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Hwang JH, Lai A, Tung JP, Harkin DG, Flower RL, Pecheniuk NM. Proteomic Characterization of Transfusable Blood Components: Fresh Frozen Plasma, Cryoprecipitate, and Derived Extracellular Vesicles via Data-Independent Mass Spectrometry. J Proteome Res 2024. [PMID: 39254217 DOI: 10.1021/acs.jproteome.4c00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Extracellular vesicles (EVs) are a heterogeneous collection of particles that play a crucial role in cell-to-cell communication, primarily due to their ability to transport molecules, such as proteins. Thus, profiling EV-associated proteins offers insight into their biological effects. EVs can be isolated from various biological fluids, including donor blood components such as cryoprecipitate and fresh frozen plasma (FFP). In this study, we conducted a proteomic analysis of five single donor units of cryoprecipitate, FFP, and EVs derived from these blood components using a quantitative mass spectrometry approach. EVs were successfully isolated from both cryoprecipitate and FFP based on community guidelines. We identified and quantified approximately 360 proteins across all sample groups. Principal component analysis and heatmaps revealed that both cryoprecipitate and FFP are similar. Similarly, EVs derived from cryoprecipitate and FFP are comparable. However, they differ between the originating fluids and their derived EVs. Using the R-package MS-DAP, differentially expressed proteins (DEPs) were identified. The DEPs for all comparisons, when submitted for gene enrichment analysis, are involved in the complement and coagulation pathways. The protein profile generated from this study will have important clinical implications in increasing our knowledge of the proteins that are associated with EVs derived from blood components.
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Affiliation(s)
- Ji Hui Hwang
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4000, Australia
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia
| | - Andrew Lai
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, QLD 4006, Australia
| | - John-Paul Tung
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4000, Australia
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD 4006, Australia
- School of Health, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Damien G Harkin
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4000, Australia
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia
| | - Robert L Flower
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4000, Australia
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia
| | - Natalie M Pecheniuk
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld 4000, Australia
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia
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2
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Zhuang T, Wang S, Yu X, He X, Guo H, Ou C. Current status and future perspectives of platelet-derived extracellular vesicles in cancer diagnosis and treatment. Biomark Res 2024; 12:88. [PMID: 39183323 PMCID: PMC11346179 DOI: 10.1186/s40364-024-00639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024] Open
Abstract
Platelets are a significant component of the cell population in the tumour microenvironment (TME). Platelets influence other immune cells and perform cross-talk with tumour cells, playing an important role in tumour development. Extracellular vesicles (EVs) are small membrane vesicles released from the cells into the TME. They can transfer biological information, including proteins, nucleic acids, and metabolites, from secretory cells to target receptor cells. This process affects the progression of various human diseases, particularly cancer. In recent years, several studies have demonstrated that platelet-derived extracellular vesicles (PEVs) can help regulate the malignant biological behaviours of tumours, including malignant proliferation, resistance to cell death, invasion and metastasis, metabolic reprogramming, immunity, and angiogenesis. Consequently, PEVs have been identified as key regulators of tumour progression. Therefore, targeting PEVs is a potential strategy for tumour treatment. Furthermore, the extensive use of nanomaterials in medical research has indicated that engineered PEVs are ideal delivery systems for therapeutic drugs. Recent studies have demonstrated that PEV engineering technologies play a pivotal role in the treatment of tumours by combining photothermal therapy, immunotherapy, and chemotherapy. In addition, aberrant changes in PEVs are closely associated with the clinicopathological features of patients with tumours, which may serve as liquid biopsy markers for early diagnosis, monitoring disease progression, and the prognostic assessment of patients with tumours. A comprehensive investigation into the role and potential mechanisms of PEVs in tumourigenesis may provide novel diagnostic biomarkers and potential therapeutic strategies for treating human tumours.
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Affiliation(s)
- Tongtao Zhuang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Shenrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiaoqian Yu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Wang Z, Zhou X, Kong Q, He H, Sun J, Qiu W, Zhang L, Yang M. Extracellular Vesicle Preparation and Analysis: A State-of-the-Art Review. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401069. [PMID: 38874129 PMCID: PMC11321646 DOI: 10.1002/advs.202401069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/11/2024] [Indexed: 06/15/2024]
Abstract
In recent decades, research on Extracellular Vesicles (EVs) has gained prominence in the life sciences due to their critical roles in both health and disease states, offering promising applications in disease diagnosis, drug delivery, and therapy. However, their inherent heterogeneity and complex origins pose significant challenges to their preparation, analysis, and subsequent clinical application. This review is structured to provide an overview of the biogenesis, composition, and various sources of EVs, thereby laying the groundwork for a detailed discussion of contemporary techniques for their preparation and analysis. Particular focus is given to state-of-the-art technologies that employ both microfluidic and non-microfluidic platforms for EV processing. Furthermore, this discourse extends into innovative approaches that incorporate artificial intelligence and cutting-edge electrochemical sensors, with a particular emphasis on single EV analysis. This review proposes current challenges and outlines prospective avenues for future research. The objective is to motivate researchers to innovate and expand methods for the preparation and analysis of EVs, fully unlocking their biomedical potential.
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Affiliation(s)
- Zesheng Wang
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000P. R. China
- Department of Biomedical Sciencesand Tung Biomedical Sciences CentreCity University of Hong KongHong Kong999077P. R. China
- Key Laboratory of Biochip TechnologyBiotech and Health CentreShenzhen Research Institute of City University of Hong KongShenzhen518057P. R. China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000P. R. China
- Department of Biomedical Sciencesand Tung Biomedical Sciences CentreCity University of Hong KongHong Kong999077P. R. China
- Key Laboratory of Biochip TechnologyBiotech and Health CentreShenzhen Research Institute of City University of Hong KongShenzhen518057P. R. China
| | - Qinglong Kong
- The Second Department of Thoracic SurgeryDalian Municipal Central HospitalDalian116033P. R. China
| | - Huimin He
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000P. R. China
- Department of Biomedical Sciencesand Tung Biomedical Sciences CentreCity University of Hong KongHong Kong999077P. R. China
- Key Laboratory of Biochip TechnologyBiotech and Health CentreShenzhen Research Institute of City University of Hong KongShenzhen518057P. R. China
| | - Jiayu Sun
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000P. R. China
- Department of Biomedical Sciencesand Tung Biomedical Sciences CentreCity University of Hong KongHong Kong999077P. R. China
| | - Wenting Qiu
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000P. R. China
- Department of Biomedical Sciencesand Tung Biomedical Sciences CentreCity University of Hong KongHong Kong999077P. R. China
| | - Liang Zhang
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000P. R. China
- Department of Biomedical Sciencesand Tung Biomedical Sciences CentreCity University of Hong KongHong Kong999077P. R. China
- Key Laboratory of Biochip TechnologyBiotech and Health CentreShenzhen Research Institute of City University of Hong KongShenzhen518057P. R. China
| | - Mengsu Yang
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000P. R. China
- Department of Biomedical Sciencesand Tung Biomedical Sciences CentreCity University of Hong KongHong Kong999077P. R. China
- Key Laboratory of Biochip TechnologyBiotech and Health CentreShenzhen Research Institute of City University of Hong KongShenzhen518057P. R. China
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Fernández‐Rhodes M, Buchan E, Gagnon SD, Qian J, Gethings L, Lees R, Peacock B, Capel AJ, Martin NRW, Oppenheimer PG, Lewis MP, Davies OG. Extracellular vesicles may provide an alternative detoxification pathway during skeletal muscle myoblast ageing. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e171. [PMID: 39169919 PMCID: PMC11336379 DOI: 10.1002/jex2.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/20/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024]
Abstract
Skeletal muscle (SM) acts as a secretory organ, capable of releasing myokines and extracellular vesicles (SM-EVs) that impact myogenesis and homeostasis. While age-related changes have been previously reported in murine SM-EVs, no study has comprehensively profiled SM-EV in human models. To this end, we provide the first comprehensive comparison of SM-EVs from young and old human primary skeletal muscle cells (HPMCs) to map changes associated with SM ageing. HPMCs, isolated from young (24 ± 1.7 years old) and older (69 ± 2.6 years old) participants, were immunomagnetically sorted based on the presence of the myogenic marker CD56 (N-CAM) and cultured as pure (100% CD56+) or mixed populations (MP: 90% CD56+). SM-EVs were isolated using an optimised protocol combining ultrafiltration and size exclusion chromatography (UF + SEC) and their biological content was extensively characterised using Raman spectroscopy (RS) and liquid chromatography mass spectrometry (LC-MS). Minimal variations in basic EV parameters (particle number, size, protein markers) were observed between young and old populations. However, biochemical fingerprinting by RS highlighted increased protein (amide I), lipid (phospholipids and phosphatidylcholine) and hypoxanthine signatures for older SM-EVs. Through LC-MS, we identified 84 shared proteins with functions principally related to cell homeostasis, muscle maintenance and transcriptional regulation. Significantly, SM-EVs from older participants were comparatively enriched in proteins involved in oxidative stress and DNA/RNA mutagenesis, such as E3 ubiquitin-protein ligase TTC3 (TTC3), little elongation complex subunit 1 (ICE1) and Acetyl-CoA carboxylase 1 (ACACA). These data suggest SM-EVs could provide an alternative pathway for homeostasis and detoxification during SM ageing.
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Affiliation(s)
| | - Emma Buchan
- School of Chemical Engineering, Advanced Nanomaterials Structures and Applications Laboratories, College of Engineering and Physical SciencesUniversity of BirminghamBirminghamUK
| | - Stephanie D. Gagnon
- School of SportExercise and Health Sciences, Loughborough UniversityLoughboroughUK
| | - Jiani Qian
- School of SportExercise and Health Sciences, Loughborough UniversityLoughboroughUK
| | - Lee Gethings
- Waters CorporationWilmslowUK
- School of Biological SciencesUniversity of ManchesterManchesterUK
- Medical SchoolUniversity of SurreySurreyUK
| | | | - Ben Peacock
- School of Biological SciencesUniversity of ManchesterManchesterUK
| | - Andrew J. Capel
- School of SportExercise and Health Sciences, Loughborough UniversityLoughboroughUK
| | - Neil R. W. Martin
- School of SportExercise and Health Sciences, Loughborough UniversityLoughboroughUK
| | - Pola Goldberg Oppenheimer
- School of Chemical Engineering, Advanced Nanomaterials Structures and Applications Laboratories, College of Engineering and Physical SciencesUniversity of BirminghamBirminghamUK
| | - Mark P. Lewis
- School of SportExercise and Health Sciences, Loughborough UniversityLoughboroughUK
| | - Owen G. Davies
- School of SportExercise and Health Sciences, Loughborough UniversityLoughboroughUK
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Morganti C, Bonora M, Ito K. Metabolism and HSC fate: what NADPH is made for. Trends Cell Biol 2024:S0962-8924(24)00141-7. [PMID: 39054107 DOI: 10.1016/j.tcb.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024]
Abstract
Mitochondrial metabolism plays a central role in the regulation of hematopoietic stem cell (HSC) biology. Mitochondrial fatty acid oxidation (FAO) is pivotal in controlling HSC self-renewal and differentiation. Herein, we discuss recent evidence suggesting that NADPH generated in the mitochondria can influence the fate of HSCs. Although NADPH has multiple functions, HSCs show high levels of NADPH that are preferentially used for cholesterol biosynthesis. Endogenous cholesterol supports the biogenesis of extracellular vesicles (EVs), which are essential for maintaining HSC properties. We also highlight the significance of EVs in hematopoiesis through autocrine signaling. Elucidating the mitochondrial NADPH-cholesterol axis as part of the metabolic requirements of healthy HSCs will facilitate the development of new therapies for hematological disorders.
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Affiliation(s)
- Claudia Morganti
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Oncology and Medicine, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY 10461, USA.
| | - Massimo Bonora
- Department of Medical Sciences, Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies, University of Ferrara, Ferrara, Italy
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Oncology and Medicine, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY 10461, USA.
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6
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Martínez-Díaz P, Parra A, Sanchez-López CM, Casas J, Lucas X, Marcilla A, Roca J, Barranco I. Small and Large Extracellular Vesicles of Porcine Seminal Plasma Differ in Lipid Profile. Int J Mol Sci 2024; 25:7492. [PMID: 39000599 PMCID: PMC11242203 DOI: 10.3390/ijms25137492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Seminal plasma contains a heterogeneous population of extracellular vesicles (sEVs) that remains poorly characterized. This study aimed to characterize the lipidomic profile of two subsets of differently sized sEVs, small (S-) and large (L-), isolated from porcine seminal plasma by size-exclusion chromatography and characterized by an orthogonal approach. High-performance liquid chromatography-high-resolution mass spectrometry was used for lipidomic analysis. A total of 157 lipid species from 14 lipid classes of 4 major categories (sphingolipids, glycerophospholipids, glycerolipids, and sterols) were identified. Qualitative differences were limited to two cholesteryl ester species present only in S-sEVs. L-sEVs had higher levels of all quantified lipid classes due to their larger membrane surface area. The distribution pattern was different, especially for sphingomyelins (more in S-sEVs) and ceramides (more in L-sEVs). In conclusion, this study reveals differences in the lipidomic profile of two subsets of porcine sEVs, suggesting that they differ in biogenesis and functionality.
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Affiliation(s)
- Pablo Martínez-Díaz
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Ana Parra
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Christian M Sanchez-López
- Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Universitat de València, 46100 Valencia, Spain
- Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute La Fe, Universitat de València, 46100 Valencia, Spain
| | - Josefina Casas
- Research Unit on BioActive Molecules (RUBAM), Institute for Advanced Chemistry (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Xiomara Lucas
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Antonio Marcilla
- Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Universitat de València, 46100 Valencia, Spain
- Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute La Fe, Universitat de València, 46100 Valencia, Spain
| | - Jordi Roca
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Isabel Barranco
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
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7
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Vaidya M, Kimura A, Bajaj A, Sugaya K. 3'-UTR Sequence of Exosomal NANOGP8 DNA as an Extracellular Vesicle-Localization Signal. Int J Mol Sci 2024; 25:7294. [PMID: 39000405 PMCID: PMC11242200 DOI: 10.3390/ijms25137294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Extracellular vesicles (EVs) are garnering attention as a safe and efficient biomolecule delivery system. EVs intrinsically play a crucial role in intercellular communication and pathophysiology by transporting functionally active DNA molecules. The internalized DNA pleiotropically affects the recipient cells. Considering these salient features, an intentional incorporation of specific DNA gene cassettes into EVs and their subsequent delivery to the target cells has potential applications in genetic engineering. Moreover, efficient ways to insert the DNA into EVs during their biogenesis is valuable. Our current research is a step in the development of this technology. As such, cancer cells are known to secrete exosomes containing increased amounts of double-stranded DNA than normal cells. The clonal analysis in our previously published data revealed that exosomes released from various cancer cells contained a significantly larger population of NANOGP8 DNA with a 22-base pair insertion in the 3'-untranslated region (UTR) compared to those secreted by normal cells. This finding led us to hypothesize that the 22-base pair insertion may act as a signal to facilitate the incorporation of NANOGP8 DNA into the exosomes. To test this hypothesis, we compared the EV localization of an Enhanced Green Fluorescent Protein (EGFP) gene fused with the NANOGP8 3'-UTR, with and without the 22-base pair insertion. The quantitative PCR analysis showed a significantly higher EGFP DNA accumulation in exosomes released from cells transfected with the gene cassette containing the 3'-UTR with the 22-base pair insertion. The discovery of a DNA localization signal in exosomal DNA's 3'-UTR could pave the way for the development of an EV-based DNA delivery system. This technology will open new possibilities in genetic engineering and innovative therapies using nucleic acid medicine.
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Affiliation(s)
| | | | | | - Kiminobu Sugaya
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA; (M.V.); (A.K.); (A.B.)
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Mashayekhi V, Schomisch A, Rasheed S, Aparicio-Puerta E, Risch T, Yildiz D, Koch M, Both S, Ludwig N, Legroux TM, Keller A, Müller R, Fuhrmann G, Hoppstädter J, Kiemer AK. The RNA binding protein IGF2BP2/IMP2 alters the cargo of cancer cell-derived extracellular vesicles supporting tumor-associated macrophages. Cell Commun Signal 2024; 22:344. [PMID: 38937789 PMCID: PMC11212187 DOI: 10.1186/s12964-024-01701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Tumor cells release extracellular vesicles (EVs) that contribute to the polarization of macrophages towards tumor-associated macrophages (TAMs). High expression levels of the RNA binding protein IGF2BP2/IMP2 are correlated with increased tumor cell proliferation, invasion, and poor prognosis in the clinic. However, there is a lack of understanding of whether IMP2 affects the cargo of cancer cell-derived EVs, thereby modulating macrophage polarization. METHODS EVs were isolated from IMP2-expressing HCT116 parental cells (WT) and CRISPR/Cas9 IMP2 knockout (KO) cells. EVs were characterized according to MISEV guidelines, microRNA cargo was assessed by microRNA-Seq, and the protein cargo was analyzed by proteomics. Primary human monocyte-derived macrophages (HMDMs) were polarized by EVs, and the expression of genes and surface markers was assessed using qPCR and flow cytometry, respectively. Morphological changes of macrophages, as well as the migratory potential of cancer cells, were assessed by the Incucyte® system and macrophage matrix degradation potential by zymography. Changes in the metabolic activity of macrophages were quantified using a Seahorse® analyzer. For in vivo studies, EVs were injected into the yolk sac of zebrafish larvae, and macrophages were isolated by fluorescence-activated cell sorting. RESULTS EVs from WT and KO cells had a similar size and concentration and were positive for 25 vesicle markers. The expression of tumor-promoting genes was higher in macrophages polarized with WT EVs than KO EVs, while the expression of TNF and IL6 was reduced. A similar pattern was observed in macrophages from zebrafish larvae treated in vivo. WT EV-polarized macrophages showed a higher abundance of TAM-like surface markers, higher matrix degrading activity, as well as a higher promotion of cancer cell migration. MicroRNA-Seq revealed a significant difference in the microRNA composition of WT and KO EVs, particularly a high abundance of miR-181a-5p in WT EVs, which was absent in KO EVs. Inhibitors of macropinocytosis and phagocytosis antagonized the delivery of miR-181a-5p into macrophages and the downregulation of the miR-181a-5p target DUSP6. Proteomics data showed differences in protein cargo in KO vs. WT EVs, with the differentially abundant proteins mainly involved in metabolic pathways. WT EV-treated macrophages exhibited a higher basal oxygen consumption rate and a lower extracellular acidification rate than KO EV-treated cells. CONCLUSION Our results show that IMP2 determines the cargo of EVs released by cancer cells, thereby modulating the EVs' actions on macrophages. Expression of IMP2 is linked to the secretion of EVs that polarize macrophages towards a tumor-promoting phenotype.
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Affiliation(s)
- Vida Mashayekhi
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Annika Schomisch
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Sari Rasheed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Brunswick, Germany
| | - Ernesto Aparicio-Puerta
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | - Timo Risch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Brunswick, Germany
| | - Daniela Yildiz
- Institute of Experimental and Clinical Pharmacology and Toxicology, PZMS, ZHMB, Saarland University, Homburg, Germany
| | - Marcus Koch
- INM - Leibniz Institute for New Materials, Saarbrücken, Germany
| | - Simon Both
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Thierry M Legroux
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Brunswick, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Gregor Fuhrmann
- Department of Pharmaceutical Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jessica Hoppstädter
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany.
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Liu Q, Zhang Q, Yao Z, Yi G, Kang Y, Qiu Y, Yang Y, Yuan H, Fu R, Sheng W, Cheng L, Wang W, Wang H, Peng C. Pushing Forward the DNA Walkers in Connection with Tumor-Derived Extracellular Vesicles. Int J Nanomedicine 2024; 19:6231-6252. [PMID: 38915916 PMCID: PMC11194468 DOI: 10.2147/ijn.s464895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/15/2024] [Indexed: 06/26/2024] Open
Abstract
Extracellular vesicles (EVs) are microparticles released from cells in both physiological and pathological conditions and could be used to monitor the progression of various pathological states, including neoplastic diseases. In various EVs, tumor-derived extracellular vesicles (TEVs) are secreted by different tumor cells and are abundant in many molecular components, such as proteins, nucleic acids, lipids, and carbohydrates. TEVs play a crucial role in forming and advancing various cancer processes. Therefore, TEVs are regarded as promising biomarkers for the early detection of cancer in liquid biopsy. However, the currently developed TEV detection methods still face several key scientific problems that need to be solved, such as low sensitivity, poor specificity, and poor accuracy. To overcome these limitations, DNA walkers have emerged as one of the most popular nanodevices that exhibit better signal amplification capability and enable highly sensitive and specific detection of the analytes. Due to their unique properties of high directionality, flexibility, and efficiency, DNA walkers hold great potential for detecting TEVs. This paper provides an introduction to EVs and DNA walker, additionally, it summarizes recent advances in DNA walker-based detection of TEVs (2018-2024). The review highlights the close relationship between TEVs and DNA walkers, aims to offer valuable insights into TEV detection and to inspire the development of reliable, efficient, simple, and innovative methods for detecting TEVs based on DNA walker in the future.
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Affiliation(s)
- Qingyi Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Qiongdan Zhang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Zhijian Yao
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Gangqiang Yi
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Yeonseok Kang
- College of Korean Medicine, Wonkwang University, Jeonbuk, Korea
| | - Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Hanwen Yuan
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Ronggeng Fu
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Wenbing Sheng
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Lidong Cheng
- Hunan Yirentang Chinese Herbal Pieces Co., Ltd, Changde, People’s Republic of China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Caiyun Peng
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- Institute of Innovation and Applied Research in Chinese Medicine Hunan University of Chinese Medicine, Changsha, People’s Republic of China
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10
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Olson C, Ivanov K, Boyes D, Bengford D, Ku J, Flojo R, Zhang P, Lu B. Dual-Omics Approach Unveils Novel Perspective on the Quality Control of Genetically Engineered Exosomes. Pharmaceutics 2024; 16:824. [PMID: 38931944 PMCID: PMC11207238 DOI: 10.3390/pharmaceutics16060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Exosomes, nanoscale vesicles derived from human cells, offer great promise for targeted drug delivery. However, their inherent diversity and genetic modifications present challenges in terms of ensuring quality in clinical use. To explore solutions, we employed advanced gene fusion and transfection techniques in human 293T cells to generate two distinct sets of genetically engineered samples. We used dual-omics analysis, combining transcriptomics and proteomics, to comprehensively assess exosome quality by comparing with controls. Transcriptomic profiling showed increased levels of engineering scaffolds in the modified groups, confirming the success of genetic manipulation. Through transcriptomic analysis, we identified 15 RNA species, including 2008 miRNAs and 13,897 mRNAs, loaded onto exosomes, with no significant differences in miRNA or mRNA levels between the control and engineered exosomes. Proteomics analysis identified changes introduced through genetic engineering and over 1330 endogenous exosome-associated proteins, indicating the complex nature of the samples. Further pathway analysis showed enrichment in a small subset of cellular signaling pathways, aiding in our understanding of the potential biological impacts on recipient cells. Detection of over 100 cow proteins highlighted the effectiveness of LC-MS for identifying potential contaminants. Our findings establish a dual-omics framework for the quality control of engineered exosome products, facilitating their clinical translation and therapeutic applications in nanomedicine.
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Affiliation(s)
- Christopher Olson
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA; (C.O.); (K.I.); (D.B.); (J.K.); (R.F.)
| | - Konstantin Ivanov
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA; (C.O.); (K.I.); (D.B.); (J.K.); (R.F.)
| | - Darin Boyes
- Department of Biology, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA;
| | - David Bengford
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA; (C.O.); (K.I.); (D.B.); (J.K.); (R.F.)
| | - Joy Ku
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA; (C.O.); (K.I.); (D.B.); (J.K.); (R.F.)
| | - Renceh Flojo
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA; (C.O.); (K.I.); (D.B.); (J.K.); (R.F.)
| | - Pengyang Zhang
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA; (C.O.); (K.I.); (D.B.); (J.K.); (R.F.)
| | - Biao Lu
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, USA; (C.O.); (K.I.); (D.B.); (J.K.); (R.F.)
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11
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Jank L, Kesharwani A, Ryu T, Joshi D, Ladakis DC, Smith MD, Singh S, Arab T, Witwer KW, Calabresi PA, Na CH, Bhargava P. Characterization of spinal cord tissue-derived extracellular vesicles in neuroinflammation. J Neuroinflammation 2024; 21:154. [PMID: 38851724 PMCID: PMC11162576 DOI: 10.1186/s12974-024-03147-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Extracellular vesicles (EVs) are released by all cells, can cross the blood-brain barrier, and have been shown to play an important role in cellular communication, substance shuttling, and immune modulation. In recent years EVs have shifted into focus in multiple sclerosis (MS) research as potential plasma biomarkers and therapeutic vehicles. Yet little is known about the disease-associated changes in EVs in the central nervous system (CNS). To address this gap, we characterized the physical and proteomic changes of mouse spinal cord-derived EVs before and at 16 and 25 days after the induction of experimental autoimmune encephalomyelitis (EAE), a neuroinflammatory model of MS. Using various bioinformatic tools, we found changes in inflammatory, glial, and synaptic proteins and pathways, as well as a shift in the predicted contribution of immune and glial cell types over time. These results show that EVs provide snapshots of crucial disease processes such as CNS-compartmentalized inflammation, re/de-myelination, and synaptic pathology, and might also mediate these processes. Additionally, inflammatory plasma EV biomarkers previously identified in people with MS were also altered in EAE spinal cord EVs, suggesting commonalities of EV-related pathological processes during EAE and MS and overlap of EV proteomic changes between CNS and circulating EVs.
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Affiliation(s)
- Larissa Jank
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ajay Kesharwani
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Taekyung Ryu
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Deepika Joshi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dimitrios C Ladakis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew D Smith
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saumitra Singh
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tanina Arab
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Witwer
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chan-Hyun Na
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pavan Bhargava
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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Ala U, Fagoonee S. RNA-binding protein transcripts as potential biomarkers for detecting Primary Sclerosing Cholangitis and for predicting its progression to Cholangiocarcinoma. Front Mol Biosci 2024; 11:1388294. [PMID: 38903178 PMCID: PMC11187294 DOI: 10.3389/fmolb.2024.1388294] [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: 02/19/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Primary Sclerosing Cholangitis (PSC) is a persistent inflammatory liver condition that affects the bile ducts and is commonly diagnosed in young individuals. Despite efforts to incorporate various clinical, biochemical and molecular parameters for diagnosing PSC, it remains challenging, and no biomarkers characteristic of the disease have been identified hitherto. PSC is linked with an uncertain prognosis, and there is a pressing need to explore multiomics databases to establish a new biomarker panel for the early detection of PSC's gradual progression into Cholangiocarcinoma (CCA) and for the development of effective therapeutic interventions. Apart from non-coding RNAs, other components of the Ribonucleoprotein (RNP) complex, such as RNA-Binding Proteins (RBPs), also hold great promise as biomarkers due to their versatile expression in pathological conditions. In the present review, an update on the RBP transcripts that show dysregulated expression in PSC and CCA is provided. Moreover, by utilizing a bioinformatic data mining approach, we give insight into those RBP transcripts that also exhibit differential expression in liver and gall bladder, as well as in body fluids, and are promising as biomarkers for diagnosing and predicting the prognosis of PSC. Expression data were bioinformatically extracted from public repositories usingTCGA Bile Duct Cancer dataset for CCA and specific NCBI GEO datasets for both PSC and CCA; more specifically, RBPs annotations were obtained from RBP World database. Interestingly, our comprehensive analysis shows an elevated expression of the non-canonical RBPs, FANCD2, as well as the microtubule dynamics regulator, ASPM, transcripts in the body fluids of patients with PSC and CCA compared with their respective controls, with the same trend in expression being observed in gall bladder and liver cancer tissues. Consequently, the manipulation of tissue expression of RBP transcripts might be considered as a strategy to mitigate the onset of CCA in PSC patients, and warrants further experimental investigation. The analysis performed herein may be helpful in the identification of non-invasive biomarkers for the early detection of PSC and for predicting its progression into CCA. In conclusion, future clinical research should investigate in more depth the full potential of RBP transcripts as biomarkers for human pathologies.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Sharmila Fagoonee
- Institute of Biostructure and Bioimaging (CNR), Molecular Biotechnology Center “Guido Tarone”, Turin, Italy
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13
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Griffin K, Mizenko R, Arun V, Carney RP, Leach JK. Extracellular Vesicles from Highly Metastatic Osteosarcoma Cells Induce Pro-Tumorigenic Macrophage Phenotypes. Adv Biol (Weinh) 2024; 8:e2300577. [PMID: 38596830 PMCID: PMC11178448 DOI: 10.1002/adbi.202300577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Metastasis is the principal factor in poor prognosis for individuals with osteosarcoma (OS). Understanding the events that lead to metastasis is critical to develop better interventions for this disease. Alveolar macrophages are potentially involved in priming the lung microenvironment for OS metastasis, yet the mechanisms involved in this process remain unclear. Since extracellular vesicles (EVs) are a known actor in primary tumor development, their potential role in OS metastagenesis through macrophage modulation is explored here. The interaction of EVs isolated from highly metastatic (K7M2) and less metastatic (K12) osteosarcoma cell lines is compared with a peritoneal macrophage cell line. An EV concentration that reproducibly induced macrophage migration is identified first, then used for later experiments. By confocal microscopy, both EV types associated with M0 or M1 macrophages; however, only K7M2-EVs are associated with M2 macrophages, an interaction that is abrogated by EV pre-treatment with anti-CD47 antibody. Interestingly, all interactions appeared to be surface binding, not internalized. In functional studies, K7M2-EVs polarized fewer macrophages to M1. Together, these data suggest that K7M2-EVs have unique interactions with macrophages that can contribute to the production of a higher proportion of pro-tumor type macrophages, thereby accelerating metastasis.
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Affiliation(s)
- Katherine Griffin
- School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Orthopaedic Surgery, UC Davis Health, Sacramento, California, USA
| | - Rachel Mizenko
- Department of Biomedical Engineering, University of California, Davis, California, USA
| | - Vishalakshi Arun
- Department of Biomedical Engineering, University of California, Davis, California, USA
| | - Randy P. Carney
- Department of Biomedical Engineering, University of California, Davis, California, USA
| | - J. Kent Leach
- Department of Orthopaedic Surgery, UC Davis Health, Sacramento, California, USA
- Department of Biomedical Engineering, University of California, Davis, California, USA
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14
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Yavuz B, Mutlu EC, Ahmed Z, Ben-Nissan B, Stamboulis A. Applications of Stem Cell-Derived Extracellular Vesicles in Nerve Regeneration. Int J Mol Sci 2024; 25:5863. [PMID: 38892052 PMCID: PMC11172915 DOI: 10.3390/ijms25115863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Extracellular vesicles (EVs), including exosomes, microvesicles, and other lipid vesicles derived from cells, play a pivotal role in intercellular communication by transferring information between cells. EVs secreted by progenitor and stem cells have been associated with the therapeutic effects observed in cell-based therapies, and they also contribute to tissue regeneration following injury, such as in orthopaedic surgery cases. This review explores the involvement of EVs in nerve regeneration, their potential as drug carriers, and their significance in stem cell research and cell-free therapies. It underscores the importance of bioengineers comprehending and manipulating EV activity to optimize the efficacy of tissue engineering and regenerative therapies.
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Affiliation(s)
- Burcak Yavuz
- Vocational School of Health Services, Altinbas University, 34147 Istanbul, Turkey;
| | - Esra Cansever Mutlu
- Biomaterials Research Group, School of Metallurgy and Materials, College of Engineering and Physical Science, University of Birmingham, Birmingham B15 2TT, UK;
| | - Zubair Ahmed
- Neuroscience & Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston B15 2TT, UK
| | - Besim Ben-Nissan
- Translational Biomaterials and Medicine Group, School of Life Sciences, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia;
| | - Artemis Stamboulis
- Biomaterials Research Group, School of Metallurgy and Materials, College of Engineering and Physical Science, University of Birmingham, Birmingham B15 2TT, UK;
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15
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Solheim ET, Gerking Y, Kråkenes T, Herdlevær I, Birkeland E, Totland C, Dick F, Vedeler CA. Multi-omics profiling reveals dysregulated ribosome biogenesis and impaired cell proliferation following knockout of CDR2L. BMC Cancer 2024; 24:645. [PMID: 38802745 PMCID: PMC11129367 DOI: 10.1186/s12885-024-12399-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Cerebellar degeneration-related (CDR) proteins are associated with paraneoplastic cerebellar degeneration (PCD) - a rare, neurodegenerative disease caused by tumour-induced autoimmunity against neural antigens resulting in degeneration of Purkinje neurons in the cerebellum. The pathogenesis of PCD is unknown, in large part due to our limited understanding of the functions of CDR proteins. To this end, we performed an extensive, multi-omics analysis of CDR-knockout cells focusing on the CDR2L protein, to gain a deeper understanding of the properties of the CDR proteins in ovarian cancer. METHODS Ovarian cancer cell lines lacking either CDR1, CDR2, or CDR2L were analysed using RNA sequencing and mass spectrometry-based proteomics to assess changes to the transcriptome, proteome and secretome in the absence of these proteins. RESULTS For each knockout cell line, we identified sets of differentially expressed genes and proteins. CDR2L-knockout cells displayed a distinct expression profile compared to CDR1- and CDR2-knockout cells. Knockout of CDR2L caused dysregulation of genes involved in ribosome biogenesis, protein translation, and cell cycle progression, ultimately causing impaired cell proliferation in vitro. Several of these genes showed a concurrent upregulation at the transcript level and downregulation at the protein level. CONCLUSIONS Our study provides the first integrative multi-omics analysis of the impact of knockout of the CDR genes, providing both new insights into the biological properties of the CDR proteins in ovarian cancer, and a valuable resource for future investigations into the CDR proteins.
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Affiliation(s)
- Eirik Tveit Solheim
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.
- Neuro-SysMed - Centre of Excellence for Experimental Therapy in Neurology, Departments of Neurology and Clinical Medicine, Bergen, Norway.
| | - Yola Gerking
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Neuro-SysMed - Centre of Excellence for Experimental Therapy in Neurology, Departments of Neurology and Clinical Medicine, Bergen, Norway
| | - Torbjørn Kråkenes
- Neuro-SysMed - Centre of Excellence for Experimental Therapy in Neurology, Departments of Neurology and Clinical Medicine, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Ida Herdlevær
- Neuro-SysMed - Centre of Excellence for Experimental Therapy in Neurology, Departments of Neurology and Clinical Medicine, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Cecilie Totland
- Neuro-SysMed - Centre of Excellence for Experimental Therapy in Neurology, Departments of Neurology and Clinical Medicine, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Fiona Dick
- Neuro-SysMed - Centre of Excellence for Experimental Therapy in Neurology, Departments of Neurology and Clinical Medicine, Bergen, Norway
| | - Christian Alexander Vedeler
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Neuro-SysMed - Centre of Excellence for Experimental Therapy in Neurology, Departments of Neurology and Clinical Medicine, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
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16
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Sharma A, Yadav A, Nandy A, Ghatak S. Insight into the Functional Dynamics and Challenges of Exosomes in Pharmaceutical Innovation and Precision Medicine. Pharmaceutics 2024; 16:709. [PMID: 38931833 PMCID: PMC11206934 DOI: 10.3390/pharmaceutics16060709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Of all the numerous nanosized extracellular vesicles released by a cell, the endosomal-originated exosomes are increasingly recognized as potential therapeutics, owing to their inherent stability, low immunogenicity, and targeted delivery capabilities. This review critically evaluates the transformative potential of exosome-based modalities across pharmaceutical and precision medicine landscapes. Because of their precise targeted biomolecular cargo delivery, exosomes are posited as ideal candidates in drug delivery, enhancing regenerative medicine strategies, and advancing diagnostic technologies. Despite the significant market growth projections of exosome therapy, its utilization is encumbered by substantial scientific and regulatory challenges. These include the lack of universally accepted protocols for exosome isolation and the complexities associated with navigating the regulatory environment, particularly the guidelines set forth by the U.S. Food and Drug Administration (FDA). This review presents a comprehensive overview of current research trajectories aimed at addressing these impediments and discusses prospective advancements that could substantiate the clinical translation of exosomal therapies. By providing a comprehensive analysis of both the capabilities and hurdles inherent to exosome therapeutic applications, this article aims to inform and direct future research paradigms, thereby fostering the integration of exosomal systems into mainstream clinical practice.
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Affiliation(s)
| | | | | | - Subhadip Ghatak
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA; (A.S.); (A.Y.); (A.N.)
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17
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Chen X, Song X, Li J, Wang J, Yan Y, Yang F. Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses of small extracellular vesicles from C2C12 myoblasts identify specific PTM patterns in ligand-receptor interactions. Cell Commun Signal 2024; 22:273. [PMID: 38755675 PMCID: PMC11097525 DOI: 10.1186/s12964-024-01640-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Small extracellular vesicles (sEVs) are important mediators of intercellular communication by transferring of functional components (proteins, RNAs, and lipids) to recipient cells. Some PTMs, including phosphorylation and N-glycosylation, have been reported to play important role in EV biology, such as biogenesis, protein sorting and uptake of sEVs. MS-based proteomic technology has been applied to identify proteins and PTM modifications in sEVs. Previous proteomic studies of sEVs from C2C12 myoblasts, an important skeletal muscle cell line, focused on identification of proteins, but no PTM information on sEVs proteins is available.In this study, we systematically analyzed the proteome, phosphoproteome, and N-glycoproteome of sEVs from C2C12 myoblasts with LC-MS/MS. In-depth analyses of the three proteomic datasets revealed that the three proteomes identified different catalogues of proteins, and PTMomic analysis could expand the identification of cargos in sEVs. At the proteomic level, a high percentage of membrane proteins, especially tetraspanins, was identified. The sEVs-derived phosphoproteome had a remarkably high level of tyrosine-phosphorylated sites. The tyrosine-phosphorylated proteins might be involved with EPH-Ephrin signaling pathway. At the level of N-glycoproteomics, several glycoforms, such as complex N-linked glycans and sialic acids on glycans, were enriched in sEVs. Retrieving of the ligand-receptor interaction in sEVs revealed that extracellular matrix (ECM) and cell adhesion molecule (CAM) represented the most abundant ligand-receptor pairs in sEVs. Mapping the PTM information on the ligands and receptors revealed that N-glycosylation mainly occurred on ECM and CAM proteins, while phosphorylation occurred on different categories of receptors and ligands. A comprehensive PTM map of ECM-receptor interaction and their components is also provided.In summary, we conducted a comprehensive proteomic and PTMomic analysis of sEVs of C2C12 myoblasts. Integrated proteomic, phosphoproteomic, and N-glycoproteomic analysis of sEVs might provide some insights about their specific uptake mechanism.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xi Song
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaran Li
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jifeng Wang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yumeng Yan
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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18
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Lofaro FD, Costa S, Simone ML, Quaglino D, Boraldi F. Fibroblasts' secretome from calcified and non-calcified dermis in Pseudoxanthoma elasticum differently contributes to elastin calcification. Commun Biol 2024; 7:577. [PMID: 38755434 PMCID: PMC11099146 DOI: 10.1038/s42003-024-06283-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
Pseudoxanthoma elasticum (PXE) is a rare disease characterized by ectopic calcification, however, despite the widely spread effect of pro/anti-calcifying systemic factors associated with this genetic metabolic condition, it is not known why elastic fibers in the same patient are mainly fragmented or highly mineralized in clinically unaffected (CUS) and affected (CAS) skin, respectively. Cellular morphology and secretome are investigated in vitro in CUS and CAS fibroblasts. Here we show that, compared to CUS, CAS fibroblasts exhibit: a) differently distributed and organized focal adhesions and stress fibers; b) modified cell-matrix interactions (i.e., collagen gel retraction); c) imbalance between matrix metalloproteinases and tissue inhibitor of metalloproteinases; d) differentially expressed pro- and anti-calcifying proteoglycans and elastic-fibers associated glycoproteins. These data emphasize that in the development of pathologic mineral deposition fibroblasts play an active role altering the stability of elastic fibers and of the extracellular matrix milieu creating a local microenvironment guiding the level of matrix remodeling at an extent that may lead to degradation (in CUS) or to degradation and calcification (in CAS) of the elastic component. In conclusion, this study contributes to a better understanding of the mechanisms of the mineral deposition that can be also associated with several inherited or age-related diseases (e.g., diabetes, atherosclerosis, chronic kidney diseases).
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Affiliation(s)
| | - Sonia Costa
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Maria Luisa Simone
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daniela Quaglino
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
| | - Federica Boraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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19
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Vo N, Tran C, Tran NHB, Nguyen NT, Nguyen T, Ho DTK, Nguyen DDN, Pham T, Nguyen TA, Phan HTN, Nguyen H, Tu LN. A novel multi-stage enrichment workflow and comprehensive characterization for HEK293F-derived extracellular vesicles. J Extracell Vesicles 2024; 13:e12454. [PMID: 38760878 PMCID: PMC11101607 DOI: 10.1002/jev2.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/19/2024] Open
Abstract
Extracellular vesicles (EVs) are emerging as a promising drug delivery vehicle as they are biocompatible and capable of targeted delivery. However, clinical translation of EVs remains challenging due to the lack of standardized and scalable manufacturing protocols to consistently isolate small EVs (sEVs) with both high yield and high purity. The heterogenous nature of sEVs leading to unknown composition of biocargos causes further pushback due to safety concerns. In order to address these issues, we developed a robust quality-controlled multi-stage process to produce and isolate sEVs from human embryonic kidney HEK293F cells. We then compared different 2-step and 3-step workflows for eliminating protein impurities and cell-free nucleic acids to meet acceptable limits of regulatory authorities. Our results showed that sEV production was maximized when HEK293F cells were grown at high-density stationary phase in semi-continuous culture. The novel 3-step workflow combining tangential flow filtration, sucrose-cushion ultracentrifugation and bind-elute size-exclusion chromatography outperformed other methods in sEV purity while still preserved high yield and particle integrity. The purified HEK293F-derived sEVs were thoroughly characterized for identity including sub-population analysis, content profiling including proteomics and miRNA sequencing, and demonstrated excellent preclinical safety profile in both in-vitro and in-vivo testing. Our rigorous enrichment workflow and comprehensive characterization will help advance the development of EVs, particularly HEK293F-derived sEVs, to be safe and reliable drug carriers for therapeutic applications.
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Affiliation(s)
- Nhan Vo
- Medical Genetics InstituteHo Chi Minh CityVietnam
| | - Chau Tran
- Medical Genetics InstituteHo Chi Minh CityVietnam
| | | | | | - Thieu Nguyen
- Medical Genetics InstituteHo Chi Minh CityVietnam
| | | | | | - Tran Pham
- Medical Genetics InstituteHo Chi Minh CityVietnam
| | | | | | | | - Lan N. Tu
- Medical Genetics InstituteHo Chi Minh CityVietnam
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20
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Carrera Páez LC, Olivier M, Gambino AS, Poklepovich T, Aguilar AP, Quiroga MP, Centrón D. Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes. Front Cell Infect Microbiol 2024; 14:1368622. [PMID: 38741889 PMCID: PMC11089171 DOI: 10.3389/fcimb.2024.1368622] [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: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.
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Affiliation(s)
- Laura Camila Carrera Páez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Martin Olivier
- The Research Institute of the McGill University Health Centre, McGill University, Montréal, QC, Canada
| | - Anahí Samanta Gambino
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Tomás Poklepovich
- Plataforma de Genómica y Bioinformática, Instituto Nacional de Enfermedades Infecciosas - La Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Andrea Pamela Aguilar
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
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21
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Smith SF, Brewer DS, Hurst R, Cooper CS. Applications of Urinary Extracellular Vesicles in the Diagnosis and Active Surveillance of Prostate Cancer. Cancers (Basel) 2024; 16:1717. [PMID: 38730670 PMCID: PMC11083542 DOI: 10.3390/cancers16091717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Prostate cancer is the most common non-cutaneous cancer among men in the UK, causing significant health and economic burdens. Diagnosis and risk prognostication can be challenging due to the genetic and clinical heterogeneity of prostate cancer as well as uncertainties in our knowledge of the underlying biology and natural history of disease development. Urinary extracellular vesicles (EVs) are microscopic, lipid bilayer defined particles released by cells that carry a variety of molecular cargoes including nucleic acids, proteins and other molecules. Urine is a plentiful source of prostate-derived EVs. In this narrative review, we summarise the evidence on the function of urinary EVs and their applications in the evolving field of prostate cancer diagnostics and active surveillance. EVs are implicated in the development of all hallmarks of prostate cancer, and this knowledge has been applied to the development of multiple diagnostic tests, which are largely based on RNA and miRNA. Common gene probes included in multi-probe tests include PCA3 and ERG, and the miRNAs miR-21 and miR-141. The next decade will likely bring further improvements in the diagnostic accuracy of biomarkers as well as insights into molecular biological mechanisms of action that can be translated into opportunities in precision uro-oncology.
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Affiliation(s)
- Stephanie F. Smith
- Metabolic Health Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK (C.S.C.)
- Department of Urology, Norfolk and Norwich University Hospitals, Norwich NR4 7UY, UK
| | - Daniel S. Brewer
- Metabolic Health Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK (C.S.C.)
| | - Rachel Hurst
- Metabolic Health Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK (C.S.C.)
| | - Colin S. Cooper
- Metabolic Health Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK (C.S.C.)
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22
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Shahi S, Kang T, Fonseka P. Extracellular Vesicles in Pathophysiology: A Prudent Target That Requires Careful Consideration. Cells 2024; 13:754. [PMID: 38727289 PMCID: PMC11083420 DOI: 10.3390/cells13090754] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Extracellular vesicles (EVs) are membrane-bound particles released by cells to perform multitudes of biological functions. Owing to their significant implications in diseases, the pathophysiological role of EVs continues to be extensively studied, leading research to neglect the need to explore their role in normal physiology. Despite this, many identified physiological functions of EVs, including, but not limited to, tissue repair, early development and aging, are attributed to their modulatory role in various signaling pathways via intercellular communication. EVs are widely perceived as a potential therapeutic strategy for better prognosis, primarily through utilization as a mode of delivery vehicle. Moreover, disease-associated EVs serve as candidates for the targeted inhibition by pharmacological or genetic means. However, these attempts are often accompanied by major challenges, such as off-target effects, which may result in adverse phenotypes. This renders the clinical efficacy of EVs elusive, indicating that further understanding of the specific role of EVs in physiology may enhance their utility. This review highlights the essential role of EVs in maintaining cellular homeostasis under different physiological settings, and also discusses the various aspects that may potentially hinder the robust utility of EV-based therapeutics.
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Affiliation(s)
| | | | - Pamali Fonseka
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; (S.S.); (T.K.)
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23
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Rizzuto AS, Gelpi G, Mangini A, Carugo S, Ruscica M, Macchi C. Exploring the role of epicardial adipose-tissue-derived extracellular vesicles in cardiovascular diseases. iScience 2024; 27:109359. [PMID: 38510143 PMCID: PMC10951984 DOI: 10.1016/j.isci.2024.109359] [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] [Indexed: 03/22/2024] Open
Abstract
Epicardial adipose tissue (EAT) is a fat depot located between the myocardium and the visceral layer of the epicardium, which, owing to its location, can influence surrounding tissues and can act as a local transducer of systemic inflammation. The mechanisms upon which such influence depends on are however unclear. Given the role EAT undoubtedly has in the scheme of cardiovascular diseases (CVDs), understanding the impact of its cellular components is of upmost importance. Extracellular vesicles (EVs) constitute promising candidates to fill the gap in the knowledge concerning the unexplored mechanisms through which EAT promotes onset and progression of CVDs. Owing to their ability of transporting active biomolecules, EAT-derived EVs have been reported to be actively involved in the pathogenesis of ischemia/reperfusion injury, coronary atherosclerosis, heart failure, and atrial fibrillation. Exploring the precise functions EVs exert in this context may aid in connecting the dots between EAT and CVDs.
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Affiliation(s)
| | - Guido Gelpi
- Department of Cardio-Thoracic-Vascular Diseases - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Mangini
- Department of Cardio-Thoracic-Vascular Diseases - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Carugo
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Department of Cardio-Thoracic-Vascular Diseases - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimiliano Ruscica
- Department of Cardio-Thoracic-Vascular Diseases - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences “Rodolfo Paoletti”, University of Milan, Milan, Italy
| | - Chiara Macchi
- Department of Pharmacological and Biomolecular Sciences “Rodolfo Paoletti”, University of Milan, Milan, Italy
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24
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Santana de Andrade JC, Benchimol M, de Souza W. Stimulation of microvesicle secretion in Trichomonas vaginalis. Exp Parasitol 2024; 259:108722. [PMID: 38395187 DOI: 10.1016/j.exppara.2024.108722] [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: 12/17/2023] [Revised: 02/03/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Trichomonas vaginalis is an extracellular flagellate protozoan and the etiological agent of human trichomoniasis, a sexually transmitted infection (STI) with a high incidence. Several reports have shown that this protozoan releases microvesicles into the culture medium, which show high potential in modulating cell-to-cell communication and the host response to infections. However, the biogenesis of these vesicles has not been analyzed in detail. In the present study, high-resolution ion scanning microscopy (SEM) and transmission electron microscopy (TEM) were used to analyze the surface of control cells and cells incubated in the presence of Ca2+ alone or with A 23187 calcium ionophore. Two different strains of T. vaginalis were analyzed. Most control cells displayed relatively smooth surfaces, whereas cells incubated with Ca2+ had many surface projections of variable shape and size (from 40 nm to around 1 μm). Quantitative analyses were performed directly in the scanning electron microscope and showed a significant increase in the number of cells with surface projections after incubation in the presence of calcium. TEM showed that treated cells presented several cytoplasmic multivesicular structures, suggesting membrane fusion and exosomes in the extracellular medium. The amount and size of the released vesicles were quantitatively analyzed using light scattering and TEM on negatively stained samples. The observations show that incubation of both parasite strains in the presence of Ca2+ significantly increased the release of microvesicles into the extracellular medium in a time-dependent process. Sequential incubation in the presence of Ca2+ and the calcium ionophore A23187 increases the presence of vesicles on the parasite surface only at a short incubation time (5 min). Transmission electron microscopy showed that at least part of the vesicles are originated from cytoplasmic multivesicular structures. This information contributes to a better understanding of the biogenesis of extracellular vesicles secreted by T. vaginalis.
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Affiliation(s)
- Júlio César Santana de Andrade
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; BIOTRANS-CAXIAS, Universidade do Grande Rio. UNIGRANRIO, Rio de Janeiro, 96200-000, Brazil.
| | - Marlene Benchimol
- BIOTRANS-CAXIAS, Universidade do Grande Rio. UNIGRANRIO, Rio de Janeiro, 96200-000, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil.
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil.
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25
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Mesquita FCP, King M, da Costa Lopez PL, Thevasagayampillai S, Gunaratne PH, Hochman-Mendez C. Laminin Alpha 2 Enhances the Protective Effect of Exosomes on Human iPSC-Derived Cardiomyocytes in an In Vitro Ischemia-Reoxygenation Model. Int J Mol Sci 2024; 25:3773. [PMID: 38612582 PMCID: PMC11011704 DOI: 10.3390/ijms25073773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Ischemic heart disease, a leading cause of death worldwide, manifests clinically as myocardial infarction. Contemporary therapies using mesenchymal stromal cells (MSCs) and their derivative (exosomes, EXOs) were developed to decrease the progression of cell damage during ischemic injury. Laminin alpha 2 (LAMA2) is an important extracellular matrix protein of the heart. Here, we generated MSC-derived exosomes cultivated under LAMA2 coating to enhance human-induced pluripotent stem cell (hiPSC)-cardiomyocyte recognition of LAMA2-EXOs, thus, increasing cell protection during ischemia reoxygenation. We mapped the mRNA content of LAMA2 and gelatin-EXOs and identified 798 genes that were differentially expressed, including genes associated with cardiac muscle development and extracellular matrix organization. Cells were treated with LAMA2-EXOs 2 h before a 4 h ischemia period (1% O2, 5% CO2, glucose-free media). LAMA2-EXOs had a two-fold protective effect compared to non-treatment on plasma membrane integrity and the apoptosis activation pathway; after a 1.5 h recovery period (20% O2, 5% CO2, cardiomyocyte-enriched media), cardiomyocytes treated with LAMA2-EXOs showed faster recovery than did the control group. Although EXOs had a protective effect on endothelial cells, there was no LAMA2-enhanced protection on these cells. This is the first report of LAMA2-EXOs used to treat cardiomyocytes that underwent ischemia-reoxygenation injury. Overall, we showed that membrane-specific EXOs may help improve cardiomyocyte survival in treating ischemic cardiovascular disease.
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Affiliation(s)
- Fernanda C. P. Mesquita
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
| | - Madelyn King
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
| | - Patricia Luciana da Costa Lopez
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
| | | | - Preethi H. Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Camila Hochman-Mendez
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
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26
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Rigden DJ, Fernández XM. The 2024 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Res 2024; 52:D1-D9. [PMID: 38035367 PMCID: PMC10767945 DOI: 10.1093/nar/gkad1173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/02/2023] Open
Abstract
The 2024 Nucleic Acids Research database issue contains 180 papers from across biology and neighbouring disciplines. There are 90 papers reporting on new databases and 83 updates from resources previously published in the Issue. Updates from databases most recently published elsewhere account for a further seven. Nucleic acid databases include the new NAKB for structural information and updates from Genbank, ENA, GEO, Tarbase and JASPAR. The Issue's Breakthrough Article concerns NMPFamsDB for novel prokaryotic protein families and the AlphaFold Protein Structure Database has an important update. Metabolism is covered by updates from Reactome, Wikipathways and Metabolights. Microbes are covered by RefSeq, UNITE, SPIRE and P10K; viruses by ViralZone and PhageScope. Medically-oriented databases include the familiar COSMIC, Drugbank and TTD. Genomics-related resources include Ensembl, UCSC Genome Browser and Monarch. New arrivals cover plant imaging (OPIA and PlantPAD) and crop plants (SoyMD, TCOD and CropGS-Hub). The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Over the last year the NAR online Molecular Biology Database Collection has been updated, reviewing 1060 entries, adding 97 new resources and eliminating 388 discontinued URLs bringing the current total to 1959 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
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Affiliation(s)
- Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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27
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Yadav A, Nandy A, Sharma A, Ghatak S. Exosome Mediated Cell-Cell Crosstalk in Tissue Injury and Repair. Results Probl Cell Differ 2024; 73:249-297. [PMID: 39242383 DOI: 10.1007/978-3-031-62036-2_12] [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] [Indexed: 09/09/2024]
Abstract
The landscape of exosome research has undergone a significant paradigm shift, with a departure from early conceptions of exosomes as vehicles for cellular waste disposal towards their recognition as integral components of cellular communication with therapeutic potential. This chapter presents an exhaustive elucidation of exosome biology, detailing the processes of exosome biogenesis, release, and uptake, and their pivotal roles in signal transduction, tissue repair, regeneration, and intercellular communication. Additionally, the chapter highlights recent innovations and anticipates future directions in exosome research, emphasizing their applicability in clinical settings. Exosomes have the unique ability to navigate through tissue spaces to enter the circulatory system, positioning them as key players in tissue repair. Their contributory role in various processes of tissue repair, although in the nascent stages of investigation, stands out as a promising area of research. These vesicles function as a complex signaling network for intracellular and organ-level communication, critical in both pathological and physiological contexts. The chapter further explores the tissue-specific functionality of exosomes and underscores the advancements in methodologies for their isolation and purification, which have been instrumental in expanding the scope of exosome research. The differential cargo profiles of exosomes, dependent on their cellular origin, position them as prospective diagnostic biomarkers for tissue damage and regenerative processes. Looking ahead, the trajectory of exosome research is anticipated to bring transformative changes to biomedical fields. This includes advancing diagnostic and prognostic techniques that utilize exosomes as non-invasive biomarkers for a plethora of diseases, such as cancer, neurodegenerative, and cardiovascular conditions. Additionally, engineering exosomes through alterations of their native content or surface properties presents a novel frontier, including the synthesis of artificial or hybrid variants with enhanced functional properties. Concurrently, the ethical and regulatory frameworks surrounding exosome research, particularly in clinical translation, will require thorough deliberation. In conclusion, the diverse aspects of exosome research are coalescing to redefine the frontiers of diagnostic and therapeutic methodologies, cementing its importance as a discipline of considerable consequence in the biomedical sciences.
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Affiliation(s)
- Anita Yadav
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Aparajita Nandy
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anu Sharma
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Subhadip Ghatak
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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28
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Agüera-Lorente A, Alonso-Pardavila A, Larrinaga M, Boyano MD, González E, Falcón-Pérez JM, Asumendi A, Apraiz A. Small extracellular vesicle-based human melanocyte and melanoma signature. Pigment Cell Melanoma Res 2023. [PMID: 38158521 DOI: 10.1111/pcmr.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/10/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Intercellular communication is a cell-type and stimulus-dependent event driven not only by soluble factors but also by extracellular vesicles (EVs). EVs include vesicles of different size and origin that contain a myriad of molecules. Among them, small EVs (sEV; <200 nm) have been shown to modulate not just regional cell responses but also distant organ behavior. In cancer, distant organ modulation by sEVs has been associated to disease dissemination, which is one of the main concerns in melanoma. Description of broadly conserved alterations in sEV-contained molecules represents a strategy to identify key modifications in cellular communication as well as new disease biomarkers. Here, we characterize proteomes of cutaneous melanocyte and melanoma-derived sEVs to deepen on the landscape of normal and disease-related cell communication. Results reveal the presence of unique protein signatures for melanocytes and melanoma cells that reflect cellular transformation-related profound modifications. Melanocyte-derived sEVs are enriched in oxidative metabolism (e.g., aconitase 2, ACO2) or pigmentation (e.g., tyrosinase, TYR) related proteins while melanoma-derived sEVs reflect a generalized decrease in mature melanocytic markers (e.g., melanoma antigen recognized by T-cells 1, MART-1, also known as MLANA) and an increase in epithelial to mesenchymal transition (EMT)-related adhesion molecules such as tenascin C (TNC).
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Affiliation(s)
- Andrea Agüera-Lorente
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
| | | | - María Larrinaga
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Esperanza González
- Exosomes Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio, Spain
| | - Juan Manuel Falcón-Pérez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
- Metabolomics Platform, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Aintzane Asumendi
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Aintzane Apraiz
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
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