@article{MTMT:34567532,
	title = {Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches},
	url = {https://m2.mtmt.hu/api/publication/34567532},
	author = {Welsh, Joshua A. and Goberdhan, Deborah C. I. and O'Driscoll, Lorraine and Buzás, Edit Irén and Blenkiron, Cherie and Bussolati, Benedetta and Cai, Houjian and Di Vizio, Dolores and Driedonks, Tom A. P. and Erdbrügger, Uta and Falcon‐Perez, Juan M. and Fu, Qing‐Ling and Hill, Andrew F. and Lenassi, Metka and Lim, Sai Kiang and Mahoney, Mỹ G. and Mohanty, Sujata and Möller, Andreas and Nieuwland, Rienk and Ochiya, Takahiro and Sahoo, Susmita and Torrecilhas, Ana C. and Zheng, Lei and Zijlstra, Andries and Abuelreich, Sarah and Bagabas, Reem and Bergese, Paolo and Bridges, Esther M. and Brucale, Marco and Burger, Dylan and Carney, Randy P. and Cocucci, Emanuele and Colombo, Federico and Crescitelli, Rossella and Hanser, Edveena and Harris, Adrian L. and Haughey, Norman J. and Hendrix, An and Ivanov, Alexander R. and Jovanovic‐Talisman, Tijana and Kruh‐Garcia, Nicole A. and Ku'ulei‐Lyn Faustino, Vroniqa and Kyburz, Diego and Lässer, Cecilia and Lennon, Kathleen M. and Lötvall, Jan and Maddox, Adam L. and Martens‐Uzunova, Elena S. and Mizenko, Rachel R. and Newman, Lauren A. and Ridolfi, Andrea and Rohde, Eva and Rojalin, Tatu and Rowland, Andrew and Saftics, Andras and Sandau, Ursula S. and Saugstad, Julie A. and Shekari, Faezeh and Swift, Simon and Ter‐Ovanesyan, Dmitry and Tosar, Juan P. and Useckaite, Zivile and Valle, Francesco and Varga, Zoltán and van der Pol, Edwin and van Herwijnen, Martijn J. C. and Wauben, Marca H. M. and Wehman, Ann M. and Williams, Sarah and Zendrini, Andrea and Zimmerman, Alan J. and Théry, Clotilde and Witwer, Kenneth W. and Haseeb, Zubair},
	doi = {10.1002/jev2.12404},
	journal-iso = {J EXTRACELLULAR VESICL},
	journal = {JOURNAL OF EXTRACELLULAR VESICLES},
	volume = {13},
	unique-id = {34567532},
	abstract = {Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year‐on‐year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non‐vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its ‘Minimal Information for Studies of Extracellular Vesicles’, which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.},
	year = {2024},
	eissn = {2001-3078},
	orcid-numbers = {Welsh, Joshua A./0000-0002-1097-9756; Goberdhan, Deborah C. I./0000-0003-0645-6714; Buzás, Edit Irén/0000-0002-3744-206X; Bussolati, Benedetta/0000-0002-3663-5134; Cai, Houjian/0000-0003-4887-2652; Falcon‐Perez, Juan M./0000-0003-3133-0670; Hill, Andrew F./0000-0001-5581-2354; Lenassi, Metka/0000-0002-9488-6855; Mohanty, Sujata/0000-0002-0047-4914; Nieuwland, Rienk/0000-0002-5671-3400; Ochiya, Takahiro/0000-0002-0776-9918; Sahoo, Susmita/0000-0002-7279-1564; Torrecilhas, Ana C./0000-0001-5724-2199; Zheng, Lei/0000-0003-2576-8780; Zijlstra, Andries/0000-0001-8460-8803; Brucale, Marco/0000-0001-7244-4389; Carney, Randy P./0000-0001-8193-1664; Crescitelli, Rossella/0000-0002-1714-3169; Haughey, Norman J./0000-0001-5194-4122; Martens‐Uzunova, Elena S./0000-0002-5363-2525; Newman, Lauren A./0000-0003-3303-1666; Rohde, Eva/0000-0001-8692-886X; Sandau, Ursula S./0000-0002-3646-7089; Saugstad, Julie A./0000-0002-2996-9611; Shekari, Faezeh/0000-0001-6026-5412; Tosar, Juan P./0000-0002-2021-2479; Varga, Zoltán/0000-0002-5741-2669; Wauben, Marca H. M./0000-0003-0360-0311; Wehman, Ann M./0000-0001-9826-4132; Zimmerman, Alan J./0000-0001-6280-4790; Théry, Clotilde/0000-0001-8294-6884; Witwer, Kenneth W./0000-0003-1664-4233; Bodnár, Bernadett Réka/0000-0003-3347-9225; Bukva, Mátyás/0000-0002-5225-0285; Buzás, Edit Irén/0000-0002-3744-206X; Buzás, Krisztina/0000-0001-8933-2033; Dobra, Gabriella/0000-0002-2814-7720; Försönits, András/0000-0002-9298-8890; Gyukity-Sebestyén, Edina/0000-0003-1383-6301; Koncz, Anna/0000-0003-2511-2394; Lőrincz, Márton Ákos/0000-0002-2819-5116; Németh, Krisztina/0000-0002-3825-2137; Oláh, Attila/0000-0003-4122-5639; Osteikoetxea, Xabier/0000-0003-3628-0174; Pálóczi, Krisztina/0000-0001-7065-3582; Stepanova, Ganna/0000-0002-8285-2762; Visnovitz, Tamás/0000-0002-7962-5083; Wiener, Zoltán/0000-0001-7056-4926; Harmati, Mária/0000-0002-4875-5723; Hegyesi, Hargita/0000-0002-8800-5169}
}

@article{MTMT:34417027,
	title = {Machine learning-based analysis of cancer cell-derived vesicular proteins revealed significant tumor-specificity and predictive potential of extracellular vesicles for cell invasion and proliferation - A meta-analysis.},
	url = {https://m2.mtmt.hu/api/publication/34417027},
	author = {Bukva, Mátyás and Dobra, Gabriella and Gyukity-Sebestyén, Edina and Böröczky, Timea and Korsós, Marietta Margaréta and David G, Meckes and Horváth, Péter and Buzás, Krisztina and Harmati, Mária},
	doi = {10.1186/s12964-023-01344-5},
	journal-iso = {CELL COMM SIGN},
	journal = {CELL COMMUNICATION AND SIGNALING},
	volume = {21},
	unique-id = {34417027},
	issn = {1478-811X},
	abstract = {Although interest in the role of extracellular vesicles (EV) in oncology is growing, not all potential aspects have been investigated. In this meta-analysis, data regarding (i) the EV proteome and (ii) the invasion and proliferation capacity of the NCI-60 tumor cell lines (60 cell lines from nine different tumor types) were analyzed using machine learning methods.On the basis of the entire proteome or the proteins shared by all EV samples, 60 cell lines were classified into the nine tumor types using multiple logistic regression. Then, utilizing the Least Absolute Shrinkage and Selection Operator, we constructed a discriminative protein panel, upon which the samples were reclassified and pathway analyses were performed. These panels were validated using clinical data (n = 4,665) from Human Protein Atlas.Classification models based on the entire proteome, shared proteins, and discriminative protein panel were able to distinguish the nine tumor types with 49.15%, 69.10%, and 91.68% accuracy, respectively. Invasion and proliferation capacity of the 60 cell lines were predicted with R2 = 0.68 and R2 = 0.62 (p < 0.0001). The results of the Reactome pathway analysis of the discriminative protein panel suggest that the molecular content of EVs might be indicative of tumor-specific biological processes.Integrating in vitro EV proteomic data, cell physiological characteristics, and clinical data of various tumor types illuminates the diagnostic, prognostic, and therapeutic potential of EVs. Video Abstract.},
	keywords = {CLASSIFICATION; PROLIFERATION; INVASION; PREDICTION; machine learning; Extracellular vesicles; NCI-60},
	year = {2023},
	eissn = {1478-811X},
	orcid-numbers = {Bukva, Mátyás/0000-0002-5225-0285; Dobra, Gabriella/0000-0002-2814-7720; Gyukity-Sebestyén, Edina/0000-0003-1383-6301; Böröczky, Timea/0009-0009-3390-7809; Buzás, Krisztina/0000-0001-8933-2033; Harmati, Mária/0000-0002-4875-5723}
}

@article{MTMT:34231255,
	title = {Extracellular vesicle-mediated intercellular communication in cancer},
	url = {https://m2.mtmt.hu/api/publication/34231255},
	author = {Harmati, Mária and Bukva, Mátyás and Dobra, Gabriella and Gyukity-Sebestyén, Edina and Böröczky, Timea and Szabó, Zoltán and Kónya, Zoltán and Horvath, Peter and Klekner, Almos and Buzás, Krisztina},
	journal-iso = {EUR J IMMUNOL},
	journal = {EUROPEAN JOURNAL OF IMMUNOLOGY},
	volume = {53},
	unique-id = {34231255},
	issn = {0014-2980},
	year = {2023},
	eissn = {1521-4141},
	pages = {39-40},
	orcid-numbers = {Harmati, Mária/0000-0002-4875-5723; Bukva, Mátyás/0000-0002-5225-0285; Dobra, Gabriella/0000-0002-2814-7720; Gyukity-Sebestyén, Edina/0000-0003-1383-6301; Böröczky, Timea/0009-0009-3390-7809; Szabó, Zoltán/0000-0001-8278-8038; Kónya, Zoltán/0000-0002-9406-8596; Buzás, Krisztina/0000-0001-8933-2033}
}

@article{MTMT:34107493,
	title = {Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2},
	url = {https://m2.mtmt.hu/api/publication/34107493},
	author = {Pietiäinen, Vilja and Polso, Minttu and Migh, Ede and Guckelsberger, Christian and Harmati, Mária and Diósdi, Ákos and Turunen, Laura and Hassinen, Antti and Potdar, Swapnil and Koponen, Annika and Gyukity-Sebestyén, Edina and Kovács, Ferenc and Kriston, András and Hollandi, Réka and Burián, Katalin and Terhes, Gabriella and Visnyovszki, Ádám and Fodor, Eszter and Lacza, Zsombor and Kantele, Anu and Kolehmainen, Pekka and Kakkola, Laura and Strandin, Tomas and Levanov, Lev and Kallioniemi, Olli and Kemény, Lajos and Julkunen, Ilkka and Vapalahti, Olli and Buzás, Krisztina and Paavolainen, Lassi and Horváth, Péter and Hepojoki, Jussi},
	doi = {10.1016/j.crmeth.2023.100565},
	journal-iso = {CELL REP METH},
	journal = {CELL REPORTS METHODS},
	volume = {3},
	unique-id = {34107493},
	year = {2023},
	eissn = {2667-2375},
	orcid-numbers = {Harmati, Mária/0000-0002-4875-5723; Gyukity-Sebestyén, Edina/0000-0003-1383-6301; Burián, Katalin/0000-0003-1300-2374; Terhes, Gabriella/0000-0002-7301-9672; Kemény, Lajos/0000-0002-2119-9501; Buzás, Krisztina/0000-0001-8933-2033}
}

@article{MTMT:33592853,
	title = {MMP-9 as Prognostic Marker for Brain Tumours: A Comparative Study on Serum-Derived Small Extracellular Vesicles},
	url = {https://m2.mtmt.hu/api/publication/33592853},
	author = {Dobra, Gabriella and Gyukity-Sebestyén, Edina and Bukva, Mátyás and Harmati, Mária and Nagy, Valentina and Szabó, Zoltán and Pankotai, Tibor and Klekner, Álmos and Buzás, Krisztina},
	doi = {10.3390/cancers15030712},
	journal-iso = {CANCERS},
	journal = {CANCERS},
	volume = {15},
	unique-id = {33592853},
	abstract = {Matrix metalloproteinase-9 (MMP-9) degrades the extracellular matrix, contributes to tumour cell invasion and metastasis, and its elevated level in brain tumour tissues indicates poor prognosis. High-risk tissue biopsy can be replaced by liquid biopsy; however, the blood–brain barrier (BBB) prevents tumour-associated components from entering the peripheral blood, making the development of blood-based biomarkers challenging. Therefore, we examined the MMP-9 content of small extracellular vesicles (sEVs)—which can cross the BBB and are stable in body fluids—to characterise tumours with different invasion capacity. From four patient groups (glioblastoma multiforme, brain metastases of lung cancer, meningioma, and lumbar disc herniation as controls), 222 serum-derived sEV samples were evaluated. After isolating and characterising sEVs, their MMP-9 content was measured by ELISA and assessed statistically (correlation, paired t-test, Welch’s test, ANOVA, ROC). We found that the MMP-9 content of sEVs is independent of gender and age, but is affected by surgical intervention, treatment, and recurrence. We found a relation between low MMP-9 level in sEVs (<28 ppm) and improved survival (8-month advantage) of glioblastoma patients, and MMP-9 levels showed a positive correlation with aggressiveness. These findings suggest that vesicular MMP-9 level might be a useful prognostic marker for brain tumours.},
	year = {2023},
	eissn = {2072-6694},
	orcid-numbers = {Dobra, Gabriella/0000-0002-2814-7720; Gyukity-Sebestyén, Edina/0000-0003-1383-6301; Bukva, Mátyás/0000-0002-5225-0285; Harmati, Mária/0000-0002-4875-5723; Szabó, Zoltán/0000-0001-8278-8038; Pankotai, Tibor/0000-0001-9810-5465; Buzás, Krisztina/0000-0001-8933-2033}
}

@article{MTMT:33554742,
	title = {Impact of Experimental Conditions on Extracellular Vesicles’ Proteome: A Comparative Study},
	url = {https://m2.mtmt.hu/api/publication/33554742},
	author = {Böröczky, Timea and Dobra, Gabriella and Bukva, Mátyás and Gyukity-Sebestyén, Edina and Hunyadi-Gulyás Éva, Csilla and Darula, Zsuzsanna and Horváth, Péter and Buzás, Krisztina and Harmati, Mária},
	doi = {10.3390/life13010206},
	journal-iso = {LIFE-BASEL},
	journal = {LIFE-BASEL},
	volume = {13},
	unique-id = {33554742},
	abstract = {Extracellular vesicle (EV) research is a rapidly developing field, mainly due to the key role of EVs in intercellular communication and pathophysiological processes. However, the heterogeneity of EVs challenges their exploration and the establishment of gold-standard methods. Here, we aimed to reveal the influence of technical changes on EV biology and the reliability of experimental data. We used B16F1 melanoma cells as a model and applied nanoparticle tracking analysis, mass spectrometry (LC-MS/MS) and pathway enrichment analysis to analyze the quantity, size distribution, proteome and function of their small EVs (sEVs) produced in sEV-depleted fetal bovine serum (FBS)-containing medium or serum-free medium. Additionally, we investigated the effects of minor technical variances on the quality of sEV preparations. We found that storage of the isolates at −80 °C has no adverse effect on LC-MS/MS analysis, and an additional washing step after differential ultracentrifugation has a minor influence on the sEV proteome. In contrast, FBS starvation affects the production and proteome of sEVs; moreover, these vesicles may have a greater impact on protein metabolism, but a smaller impact on cell adhesion and membrane raft assembly, than the control sEVs. As we demonstrated that FBS starvation has a strong influence on sEV biology, applying serum-free conditions might be considered in in vitro sEV studies.},
	year = {2023},
	eissn = {2075-1729},
	orcid-numbers = {Böröczky, Timea/0009-0009-3390-7809; Dobra, Gabriella/0000-0002-2814-7720; Bukva, Mátyás/0000-0002-5225-0285; Gyukity-Sebestyén, Edina/0000-0003-1383-6301; Buzás, Krisztina/0000-0001-8933-2033; Harmati, Mária/0000-0002-4875-5723}
}

@article{MTMT:32557474,
	title = {The role of the metabolite cargo of extracellular vesicles in tumor progression},
	url = {https://m2.mtmt.hu/api/publication/32557474},
	author = {Harmati, Mária and Bukva, Mátyás and Böröczky, Timea and Buzás, Krisztina and Gyukity-Sebestyén, Edina},
	doi = {10.1007/s10555-021-10014-2},
	journal-iso = {CANCER METAST REV},
	journal = {CANCER AND METASTASIS REVIEWS},
	volume = {40},
	unique-id = {32557474},
	issn = {0167-7659},
	abstract = {Metabolomic reprogramming in tumor and stroma cells is a hallmark of cancer but understanding its effects on the metabolite composition and function of tumor-derived extracellular vesicles (EVs) is still in its infancy. EVs are membrane-bound sacs with a complex molecular composition secreted by all living cells. They are key mediators of intercellular communication both in normal and pathological conditions and play a crucial role in tumor development. Although lipids are major components of EVs, most of the EV cargo studies have targeted proteins and nucleic acids. The potential of the EV metabolome as a source for biomarker discovery has gained recognition recently, but knowledge on the biological activity of tumor EV metabolites still remains limited. Therefore, we aimed (i) to compile the list of metabolites identified in tumor EVs isolated from either clinical specimens or in vitro samples and (ii) describe their role in tumor progression through literature search and pathway analysis.},
	keywords = {EXPRESSION; METABOLITES; CANCER; proteomics; FATTY-ACID; HYPOXIA; CELL LUNG-CANCER; INTERCELLULAR COMMUNICATION; Exosomes; Extracellular vesicles; POTENTIAL BIOMARKERS; ALPHA-AMINOADIPATE},
	year = {2021},
	eissn = {1573-7233},
	pages = {1203-1221},
	orcid-numbers = {Harmati, Mária/0000-0002-4875-5723; Bukva, Mátyás/0000-0002-5225-0285; Böröczky, Timea/0009-0009-3390-7809; Buzás, Krisztina/0000-0001-8933-2033; Gyukity-Sebestyén, Edina/0000-0003-1383-6301}
}

@article{MTMT:32129396,
	title = {SpheroidPicker for automated 3D cell culture manipulation using deep learning},
	url = {https://m2.mtmt.hu/api/publication/32129396},
	author = {Grexa, István and Diósdi, Ákos and Harmati, Mária and Kriston, András and Moshkov, Nikita and Buzás, Krisztina and Pietiäinen, Vilja and Koós, Krisztián and Horváth, Péter},
	doi = {10.1038/s41598-021-94217-1},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {11},
	unique-id = {32129396},
	issn = {2045-2322},
	year = {2021},
	eissn = {2045-2322},
	orcid-numbers = {Harmati, Mária/0000-0002-4875-5723; Buzás, Krisztina/0000-0001-8933-2033}
}

@article{MTMT:32106323,
	title = {Cell lines and clearing approaches: a single-cell level 3D light-sheet fluorescence microscopy dataset of multicellular spheroids},
	url = {https://m2.mtmt.hu/api/publication/32106323},
	author = {Diósdi, Ákos and Hirling, Dominik and Kovács, Mária and Tóth, Tímea and Harmati, Mária and Koós, Krisztián and Buzás, Krisztina and Piccinini, Filippo and Horváth, Péter},
	doi = {10.1016/j.dib.2021.107090},
	journal-iso = {DATA BRIEF},
	journal = {DATA IN BRIEF},
	volume = {36},
	unique-id = {32106323},
	abstract = {Nowadays, three dimensional (3D) cell cultures are widely used in the biological laboratories and several optical clearing approaches have been proposed to visualize individual cells in the deepest layers of cancer multicellular spheroids. However, defining the most appropriate clearing approach for the different cell lines is an open issue due to the lack of a gold standard quantitative metric. In this article, we describe and share a single-cell resolution 3D image dataset of human carcinoma spheroids imaged using a light-sheet fluorescence microscope. The dataset contains 90 multicellular cancer spheroids derived from 3 cell lines (i.e. T-47D, 5-8F, and Huh-7D12) and cleared with 5 different protocols, precisely Clear(T) , Clear(T2) , CUBIC, ScaleA2, and Sucrose. To evaluate image quality and light penetration depth of the cleared 3D samples, all the spheroids have been imaged under the same experimental conditions, labelling the nuclei with the DRAQ(5) stain and using a Leica SP8 Digital LightSheet microscope. The clearing quality of this dataset was annotated by 10 independent experts and thus allows microscopy users to qualitatively compare the effects of different optical clearing protocols on different cell lines. It is also an optimal testbed to quantitatively assess different com putational metrics evaluating the image quality in the deepest layers of the spheroids. (C) 2021 The Author(s). Published by Elsevier Inc.},
	keywords = {multicellular spheroids; Carcinoma cell lines; light-sheet fluorescence microscopy; optical tissue clearing},
	year = {2021},
	eissn = {2352-3409},
	orcid-numbers = {Harmati, Mária/0000-0002-4875-5723; Buzás, Krisztina/0000-0001-8933-2033}
}

@article{MTMT:31981009,
	title = {A quantitative metric for the comparative evaluation of optical clearing protocols for 3D multicellular spheroids},
	url = {https://m2.mtmt.hu/api/publication/31981009},
	author = {Diósdi, Ákos and Hirling, Dominik and Kovács, Mária and Tóth, Tímea and Harmati, Mária and Koós, Krisztián and Buzás, Krisztina and Piccinini, F. and Horváth, Péter},
	doi = {10.1016/j.csbj.2021.01.040},
	journal-iso = {CSBJ},
	journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
	volume = {19},
	unique-id = {31981009},
	issn = {2001-0370},
	abstract = {3D multicellular spheroids quickly emerged as in vitro models because they represent the in vivo tumor environment better than standard 2D cell cultures. However, with current microscopy technologies, it is difficult to visualize individual cells in the deeper layers of 3D samples mainly because of limited light penetration and scattering. To overcome this problem several optical clearing methods have been proposed but defining the most appropriate clearing approach is an open issue due to the lack of a gold standard metric. Here, we propose a guideline for 3D light microscopy imaging to achieve single-cell resolution. The guideline includes a validation experiment focusing on five optical clearing protocols. We review and compare seven quality metrics which quantitatively characterize the imaging quality of spheroids. As a test environment, we have created and shared a large 3D dataset including approximately hundred fluorescently stained and optically cleared spheroids. Based on the results we introduce the use of a novel quality metric as a promising method to serve as a gold standard, applicable to compare optical clearing protocols, and decide on the most suitable one for a particular experiment. © 2021 The Authors},
	keywords = {ARTICLE; MICROSCOPY; human; quantitative analysis; case report; clinical article; human cell; cell culture; practice guideline; validation process; gold standard; Statistical tests; Comparative evaluations; Large dataset; multicellular spheroid; multicellular spheroid; Light-sheet microscopy; Spheroid; Optical clearing; Single cell resolution; Quality metrices; Microscopy imaging; light penetration; optical tissue clearing; Focus metrics; Quantitative metric},
	year = {2021},
	eissn = {2001-0370},
	pages = {1233-1243},
	orcid-numbers = {Harmati, Mária/0000-0002-4875-5723; Buzás, Krisztina/0000-0001-8933-2033}
}