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Article ; Online: DNA sequence context as a marker of CpG methylation instability in normal and cancer tissues.

Scala, Giovanni / Federico, Antonio / Palumbo, Domenico / Cocozza, Sergio / Greco, Dario

2020 Volume 10, Issue 1, Page(s) 1721

Abstract: DNA methylation alterations are related to multiple molecular mechanisms. The DNA context of CpG sites plays a crucial role in the maintenance and stability of methylation patterns. The quantitative relationship between DNA composition and DNA ... ...

Abstract	DNA methylation alterations are related to multiple molecular mechanisms. The DNA context of CpG sites plays a crucial role in the maintenance and stability of methylation patterns. The quantitative relationship between DNA composition and DNA methylation has been studied in normal as well as pathological conditions, showing that DNA methylation status is highly dependent on the local sequence context. In this work, we describe this relationship by analyzing the DNA sequence context associated to methylation profiles in both physiological and pathological conditions. In particular, we used DNA motifs to describe methylation stability patterns in normal tissues and aberrant methylation events in cancer lesions. In this manuscript, we show how different groups of DNA sequences can be related to specific epigenetic events, across normal and cancer tissues, and provide a thorough structural and functional characterization of these sequences.
MeSH term(s)	Base Sequence/genetics ; CpG Islands/genetics ; DNA Methylation/genetics ; Epigenesis, Genetic ; Genetic Markers ; Genomic Instability ; Humans ; Neoplasms/genetics ; Nucleotide Motifs ; Oligonucleotide Array Sequence Analysis
Chemical Substances	Genetic Markers
Language	English
Publishing date	2020-02-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-58331-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Differential proteomics argues against a general role for CD9, CD81 or CD63 in the sorting of proteins into extracellular vesicles.

Fan, Yé / Pionneau, Cédric / Cocozza, Federico / Boëlle, Pierre-Yves / Chardonnet, Solenne / Charrin, Stéphanie / Théry, Clotilde / Zimmermann, Pascale / Rubinstein, Eric

Journal of extracellular vesicles

2023 Volume 12, Issue 8, Page(s) e12352

Abstract: The tetraspanins CD9, CD81 and CD63 are major components of extracellular vesicles (EVs). Yet, their impact on EV composition remains under-investigated. In the MCF7 breast cancer cell line CD63 was as expected predominantly intracellular. In contrast ... ...

Abstract	The tetraspanins CD9, CD81 and CD63 are major components of extracellular vesicles (EVs). Yet, their impact on EV composition remains under-investigated. In the MCF7 breast cancer cell line CD63 was as expected predominantly intracellular. In contrast CD9 and CD81 strongly colocalized at the plasma membrane, albeit with different ratios at different sites, which may explain a higher enrichment of CD81 in EVs. Absence of these tetraspanins had little impact on the EV protein composition as analysed by quantitative mass spectrometry. We also analysed the effect of concomitant knock-out of CD9 and CD81 because these two tetraspanins play similar roles in several cellular processes and associate directly with two Ig domain proteins, CD9P-1/EWI-F/PTGFRN and EWI-2/IGSF8. These were the sole proteins significantly decreased in the EVs of double CD9- and CD81-deficient cells. In the case of EWI-2, this is primarily a consequence of a decreased cell expression level. In conclusion, this study shows that CD9, CD81 and CD63, commonly used as EV protein markers, play a marginal role in determining the protein composition of EVs released by MCF7 cells and highlights a regulation of the expression level and/or trafficking of CD9P-1 and EWI-2 by CD9 and CD81.
MeSH term(s)	Cell Movement ; Extracellular Vesicles/metabolism ; Proteomics ; Tetraspanin 28/metabolism ; Humans ; MCF-7 Cells ; Tetraspanin 29/metabolism ; Tetraspanin 30/metabolism
Chemical Substances	Tetraspanin 28 ; Tetraspanin 29 ; CD63 protein, human ; Tetraspanin 30
Language	English
Publishing date	2023-08-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2683797-3
ISSN	2001-3078 ; 2001-3078
ISSN (online)	2001-3078
ISSN	2001-3078
DOI	10.1002/jev2.12352
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Article ; Online: Root Exposure to 5-Aminolevulinic Acid (ALA) Affects Leaf Element Accumulation, Isoprene Emission, Phytohormonal Balance, and Photosynthesis of Salt-Stressed

Brilli, Federico / Pignattelli, Sara / Baraldi, Rita / Neri, Luisa / Pollastri, Susanna / Gonnelli, Cristina / Giovannelli, Alessio / Loreto, Francesco / Cocozza, Claudia

International journal of molecular sciences

2022 Volume 23, Issue 8

Abstract: ... Arundo ... ...

Abstract	Arundo donax
MeSH term(s)	Abscisic Acid/metabolism ; Aminolevulinic Acid/metabolism ; Butadienes ; Hemiterpenes ; Photosynthesis ; Plant Growth Regulators ; Plant Leaves/metabolism ; Plant Roots/metabolism ; Poaceae/metabolism ; Salt Stress
Chemical Substances	Butadienes ; Hemiterpenes ; Plant Growth Regulators ; isoprene (0A62964IBU) ; Abscisic Acid (72S9A8J5GW) ; Aminolevulinic Acid (88755TAZ87)
Language	English
Publishing date	2022-04-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23084311
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Article ; Online: Management of Renal Cell Carcinoma With Extensive Caval Thrombosis Utilizing a Temporary Atrial Caval Filter Through a Combined Endovascular and Open Surgical Technique.

Fontana, Federico / Deho, Federico / Piacentino, Filippo / Curti, Marco / Capogrosso, Paolo / Coppola, Andrea / Cocozza, Eugenio / Tozzi, Matteo / Venturini, Massimo

Vascular and endovascular surgery

2021 Volume 55, Issue 5, Page(s) 505–509

Abstract: The most common cause of neoplastic thrombotic infiltration of the inferior vena cava is renal cell carcinoma (RCC). In the present report we described a case of a patient with massive RCC and extensive neoplastic thrombosis reaching the retrohepatic ... ...

Abstract	The most common cause of neoplastic thrombotic infiltration of the inferior vena cava is renal cell carcinoma (RCC). In the present report we described a case of a patient with massive RCC and extensive neoplastic thrombosis reaching the retrohepatic tract of the inferior vena cava. After a discussion in a multidisciplinary team meeting we decided to perform a radical nephrectomy with vena cava thrombectomy along with the support of a novel removable vena cava filter in order to avoid thromboembolism during the surgical procedure. Furthermore, a preoperative renal artery embolization with a non-adhesive liquid embolic agent was performed ahead of the surgical procedure in order to reduce the risk of intraoperative bleeding. The surgical procedure performed the day after was based on a hybrid endovascular-surgical approach consisting in nephrectomy, liver derotation, cavotomy with the additional use of a novel temporary caval filter, thus reducing the risk of intraoperative thromboembolic dissemination.
MeSH term(s)	Aged ; Carcinoma, Renal Cell/diagnostic imaging ; Carcinoma, Renal Cell/pathology ; Carcinoma, Renal Cell/surgery ; Device Removal ; Embolization, Therapeutic ; Humans ; Kidney Neoplasms/diagnostic imaging ; Kidney Neoplasms/pathology ; Kidney Neoplasms/surgery ; Male ; Neoplasm Invasiveness ; Nephrectomy ; Prosthesis Implantation/instrumentation ; Thrombectomy/instrumentation ; Treatment Outcome ; Vena Cava Filters ; Vena Cava, Inferior/diagnostic imaging ; Vena Cava, Inferior/pathology ; Vena Cava, Inferior/surgery ; Venous Thrombosis/diagnostic imaging ; Venous Thrombosis/pathology ; Venous Thrombosis/surgery
Language	English
Publishing date	2021-02-04
Publishing country	United States
Document type	Case Reports
ZDB-ID	2076272-0
ISSN	1938-9116 ; 1538-5744
ISSN (online)	1938-9116
ISSN	1538-5744
DOI	10.1177/1538574421989862
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Article: SnapShot: Extracellular Vesicles

Cocozza, Federico / Grisard, Eleonora / Martin-Jaular, Lorena / Mathieu, Mathilde / Théry, Clotilde

Cell. 2020 July 09, v. 182, no. 1

2020

Abstract: Cells release a variety of extracellular vesicles (EVs; including exosomes, microvesicles, and many others) into their environment. EVs can bud in endosomes or directly at the plasma membrane, carrying a selection of components from the cell and ... ...

Abstract	Cells release a variety of extracellular vesicles (EVs; including exosomes, microvesicles, and many others) into their environment. EVs can bud in endosomes or directly at the plasma membrane, carrying a selection of components from the cell and displaying various functional properties. Different techniques can be used to separate EV subtypes and EVs from co-isolated components, resulting in preparations of different abundance and purity.
Keywords	endosomes ; exosomes ; functional properties ; plasma membrane
Language	English
Dates of publication	2020-0709
Size	p. 262-262.e1.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2020.04.054
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: SnapShot: Extracellular Vesicles.

Cocozza, Federico / Grisard, Eleonora / Martin-Jaular, Lorena / Mathieu, Mathilde / Théry, Clotilde

Cell

2020 Volume 182, Issue 1, Page(s) 262–262.e1

Abstract	Cells release a variety of extracellular vesicles (EVs; including exosomes, microvesicles, and many others) into their environment. EVs can bud in endosomes or directly at the plasma membrane, carrying a selection of components from the cell and displaying various functional properties. Different techniques can be used to separate EV subtypes and EVs from co-isolated components, resulting in preparations of different abundance and purity.
MeSH term(s)	Endosomes/metabolism ; Extracellular Vesicles/metabolism ; Humans
Language	English
Publishing date	2020-07-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2020.04.054
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Article ; Online: Real-time monitoring of Arundo donax response to saline stress through the application of in vivo sensing technology.

Michela, Janni / Claudia, Cocozza / Federico, Brilli / Sara, Pignattelli / Filippo, Vurro / Nicola, Coppede / Manuele, Bettelli / Davide, Calestani / Loreto, Francesco / Zappettini, Andrea

Scientific reports

2021 Volume 11, Issue 1, Page(s) 18598

Abstract: One of the main impacts of climate change on agriculture production is the dramatic increase of saline ( ... ...

Abstract	One of the main impacts of climate change on agriculture production is the dramatic increase of saline (Na
Language	English
Publishing date	2021-09-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-97872-6
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Article ; Online: Root Exposure to 5-Aminolevulinic Acid (ALA) Affects Leaf Element Accumulation, Isoprene Emission, Phytohormonal Balance, and Photosynthesis of Salt-Stressed Arundo donax

Federico Brilli / Sara Pignattelli / Rita Baraldi / Luisa Neri / Susanna Pollastri / Cristina Gonnelli / Alessio Giovannelli / Francesco Loreto / Claudia Cocozza

International Journal of Molecular Sciences, Vol 23, Iss 4311, p

2022 Volume 4311

Abstract: Arundo donax has been recognized as a promising crop for biomass production on marginal lands due to its superior productivity and stress tolerance. However, salt stress negatively impacts A. donax growth and photosynthesis. In this study, we tested ... ...

Abstract	Arundo donax has been recognized as a promising crop for biomass production on marginal lands due to its superior productivity and stress tolerance. However, salt stress negatively impacts A. donax growth and photosynthesis. In this study, we tested whether the tolerance of A. donax to salinity stress can be enhanced by the addition of 5-aminolevulinic acid (ALA), a known promoter of plant growth and abiotic stress tolerance. Our results indicated that root exposure to ALA increased the ALA levels in leaves along the A. donax plant profile. ALA enhanced Na + accumulation in the roots of salt-stressed plants and, at the same time, lowered Na + concentration in leaves, while a reduced callose amount was found in the root tissue. ALA also improved the photosynthetic performance of salt-stressed apical leaves by stimulating stomatal opening and preventing an increase in the ratio between abscisic acid (ABA) and indol-3-acetic acid (IAA), without affecting leaf methanol emission and plant growth. Supply of ALA to the roots reduced isoprene fluxes from leaves of non-stressed plants, while it sustained isoprene fluxes along the profile of salt-stressed A. donax . Thus, ALA likely interacted with the methylerythritol 4-phosphate (MEP) pathway and modulate the synthesis of either ABA or isoprene under stressful conditions. Overall, our study highlights the effectiveness of ALA supply through soil fertirrigation in preserving the young apical developing leaves from the detrimental effects of salt stress, thus helping of A. donax to cope with salinity and favoring the recovery of the whole plant once the stress is removed.
Keywords	volatile organic compounds (VOCs) ; indol-3-acetic acid (IAA) ; abscisic acid (ABA) ; growth ; sodium (Na + ) ; stress tolerance ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Extracellular vesicles and co-isolated endogenous retroviruses from murine cancer cells differentially affect dendritic cells.

Cocozza, Federico / Martin-Jaular, Lorena / Lippens, Lien / Di Cicco, Aurelie / Arribas, Yago A / Ansart, Nicolas / Dingli, Florent / Richard, Michael / Merle, Louise / Jouve San Roman, Mabel / Poullet, Patrick / Loew, Damarys / Lévy, Daniel / Hendrix, An / Kassiotis, George / Joliot, Alain / Tkach, Mercedes / Théry, Clotilde

The EMBO journal

2023 Volume 42, Issue 24, Page(s) e113590

Abstract: Cells secrete extracellular vesicles (EVs) and non-vesicular extracellular (nano)particles (NVEPs or ENPs) that may play a role in intercellular communication. Tumor-derived EVs have been proposed to induce immune priming of antigen presenting cells or ... ...

Abstract	Cells secrete extracellular vesicles (EVs) and non-vesicular extracellular (nano)particles (NVEPs or ENPs) that may play a role in intercellular communication. Tumor-derived EVs have been proposed to induce immune priming of antigen presenting cells or to be immuno-suppressive agents. We suspect that such disparate functions are due to variable compositions in EV subtypes and ENPs. We aimed to characterize the array of secreted EVs and ENPs of murine tumor cell lines. Unexpectedly, we identified virus-like particles (VLPs) from endogenous murine leukemia virus in preparations of EVs produced by many tumor cells. We established a protocol to separate small EVs from VLPs and ENPs. We compared their protein composition and analyzed their functional interaction with target dendritic cells. ENPs were poorly captured and did not affect dendritic cells. Small EVs specifically induced dendritic cell death. A mixed large/dense EV/VLP preparation was most efficient to induce dendritic cell maturation and antigen presentation. Our results call for systematic re-evaluation of the respective proportions and functions of non-viral EVs and VLPs produced by murine tumors and their contribution to tumor progression.
MeSH term(s)	Animals ; Mice ; Endogenous Retroviruses ; Extracellular Vesicles/metabolism ; Cell Line, Tumor ; Cell Differentiation ; Dendritic Cells ; Neoplasms/metabolism
Language	English
Publishing date	2023-12-10
Publishing country	England
Document type	Journal Article
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2023113590
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Article ; Online: Systemic administration of imiquimod as an adjuvant improves immunogenicity of a tumor-lysate vaccine inducing the rejection of a highly aggressive T-cell lymphoma.

Sciullo, Paula Di / Menay, Florencia / Cocozza, Federico / Gravisaco, María José / Waldner, Claudia I / Mongini, Claudia

Clinical immunology (Orlando, Fla.)

2019 Volume 203, Page(s) 154–161

Abstract: T-cell lymphomas include diverse malignancies. They are rare, some have low survival rates and they lack curative therapies. The aim of this work was to assess whether employing the TLR7 agonist imiquimod and the T-cell costimulatory molecule CD40 or the ...

Abstract	T-cell lymphomas include diverse malignancies. They are rare, some have low survival rates and they lack curative therapies. The aim of this work was to assess whether employing the TLR7 agonist imiquimod and the T-cell costimulatory molecule CD40 or the combination of both as adjuvants of a cell lysate vaccine could enhance the antitumor immune response using a murine T-cell lymphoma model. Immunization with LBC-lysate and imiquimod protected almost all vaccinated animals. A specific humoral and a Th1-type cellular immunity were induced in mice that rejected the lymphoma, characterized by an elevated number of CD4 + T-cells and secretion of IFN-γ, locally and systemically. In contrast, CD40 alone or in combination with imiquimod did not improve the protective response obtained with LBC-lysate and imiquimod. Systemic administration of imiquimod proved to have high potential to serve as a vaccine adjuvant for the treatment of T-cell lymphomas and was effective in this immunotherapy model.
MeSH term(s)	Adjuvants, Immunologic/therapeutic use ; Animals ; Antigens, Neoplasm/immunology ; Cancer Vaccines/immunology ; Cell Extracts/immunology ; Cell Line, Tumor ; Disease Models, Animal ; Female ; Graft vs Tumor Effect/immunology ; Humans ; Imiquimod/pharmacology ; Imiquimod/therapeutic use ; Lymphoma, T-Cell/immunology ; Lymphoma, T-Cell/therapy ; Mice ; Mice, Inbred BALB C ; Toll-Like Receptor 7/agonists
Chemical Substances	Adjuvants, Immunologic ; Antigens, Neoplasm ; Cancer Vaccines ; Cell Extracts ; Toll-Like Receptor 7 ; Imiquimod (P1QW714R7M)
Language	English
Publishing date	2019-04-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1459903-x
ISSN	1521-7035 ; 1521-6616
ISSN (online)	1521-7035
ISSN	1521-6616
DOI	10.1016/j.clim.2019.04.013
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