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Article: On the risk of further excluding outcast patient populations in South America.

Ruiz, Eloy / Fernández, Ramiro / Berrospi, Francisco / Casavilca-Zambrano, Sandro / Contreras-Mancilla, Juan / Cerapio, Juan Pablo / Pineau, Pascal / Bertani, Stéphane

Annals of hepatology

2023 Volume 28, Issue 2, Page(s) 100901

MeSH term(s)	Humans ; South America/epidemiology ; Genetic Variation ; Phylogeny
Language	English
Publishing date	2023-02-07
Publishing country	Mexico
Document type	Letter ; Comment
ZDB-ID	2188733-0
ISSN	1665-2681
ISSN	1665-2681
DOI	10.1016/j.aohep.2023.100901
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Article ; Online: On the risk of further excluding outcast patient populations in South America

Eloy Ruiz / Ramiro Fernández / Francisco Berrospi / Sandro Casavilca-Zambrano / Juan Contreras-Mancilla / Juan Pablo Cerapio / Pascal Pineau / Stéphane Bertani

Annals of Hepatology, Vol 28, Iss 2, Pp 100901- (2023)

2023

Keywords	Specialties of internal medicine ; RC581-951
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The STEMRI trial: Magnetic resonance spectroscopy imaging can define tumor areas enriched in glioblastoma stem-like cells.

Lemarié, Anthony / Lubrano, Vincent / Delmas, Caroline / Lusque, Amélie / Cerapio, Juan-Pablo / Perrier, Marion / Siegfried, Aurore / Arnauduc, Florent / Nicaise, Yvan / Dahan, Perrine / Filleron, Thomas / Mounier, Muriel / Toulas, Christine / Cohen-Jonathan Moyal, Elizabeth

Science advances

2023 Volume 9, Issue 44, Page(s) eadi0114

Abstract: Despite maximally safe resection of the magnetic resonance imaging (MRI)-defined contrast-enhanced (CE) central tumor area and chemoradiotherapy, most patients with glioblastoma (GBM) relapse within a year in peritumoral FLAIR regions. Magnetic resonance ...

Abstract	Despite maximally safe resection of the magnetic resonance imaging (MRI)-defined contrast-enhanced (CE) central tumor area and chemoradiotherapy, most patients with glioblastoma (GBM) relapse within a year in peritumoral FLAIR regions. Magnetic resonance spectroscopy imaging (MRSI) can discriminate metabolic tumor areas with higher recurrence potential as CNI+ regions (choline/
MeSH term(s)	Humans ; Brain Neoplasms/pathology ; Glioblastoma/metabolism ; Magnetic Resonance Imaging/methods ; Magnetic Resonance Spectroscopy/methods ; Neoplasm Recurrence, Local/pathology ; Neoplastic Stem Cells/metabolism ; Prospective Studies ; Recurrence
Language	English
Publishing date	2023-11-03
Publishing country	United States
Document type	Clinical Trial ; Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adi0114
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics.

Pont, Frédéric / Cerapio, Juan Pablo / Gravelle, Pauline / Ligat, Laetitia / Valle, Carine / Sarot, Emeline / Perrier, Marion / Lopez, Frédéric / Laurent, Camille / Fournié, Jean Jacques / Tosolini, Marie

BMC bioinformatics

2023 Volume 24, Issue 1, Page(s) 30

Abstract: Background: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called 'spatial transcriptomics'. Currently ... ...

Abstract	Background: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called 'spatial transcriptomics'. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. Results: Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies. Conclusions: Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.
MeSH term(s)	Humans ; Animals ; Mice ; Transcriptome ; Software ; Gene Expression Profiling ; Spatial Analysis ; Single-Cell Analysis
Language	English
Publishing date	2023-01-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-023-05150-1
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Article ; Online: The proteome and transcriptome of stress granules and P bodies during human T lymphocyte activation.

Curdy, Nicolas / Lanvin, Olivia / Cerapio, Juan-Pablo / Pont, Fréderic / Tosolini, Marie / Sarot, Emeline / Valle, Carine / Saint-Laurent, Nathalie / Lhuillier, Emeline / Laurent, Camille / Fournié, Jean-Jacques / Franchini, Don-Marc

Cell reports

2023 Volume 42, Issue 3, Page(s) 112211

Abstract: Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their ... ...

Abstract	Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their immune functions under regulatory mechanisms involving SGs and PBs. However, the impact of T cell activation on such complexes in terms of formation, constitution, and relationship remains unknown. Here, by combining proteomic, transcriptomic, and immunofluorescence approaches, we simultaneously characterized the SGs and PBs from primary human T lymphocytes pre and post stimulation. The identification of the proteomes and transcriptomes of SGs and PBs indicate an unanticipated molecular and functional complementarity. Notwithstanding, these granules keep distinct spatial organizations and abilities to interact with mRNAs. This comprehensive characterization of the RNP granule proteomic and transcriptomic landscapes provides a unique resource for future investigations on SGs and PBs in T lymphocytes.
MeSH term(s)	Stress Granules/metabolism ; T-Lymphocytes/cytology ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism ; Lymphocyte Activation ; Processing Bodies/metabolism ; Proteome/metabolism ; Transcriptome/genetics ; Proteomics ; Gene Expression Profiling ; Humans ; Male ; Female ; Adult ; Cells, Cultured ; RNA/analysis ; Protein Biosynthesis ; Transcription, Genetic ; Cell Fractionation
Chemical Substances	Proteome ; RNA (63231-63-0)
Language	English
Publishing date	2023-03-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.112211
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Single-Cell RNAseq Profiling of Human γδ T Lymphocytes in Virus-Related Cancers and COVID-19 Disease

Cerapio, Juan Pablo / Perrier, Marion / Pont, Fréderic / Tosolini, Marie / Laurent, Camille / Bertani, Stéphane / Fournie, Jean-Jacques

Viruses. 2021 Nov. 03, v. 13, no. 11

2021

Abstract: The detailed characterization of human γδ T lymphocyte differentiation at the single-cell transcriptomic (scRNAseq) level in tumors and patients with coronavirus disease 2019 (COVID-19) requires both a reference differentiation trajectory of γδ T cells ... ...

Abstract	The detailed characterization of human γδ T lymphocyte differentiation at the single-cell transcriptomic (scRNAseq) level in tumors and patients with coronavirus disease 2019 (COVID-19) requires both a reference differentiation trajectory of γδ T cells and a robust mapping method for additional γδ T lymphocytes. Here, we incepted such a method to characterize thousands of γδ T lymphocytes from (n = 95) patients with cancer or adult and pediatric COVID-19 disease. We found that cancer patients with human papillomavirus-positive head and neck squamous cell carcinoma and Epstein–Barr virus-positive Hodgkin’s lymphoma have γδ tumor-infiltrating T lymphocytes that are more prone to recirculate from the tumor and avoid exhaustion. In COVID-19, both TCRVγ9 and TCRVγnon9 subsets of γδ T lymphocytes relocalize from peripheral blood mononuclear cells (PBMC) to the infected lung tissue, where their advanced differentiation, tissue residency, and exhaustion reflect T cell activation. Although severe COVID-19 disease increases both recruitment and exhaustion of γδ T lymphocytes in infected lung lesions but not blood, the anti-IL6R therapy with Tocilizumab promotes γδ T lymphocyte differentiation in patients with COVID-19. PBMC from pediatric patients with acute COVID-19 disease display similar γδ T cell lymphopenia to that seen in adult patients. However, blood γδ T cells from children with the COVID-19-related multisystem inflammatory syndrome are not lymphodepleted, but they are differentiated as in healthy PBMC. These findings suggest that some virus-induced memory γδ T lymphocytes durably persist in the blood of adults and could subsequently infiltrate and recirculate in tumors.
Keywords	COVID-19 infection ; T-lymphocytes ; adults ; head and neck squamous cell carcinoma ; humans ; lungs ; memory ; therapeutics ; transcriptomics
Language	English
Dates of publication	2021-1103
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112212
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Cytidine Deaminase Resolves Replicative Stress and Protects Pancreatic Cancer from DNA-Targeting Drugs.

Lumeau, Audrey / Bery, Nicolas / Francès, Audrey / Gayral, Marion / Labrousse, Guillaume / Ribeyre, Cyril / Lopez, Charlene / Nevot, Adele / El Kaoutari, Abdessamad / Hanoun, Naima / Sarot, Emeline / Perrier, Marion / Pont, Frederic / Cerapio, Juan-Pablo / Fournié, Jean-Jacques / Lopez, Frederic / Madrid-Mencia, Miguel / Pancaldi, Vera / Pillaire, Marie-Jeanne /

Bergoglio, Valerie / Torrisani, Jerome / Dusetti, Nelson / Hoffmann, Jean-Sebastien / Buscail, Louis / Lutzmann, Malik / Cordelier, Pierre

Cancer research

2024 Volume 84, Issue 7, Page(s) 1013–1028

Abstract: Cytidine deaminase (CDA) functions in the pyrimidine salvage pathway for DNA and RNA syntheses and has been shown to protect cancer cells from deoxycytidine-based chemotherapies. In this study, we observed that CDA was overexpressed in pancreatic ... ...

Abstract	Cytidine deaminase (CDA) functions in the pyrimidine salvage pathway for DNA and RNA syntheses and has been shown to protect cancer cells from deoxycytidine-based chemotherapies. In this study, we observed that CDA was overexpressed in pancreatic adenocarcinoma from patients at baseline and was essential for experimental tumor growth. Mechanistic investigations revealed that CDA localized to replication forks where it increased replication speed, improved replication fork restart efficiency, reduced endogenous replication stress, minimized DNA breaks, and regulated genetic stability during DNA replication. In cellular pancreatic cancer models, high CDA expression correlated with resistance to DNA-damaging agents. Silencing CDA in patient-derived primary cultures in vitro and in orthotopic xenografts in vivo increased replication stress and sensitized pancreatic adenocarcinoma cells to oxaliplatin. This study sheds light on the role of CDA in pancreatic adenocarcinoma, offering insights into how this tumor type modulates replication stress. These findings suggest that CDA expression could potentially predict therapeutic efficacy and that targeting CDA induces intolerable levels of replication stress in cancer cells, particularly when combined with DNA-targeted therapies. Significance: Cytidine deaminase reduces replication stress and regulates DNA replication to confer resistance to DNA-damaging drugs in pancreatic cancer, unveiling a molecular vulnerability that could enhance treatment response.
MeSH term(s)	Humans ; Adenocarcinoma/drug therapy ; Adenocarcinoma/metabolism ; Adenocarcinoma/pathology ; Cytidine Deaminase/metabolism ; DNA ; Pancreatic Neoplasms/drug therapy ; Pancreatic Neoplasms/genetics ; Pancreatic Neoplasms/pathology ; DNA Replication ; Nucleic Acid Synthesis Inhibitors/therapeutic use
Chemical Substances	Cytidine Deaminase (EC 3.5.4.5) ; DNA (9007-49-2) ; Nucleic Acid Synthesis Inhibitors
Language	English
Publishing date	2024-01-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	1432-1
ISSN	1538-7445 ; 0008-5472
ISSN (online)	1538-7445
ISSN	0008-5472
DOI	10.1158/0008-5472.CAN-22-3219
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Article ; Online: Single-Cell RNAseq Profiling of Human γδ T Lymphocytes in Virus-Related Cancers and COVID-19 Disease.

Cerapio, Juan Pablo / Perrier, Marion / Pont, Fréderic / Tosolini, Marie / Laurent, Camille / Bertani, Stéphane / Fournie, Jean-Jacques

Viruses

2021 Volume 13, Issue 11

Abstract	The detailed characterization of human γδ T lymphocyte differentiation at the single-cell transcriptomic (scRNAseq) level in tumors and patients with coronavirus disease 2019 (COVID-19) requires both a reference differentiation trajectory of γδ T cells and a robust mapping method for additional γδ T lymphocytes. Here, we incepted such a method to characterize thousands of γδ T lymphocytes from (
MeSH term(s)	Adult ; Bronchoalveolar Lavage Fluid/immunology ; COVID-19/complications ; COVID-19/immunology ; Cell Differentiation ; Child ; Head and Neck Neoplasms/immunology ; Head and Neck Neoplasms/virology ; Herpesvirus 4, Human/isolation & purification ; Hodgkin Disease/immunology ; Hodgkin Disease/virology ; Humans ; Lung/immunology ; Lymphocyte Activation ; Lymphocyte Count ; Lymphocytes, Tumor-Infiltrating/immunology ; Lymphocytes, Tumor-Infiltrating/metabolism ; Lymphocytes, Tumor-Infiltrating/physiology ; Neoplasms/immunology ; Neoplasms/virology ; Papillomaviridae/isolation & purification ; RNA-Seq ; Receptors, Antigen, T-Cell, gamma-delta/immunology ; Severity of Illness Index ; Single-Cell Analysis ; Systemic Inflammatory Response Syndrome/immunology ; T-Lymphocyte Subsets/immunology ; T-Lymphocyte Subsets/metabolism ; T-Lymphocyte Subsets/physiology
Chemical Substances	Receptors, Antigen, T-Cell, gamma-delta
Language	English
Publishing date	2021-11-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112212
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Single-cell spatial explorer

Frédéric Pont / Juan Pablo Cerapio / Pauline Gravelle / Laetitia Ligat / Carine Valle / Emeline Sarot / Marion Perrier / Frédéric Lopez / Camille Laurent / Jean Jacques Fournié / Marie Tosolini

BMC Bioinformatics, Vol 24, Iss 1, Pp 1-

easy exploration of spatial and multimodal transcriptomics

2023 Volume 12

Abstract: Abstract Background: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. ... ...

Abstract	Abstract Background: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. Results: Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies. Conclusions: Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.
Keywords	Spatial transcriptomics ; Single-cell ; Multimodal analysis ; Visualization ; Open-source ; Freeware ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	004
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The proteome and transcriptome of stress granules and P bodies during human T lymphocyte activation

Nicolas Curdy / Olivia Lanvin / Juan-Pablo Cerapio / Fréderic Pont / Marie Tosolini / Emeline Sarot / Carine Valle / Nathalie Saint-Laurent / Emeline Lhuillier / Camille Laurent / Jean-Jacques Fournié / Don-Marc Franchini

Cell Reports, Vol 42, Iss 3, Pp 112211- (2023)

2023

Abstract: Summary: Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate ... ...

Abstract	Summary: Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their immune functions under regulatory mechanisms involving SGs and PBs. However, the impact of T cell activation on such complexes in terms of formation, constitution, and relationship remains unknown. Here, by combining proteomic, transcriptomic, and immunofluorescence approaches, we simultaneously characterized the SGs and PBs from primary human T lymphocytes pre and post stimulation. The identification of the proteomes and transcriptomes of SGs and PBs indicate an unanticipated molecular and functional complementarity. Notwithstanding, these granules keep distinct spatial organizations and abilities to interact with mRNAs. This comprehensive characterization of the RNP granule proteomic and transcriptomic landscapes provides a unique resource for future investigations on SGs and PBs in T lymphocytes.
Keywords	CP: Immunology ; CP: Molecular biology ; Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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