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Schmidt J, Chiffelle J, Perez MAS, Magnin M, Bobisse S, Arnaud M, Genolet R, Cesbron J, Barras D, Navarro Rodrigo B, Benedetti F, Michel A, Queiroz L, Baumgaertner P, Guillaume P, Hebeisen M, Michielin O, Nguyen-Ngoc T, Huber F, Irving M, Tissot-Renaud S, Stevenson BJ, Rusakiewicz S, Dangaj Laniti D, Bassani-Sternberg M, Rufer N, Gfeller D, Kandalaft LE, Speiser DE, Zoete V, Coukos G, Harari A. Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors. Nat Commun 2023; 14:3188. [PMID: 37280206 DOI: 10.1038/s41467-023-38946-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
The success of cancer immunotherapy depends in part on the strength of antigen recognition by T cells. Here, we characterize the T cell receptor (TCR) functional (antigen sensitivity) and structural (monomeric pMHC-TCR off-rates) avidities of 371 CD8 T cell clones specific for neoantigens, tumor-associated antigens (TAAs) or viral antigens isolated from tumors or blood of patients and healthy donors. T cells from tumors exhibit stronger functional and structural avidity than their blood counterparts. Relative to TAA, neoantigen-specific T cells are of higher structural avidity and, consistently, are preferentially detected in tumors. Effective tumor infiltration in mice models is associated with high structural avidity and CXCR3 expression. Based on TCR biophysicochemical properties, we derive and apply an in silico model predicting TCR structural avidity and validate the enrichment in high avidity T cells in patients' tumors. These observations indicate a direct relationship between neoantigen recognition, T cell functionality and tumor infiltration. These results delineate a rational approach to identify potent T cells for personalized cancer immunotherapy.
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Affiliation(s)
- Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marta A S Perez
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Morgane Magnin
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Cesbron
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Blanca Navarro Rodrigo
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Petra Baumgaertner
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Michael Hebeisen
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Olivier Michielin
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Tu Nguyen-Ngoc
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Florian Huber
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Stéphanie Tissot-Renaud
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Brian J Stevenson
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sylvie Rusakiewicz
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Nathalie Rufer
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - David Gfeller
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniel E Speiser
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland.
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland.
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2
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Genolet R, Bobisse S, Chiffelle J, Arnaud M, Petremand R, Queiroz L, Michel A, Reichenbach P, Cesbron J, Auger A, Baumgaertner P, Guillaume P, Schmidt J, Irving M, Kandalaft LE, Speiser DE, Coukos G, Harari A. TCR sequencing and cloning methods for repertoire analysis and isolation of tumor-reactive TCRs. Cell Rep Methods 2023; 3:100459. [PMID: 37159666 PMCID: PMC10163020 DOI: 10.1016/j.crmeth.2023.100459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
T cell receptor (TCR) technologies, including repertoire analyses and T cell engineering, are increasingly important in the clinical management of cellular immunity in cancer, transplantation, and other immune diseases. However, sensitive and reliable methods for repertoire analyses and TCR cloning are still lacking. Here, we report on SEQTR, a high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible, and accurate as compared with commonly used assays, and thus more reliably captures the complexity of blood and tumor TCR repertoires. We also present a TCR cloning strategy to specifically amplify TCRs from T cell populations. Positioned downstream of single-cell or bulk TCR sequencing, it allows time- and cost-effective discovery, cloning, screening, and engineering of tumor-specific TCRs. Together, these methods will accelerate TCR repertoire analyses in discovery, translational, and clinical settings and permit fast TCR engineering for cellular therapies.
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Affiliation(s)
- Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Rémy Petremand
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Patrick Reichenbach
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Cesbron
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Aymeric Auger
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Petra Baumgaertner
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Lana E. Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Daniel E. Speiser
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
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3
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Gfeller D, Schmidt J, Croce G, Guillaume P, Bobisse S, Genolet R, Queiroz L, Cesbron J, Racle J, Harari A. Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8 + T-cell epitopes. Cell Syst 2023; 14:72-83.e5. [PMID: 36603583 PMCID: PMC9811684 DOI: 10.1016/j.cels.2022.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
The recognition of pathogen or cancer-specific epitopes by CD8+ T cells is crucial for the clearance of infections and the response to cancer immunotherapy. This process requires epitopes to be presented on class I human leukocyte antigen (HLA-I) molecules and recognized by the T-cell receptor (TCR). Machine learning models capturing these two aspects of immune recognition are key to improve epitope predictions. Here, we assembled a high-quality dataset of naturally presented HLA-I ligands and experimentally verified neo-epitopes. We then integrated these data in a refined computational framework to predict antigen presentation (MixMHCpred2.2) and TCR recognition (PRIME2.0). The depth of our training data and the algorithmic developments resulted in improved predictions of HLA-I ligands and neo-epitopes. Prospectively applying our tools to SARS-CoV-2 proteins revealed several epitopes. TCR sequencing identified a monoclonal response in effector/memory CD8+ T cells against one of these epitopes and cross-reactivity with the homologous peptides from other coronaviruses.
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Affiliation(s)
- David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland,Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland,Corresponding author
| | - Julien Schmidt
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Giancarlo Croce
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland,Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Sara Bobisse
- Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Raphael Genolet
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Lise Queiroz
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Julien Cesbron
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland,Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Alexandre Harari
- Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
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4
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Rodrigues J, Sá A, Fontes R, Barbosa A, Barbosa-Martins J, Oliveira C, Peixoto M, Santos S, Rocha J, Almeida M, Carvalho C, Queiroz L, Fernandes R, Faustino I, Portela C, Coutinho C, Nabiço R. Anxiety and depression screening during neoadjuvant chemotherapy treatment in early breast cancer patients: a multicenter longitudinal observational study. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)01446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Galaine J, Turco C, Vauchy C, Royer B, Mercier-Letondal P, Queiroz L, Loyon R, Mouget V, Boidot R, Laheurte C, Lakkis Z, Jary M, Adotévi O, Borg C, Godet Y. CD4 T cells target colorectal cancer antigens upregulated by oxaliplatin. Int J Cancer 2019; 145:3112-3125. [PMID: 31396953 DOI: 10.1002/ijc.32620] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/07/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
Immune checkpoint blockade has proven its efficacy in hypermutated subtypes of metastatic colorectal cancers (mCRC). Immunogenic potential can also be observed with conventional chemotherapies, but this property has never been explored thoroughly in CRC patients. The CRC therapeutic arsenal includes oxaliplatin, a well-characterized platinum drug already described as immunogenic. Here, we investigated the impact of the oxaliplatin-based treatment on mCRC immunopeptidome. We demonstrated that oxaliplatin-resistant CRC cell lines overexpressed telomerase reverse transcriptase (TERT), colorectal-associated-tumor antigen-1 (COA-1) and mesothelin tumor-associated antigens. We identified new HLA class-II-restricted and promiscuous peptides derived from COA-1 and mesothelin. The two naturally processed peptides COA-1331-345 and Meso366-380 appear to be the most immunogenic in mCRC patients. A prospective cohort of 162 mCRC patients enabled us to explore the impact of oxaliplatin exposure on the antitumor-specific immune response. Interestingly, chemotherapy-naive mCRC patients present high immune CD4 T-cell responses directed against TERT, COA-1 and mesothelin-derived peptides. These antitumor T-cell responses were maintained after 3 months of oxaliplatin-based treatment. Altogether, these findings highlight the interest of immunostimulatory agents to improve the management of chemoresistant mCRC patients. Finally, the high frequency of immune responses targeting the new immunogenic peptides derived from COA-1 and mesothelin support their use in immunomonitoring strategies.
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Affiliation(s)
- Jeanne Galaine
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Célia Turco
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,University Hospital of Besançon, Department of Gastrointestinal Surgery, Besançon, France
| | - Charline Vauchy
- INSERM CIC-1431, University Hospital of Besançon, Clinical Investigation Center un Biotherapy, Fédération Hospitalo-Universitaire INCREASE, LabEx LipSTIC, Besançon, France
| | - Bernard Royer
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,University Hospital of Besançon, Department of pharmacotoxicology, Besançon, France
| | - Patricia Mercier-Letondal
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Lise Queiroz
- INSERM CIC-1431, University Hospital of Besançon, Clinical Investigation Center un Biotherapy, Fédération Hospitalo-Universitaire INCREASE, LabEx LipSTIC, Besançon, France
| | - Romain Loyon
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Virginie Mouget
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Romain Boidot
- Centre Georges-François Leclerc, Platform for Transfer to Cancer Biology, Dijon, France
| | - Caroline Laheurte
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,EFS Bourgogne Franche-Comté, INSERM CIC-1431, CHRU Besançon, Plateforme de BioMonitoring, Besançon, France
| | - Zaher Lakkis
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,University Hospital of Besançon, Department of Gastrointestinal Surgery, Besançon, France
| | - Marine Jary
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,University Hospital of Besançon, Department of Medical Oncology, Besançon, France
| | - Olivier Adotévi
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,University Hospital of Besançon, Department of Medical Oncology, Besançon, France
| | - Christophe Borg
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,University Hospital of Besançon, Department of Medical Oncology, Besançon, France
| | - Yann Godet
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
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6
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Rosa T, Domingues J, Martins Jr C, Domingos J, Iwabe-Marchese C, Pacheco E, Queiroz L, França Jr M, Nucci A. CONGENITAL MYOPATHIES (CNM). Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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Rosa T, Iwabe-Marchese C, Queiroz L, França M, Nucci A. Clinimetric studies in centronuclear myopathies. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Jary M, Lecomte T, Bouché O, Kim S, Dobi E, Queiroz L, Ghiringhelli F, Etienne H, Léger J, Godet Y, Balland J, Lakkis Z, Adotevi O, Bonnetain F, Borg C, Vernerey D. Prognostic value of baseline seric Syndecan-1 in initially unresectable metastatic colorectal cancer patients: a simple biological score. Int J Cancer 2016; 139:2325-35. [PMID: 27472156 DOI: 10.1002/ijc.30367] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/24/2016] [Accepted: 07/01/2016] [Indexed: 01/17/2023]
Abstract
In first-line metastatic colorectal cancer (mCRC), baseline prognostic factors allowing death risk and treatment strategy stratification are lacking. Syndecan-1 (CD138) soluble form was never described as a prognostic biomarker in mCRC. We investigated its additional prognostic value for overall survival (OS). mCRC patients with unresectable disease at diagnosis were treated with bevacizumab-based chemotherapy in two independent prospective clinical trials (development set: n = 126, validation set: n = 51, study NCT00489697 and study NCT00544011, respectively). Serums were collected at baseline for CD138 measurement. OS determinants were assessed and, based on the final multivariate model, a prognostic score was proposed. Two independent OS prognostic factors were identified: Lactate Dehydrogenase (LDH) high level (p = 0.0066) and log-CD138 high level (p = 0.0190). The determination of CD138 binary information (cutoff: 75 ng/mL) allowed the assessment of a biological prognostic score with CD138 and LDH values, identifying three risk groups for death (median OS= 38.9, 30.1 and 19.8 months for the low, intermediate and high risk groups, respectively; p < 0.0001). This score had a good discrimination ability (C-index = 0.63). These results were externally confirmed in the validation set. Our study provides robust evidence in favor of the additional baseline soluble CD138 prognostic value for OS, in mCRC patients. A simple biological scoring system is proposed including LDH and CD138 binary status values.
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Affiliation(s)
- Marine Jary
- Department of Medical Oncology, University Hospital, Besançon, France. .,INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France. .,Clinical Investigation Center 1431, EFS Bourgogne-Franche Comté, Besançon, France.
| | - Thierry Lecomte
- CNRS, Unit 7292, University François-Rabelais, Tours, France.,Department of HepatoGastroenterology and Digestive Oncology, University Hospital, Tours, France
| | - Olivier Bouché
- Department of HepatoGastroenterology and Digestive Oncology, University Hospital Robert Debré, Reims, France
| | - Stefano Kim
- Department of Medical Oncology, University Hospital, Besançon, France.,Clinical Investigation Center 1431, EFS Bourgogne-Franche Comté, Besançon, France
| | - Erion Dobi
- Department of Medical Oncology, University Hospital, Besançon, France
| | - Lise Queiroz
- INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France
| | | | - Hélène Etienne
- Department of Medical Oncology, University Hospital, Besançon, France.,Department of Gastroenterology, University Hospital, Besançon, France
| | - Julie Léger
- INSERM, Clinical Investigational Center CIC 1415, Tours, France
| | - Yann Godet
- INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France
| | - Jérémy Balland
- INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France
| | - Zaher Lakkis
- Department of Digestive Surgery and Liver Transplantation, University Hospital, Besançon, France
| | - Olivier Adotevi
- Department of Medical Oncology, University Hospital, Besançon, France.,INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France
| | - Franck Bonnetain
- INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France.,Clinical Investigation Center 1431, EFS Bourgogne-Franche Comté, Besançon, France.,Methodological and Quality of Life in Oncology Unit, EA 3181, University Hospital, Besançon, France
| | - Christophe Borg
- Department of Medical Oncology, University Hospital, Besançon, France.,INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France.,Clinical Investigation Center 1431, EFS Bourgogne-Franche Comté, Besançon, France
| | - Dewi Vernerey
- INSERM, Unit 1098, University of Bourgogne- Franche Comté, Besançon, France.,Clinical Investigation Center 1431, EFS Bourgogne-Franche Comté, Besançon, France.,Methodological and Quality of Life in Oncology Unit, EA 3181, University Hospital, Besançon, France
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9
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Galaine J, Kellermann G, Guillaume Y, Boidot R, Picard E, Loyon R, Queiroz L, Boullerot L, Beziaud L, Jary M, Mansi L, André C, Lethier L, Ségal-Bendirdjian E, Borg C, Godet Y, Adotévi O. Heparan Sulfate Proteoglycans Promote Telomerase Internalization and MHC Class II Presentation on Dendritic Cells. J I 2016; 197:1597-608. [DOI: 10.4049/jimmunol.1502633] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/01/2016] [Indexed: 01/18/2023]
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10
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Loyon R, Picard E, Mauvais O, Queiroz L, Mougey V, Pallandre JR, Galaine J, Mercier-Letondal P, Kellerman G, Chaput N, Wijdenes J, Adotévi O, Ferrand C, Romero P, Godet Y, Borg C. IL-21-Induced MHC Class II+ NK Cells Promote the Expansion of Human Uncommitted CD4+ Central Memory T Cells in a Macrophage Migration Inhibitory Factor-Dependent Manner. J Immunol 2016; 197:85-96. [PMID: 27233967 DOI: 10.4049/jimmunol.1501147] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 04/18/2016] [Indexed: 01/15/2023]
Abstract
NK cells are critical for innate immunity-mediated protection. The main roles of NK cells rely on their cytotoxic functions or depend on the tuning of Th1 adaptive immunity by IFN-γ. However, the precise influence of inflammatory cytokines on NK cell and CD4 T lymphocyte interactions was never investigated. In this study, we provide evidence that IL-21, a cytokine produced during chronic inflammation or infectious diseases, promotes the differentiation of a specific subset of NK cells coexpressing CD86 and HLA-DR and lacking NKp44. More importantly, IL-21-propagated HLA-DR(+) NK cells produce macrophage migration inhibitory factor and provide costimulatory signaling during naive CD4(+) T cell priming inducing the differentiation of uncommitted central memory T cells. Central memory T cells expanded in the presence of HLA-DR(+) NK cells are CXCR3(+)CCR6(-)CCR4(-)CXCR5(-) and produce IL-2, as well as low levels of TNF-α. Costimulation of CD4(+) T cells by HLA-DR(+) NK cells prevents the acquisition of effector memory phenotype induced by IL-2. Moreover, we identified this population of NK HLA-DR(+) macrophage migration inhibitory factor(+) cells in inflammatory human appendix. Collectively, these results demonstrate a novel function for IL-21 in tuning NK and CD4(+) T cell interactions promoting a specific expansion of central memory lymphocytes.
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Affiliation(s)
- Romain Loyon
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France
| | - Emilie Picard
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France
| | - Olivier Mauvais
- Department of Head and Neck Surgery, University Hospital of Besançon, 25000 Besançon, France
| | - Lise Queiroz
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France; Clinical Investigation Center for Biotherapies, 25000 Besançon, France
| | - Virginie Mougey
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France; Etablissement Français du Sang, 25000 Besançon, France
| | - Jean-René Pallandre
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France; INSERM Unit 1007, University of Paris Descartes, 75270 Paris, France
| | - Jeanne Galaine
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France
| | - Patricia Mercier-Letondal
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France; Etablissement Français du Sang, 25000 Besançon, France
| | | | - Nathalie Chaput
- INSERM Unit 1015, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - John Wijdenes
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France
| | - Olivier Adotévi
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France; Clinical Investigation Center for Biotherapies, 25000 Besançon, France; Department of Medical Oncology, University Hospital of Besançon, 25000 Besançon, France; and
| | - Christophe Ferrand
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France; Etablissement Français du Sang, 25000 Besançon, France
| | - Pedro Romero
- Ludwig Center for Cancer Research of the University of Lausanne, Lausanne 1066, Switzerland
| | - Yann Godet
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France
| | - Christophe Borg
- INSERM Unit 1098, University of Franche-Comté, 25000 Besançon, France; Clinical Investigation Center for Biotherapies, 25000 Besançon, France; Etablissement Français du Sang, 25000 Besançon, France; Department of Medical Oncology, University Hospital of Besançon, 25000 Besançon, France; and
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11
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Beziaud L, Mansi L, Ravel P, Marie-Joseph EL, Laheurte C, Rangan L, Bonnefoy F, Pallandre JR, Boullerot L, Gamonet C, Vrecko S, Queiroz L, Maurina T, Mouillet G, Hon TNT, Curtit E, Royer B, Gaugler B, Bayry J, Tartour E, Thiery-Vuillemin A, Pivot X, Borg C, Godet Y, Adotévi O. Rapalogs Efficacy Relies on the Modulation of Antitumor T-cell Immunity. Cancer Res 2016; 76:4100-12. [DOI: 10.1158/0008-5472.can-15-2452] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 04/27/2016] [Indexed: 11/16/2022]
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12
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Cárcano FM, Lengert AH, Vidal DO, Scapulatempo Neto C, Queiroz L, Marques H, Baltazar F, Berardinelli GN, Martinelli CMS, da Silva ECA, Reis RM, Lopes LF. Absence of microsatellite instability and BRAF (V600E) mutation in testicular germ cell tumors. Andrology 2016; 4:866-72. [PMID: 27153176 DOI: 10.1111/andr.12200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 12/27/2022]
Abstract
Testicular germ cell tumors (TGCT) are the most common malignant neoplasm in young men. DNA mismatch repair deficiency can lead to microsatellite instability (MSI), an important mechanism of genetic instability. A mutation of the BRAF gene has been implicated in the pathogenesis of several solid tumors and has recently become an important therapeutic target. The role of MSI and BRAF gene mutation in TGCT, particularly in refractory disease, is poorly understood and reported findings are controversial. In this study, we aimed to determine the frequency and clinical impact of MSI status and BRAF mutations in TGCT. DNA was isolated from formalin-fixed paraffin embedded (FFPE) tissue from 150 TGCT cases. The MSI phenotype was evaluated using multiplex PCR for five quasimonomorphic mononucleotide repeat markers. Exon 15 of the BRAF oncogene (V600E) was analyzed by PCR, followed by direct sequencing. Sixteen percent of cases were considered to have refractory disease. In a small subset of cases (17 for MSI and 18 for BRAF), the quantity and quality of DNA recovery were poor and therefore, were unable to be analyzed. The remaining 133 TGCT cases showed a complete absence of MSI. Of the 132 cases successfully evaluated for BRAF mutations, all were V600E wild-type. In conclusion, despite a distinct response of testicular germ cell tumors to therapy, microsatellite instability, and the BRAF V600E mutation were absent in all testicular germ cell tumors tested in this study.
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Affiliation(s)
- F M Cárcano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - A H Lengert
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos Children's Cancer Hospital, Barretos, Brazil
| | - D O Vidal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos Children's Cancer Hospital, Barretos, Brazil
| | - C Scapulatempo Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - L Queiroz
- Department of Medical Oncology, Hospital de Braga, Braga, Guimarães, Portugal
| | - H Marques
- Department of Medical Oncology, Hospital de Braga, Braga, Guimarães, Portugal
| | - F Baltazar
- Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - G N Berardinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - C M S Martinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - E C A da Silva
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - R M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - L F Lopes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos Children's Cancer Hospital, Barretos, Brazil
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Moreira C, Marinho A, Gil L, Bairrão M, Queiroz L. Psychiatric disorders among asthmatic patients: Literature review. Eur Psychiatry 2016. [DOI: 10.1016/j.eurpsy.2016.01.1350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
IntroductionAsthma is a major public health problem and its prevalence has increased in both developed and developing countries during the last few years. Once it is a chronic illness, it has also revealed psychological consequences. Moreover, recent studies have suggested an association between asthma (especially of severe grade) and mental disorders.ObjectivesThe authors pretend to make a brief review concerning psychiatric disorders among asthmatic patients.AimsTo understand and to be able to deal with the psychiatric disorders among chronic asthmatic patients.MethodsThe review was based on scientific documentation published in PubMed database, using the following terms as keywords: “asthma”, “depression”, “anxiety” and “panic disorder”.ResultsCompared to the general population, both anxiety and mood disorders rates are at least two times those observed in asthmatic patients. Moreover, certain psychiatric disorders rates, including panic disorder (PD) and major depressive disorder, are as much as six times more prevalent among asthmatics when compared to the general population. The association between psychiatric disorders and poor asthma control and asthma-related quality of life could occur through several pathways, such as behavioural pathways; cognitive or perceptual pathways; or through the direct physiological effects of depression and anxiety on the autonomic nervous system (ANS) and immune systems which increase asthma symptomatology.Discussions/ConclusionsThere is a close correlation between anxiety, PD and depression, and a poor controlled asthma. A better understanding of this association may have major clinical implications, mainly in patients with poor controlled asthma in whom the presence of anxiety and depression should be investigated.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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14
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Palma M, Roque FDC, Guerreiro JF, Mira NP, Queiroz L, Sá-Correia I. Search for genes responsible for the remarkably high acetic acid tolerance of a Zygosaccharomyces bailii-derived interspecies hybrid strain. BMC Genomics 2015; 16:1070. [PMID: 26673744 PMCID: PMC4681151 DOI: 10.1186/s12864-015-2278-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022] Open
Abstract
Background Zygosaccharomyces bailii is considered the most problematic acidic food spoilage yeast species due to its exceptional capacity to tolerate high concentrations of weak acids used as fungistatic preservatives at low pH. However, the mechanisms underlying its intrinsic remarkable tolerance to weak acids remain poorly understood. The identification of genes and mechanisms involved in Z. bailii acetic acid tolerance was on the focus of this study. For this, a genomic library from the highly acetic acid tolerant hybrid strain ISA1307, derived from Z. bailii and a closely related species and isolated from a sparkling wine production plant, was screened for acetic acid tolerance genes. This screen was based on the transformation of an acetic acid susceptible Saccharomyces cerevisiae mutant deleted for the gene encoding the acetic acid resistance determinant transcription factor Haa1. Results The expression of 31 different DNA inserts from ISA1307 strain genome was found to significantly increase the host cell tolerance to acetic acid. The in silico analysis of these inserts was facilitated by the recently available genome sequence of this strain. In total, 65 complete or truncated ORFs were identified as putative determinants of acetic acid tolerance and an S. cerevisiae gene homologous to most of them was found. These include genes involved in cellular transport and transport routes, protein fate, protein synthesis, amino acid metabolism and transcription. The role of strong candidates in Z. bailii and S. cerevisiae acetic acid tolerance was confirmed based on homologous and heterologous expression analyses. Conclusions ISA1307 genes homologous to S. cerevisiae genes GYP8, WSC4, PMT1, KTR7, RKR1, TIF3, ILV3 and MSN4 are proposed as strong candidate determinants of acetic acid tolerance. The ORF ZBAI_02295 that contains a functional domain associated to the uncharacterised integral membrane proteins of unknown function of the DUP family is also suggested as a relevant tolerance determinant. The genes ZbMSN4 and ZbTIF3, encoding a putative stress response transcription factor and a putative translation initiation factor, were confirmed as determinants of acetic acid tolerance in both Z. bailii and S. cerevisiae. This study provides valuable indications on the cellular components, pathways and processes to be targeted in order to control food spoilage by the highly acetic acid tolerant Z. bailii and Z. bailii-derived strains. Additionally, this information is essential to guide the improvement of yeast cells robustness against acetic acid if the objective is their use as cell factories. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2278-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margarida Palma
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Filipa de Canaveira Roque
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Joana Fernandes Guerreiro
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Nuno Pereira Mira
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Lise Queiroz
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Isabel Sá-Correia
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
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15
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Adotevi O, Beziaud L, Mansi L, Laheurte C, Nguyen T, Maurina T, Mouillet G, Queiroz L, Jacquemard C, Godet Y, Royer B, Thiery-Vuillemin A, Borg C. Modulation of antitumor T cell responses induced by everolimus in metastatic Renal Cell Carcinoma patients. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e22113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Laura Mansi
- Medical Oncology CHRU Jean Minjoz, Besançon, France
| | | | | | | | | | | | | | - Yann Godet
- UMR1098 INSERM/EFS/UFC, Besançon, France
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16
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Jary M, Vernerey D, Lecomte T, Dobi E, Ghiringhelli F, Monnien F, Godet Y, Kim S, Bouché O, Fratte S, Gonçalves A, Leger J, Queiroz L, Adotevi O, Bonnetain F, Borg C. Prognostic value of angiopoietin-2 for death risk stratification in patients with metastatic colorectal carcinoma. Cancer Epidemiol Biomarkers Prev 2015; 24:603-12. [PMID: 25583947 DOI: 10.1158/1055-9965.epi-14-1059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Baseline prognostic biomarkers stratifying treatment strategies in first-line metastatic colorectal cancer (mCRC) are lacking. Angiopoietin-2 (Ang-2) is proposed as a potential biomarker in several cancers. We therefore decided to establish the additional prognostic value of Ang-2 for overall survival (OS) in patients with first-line mCRC. METHODS We enrolled 177 patients treated with a bevacizumab containing chemotherapy in two prospective phase II clinical trials. Patient plasma samples were collected at baseline. ELISAs were used to measure Ang-2. RESULTS The multivariable Cox model identified increased lactate dehydrogenase [HR, 1.60; 95% confidence interval (CI), 1.04-2.45; P = 0.03] and Ang-2 log-transformation level (HR, 1.59; 95% CI, 1.14-2.21; P = 0.0065) as two significant independent OS prognostic factors. It exhibited good calibration (P = 0.8) and discrimination (C-index: 0.64; 95% CI, 0.58-0.68). Ang-2 parameter inclusion in the GERCOR reference model significantly and strongly improved its discriminative ability because the C-statistic increased significantly from 0.61 to 0.63 (bootstrap mean difference = 0.07; 95% CI, 0.069-0.077). Interestingly, the addition of Ang-2 binary information with a 5 ng/mL cutoff value to the GERCOR model allowed the reclassification of intermediate-risk profile patients (41%) into two subsets of low and high risks. CONCLUSIONS Our study provides robust evidence in favor of baseline Ang-2 prognostic value for OS adding to the conventional factors. Its assessment appears to be useful for the improvement in risk stratification for patients with intermediate-risk profile. IMPACT Ang-2 ability to predict OS at diagnosis could be of interest in the selection of patients eligible for intermittent or sequential therapeutic strategies dedicated to the optimization of patients' quality of life and chemotherapy cost-effectiveness. Cancer Epidemiol Biomarkers Prev; 24(3); 603-12. ©2015 AACR.
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Affiliation(s)
- Marine Jary
- Department of Medical Oncology, University Hospital, Besançon, France. INSERM, Unit 1098, University of Franche-Comté, Besançon, France.
| | - Dewi Vernerey
- Methodological and Quality of Life in Oncology Unit, University Hospital of Besançon, Besançon, France
| | - Thierry Lecomte
- INSERM, Unit 7292, University François-Rabelais, CNRS, Tours, France. Department of Hepatogastroenterology and Digestive Oncology, University Hospital, Tours, France
| | - Erion Dobi
- Department of Medical Oncology, University Hospital, Besançon, France
| | | | - Franck Monnien
- Department of Medical Oncology, University Hospital, Besançon, France
| | - Yann Godet
- INSERM, Unit 1098, University of Franche-Comté, Besançon, France
| | - Stefano Kim
- Department of Medical Oncology, University Hospital, Besançon, France. Department of Oncology and Radiotherapy, Hospital of Belfort-Montbeliard, Montbeliard, France
| | - Olivier Bouché
- Department of Hepatogastroenterology and Digestive Oncology, University Hospital Robert Debré, Reims, France
| | - Serge Fratte
- Department of Gastroenterology, Hospital of Belfort-Montbeliard, Montbeliard, France
| | - Anthony Gonçalves
- Department of Medical Oncology, Paoli-Calmettes Institute, Marseille, France
| | - Julie Leger
- INSERM, Clinical Investigational Center CIC 1415, Tours, France
| | - Lise Queiroz
- INSERM, Unit 1098, University of Franche-Comté, Besançon, France. Clinical Investigational Center, CIC-Biotherapy-506, University Hospital of Besançon, Besançon, France
| | - Olivier Adotevi
- Department of Medical Oncology, University Hospital, Besançon, France. INSERM, Unit 1098, University of Franche-Comté, Besançon, France
| | - Franck Bonnetain
- Methodological and Quality of Life in Oncology Unit, University Hospital of Besançon, Besançon, France
| | - Christophe Borg
- Department of Medical Oncology, University Hospital, Besançon, France. INSERM, Unit 1098, University of Franche-Comté, Besançon, France
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17
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Stovner L, Al Jumah M, Birbeck G, Gururaj G, Jensen R, Katsarava Z, Queiroz L, Scher A, Tekle-Haimanot R, Wang S, Steiner T. EHMTI-0205. Methodology guidelines for population surveys of headache prevalence, burden and cost. J Headache Pain 2014. [PMCID: PMC4180631 DOI: 10.1186/1129-2377-15-s1-b36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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18
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Jary M, Vernerey D, Dobi E, Monnien F, Godet Y, Kim S, Bouché O, Fratte S, Ghiringhelli F, Goncalvez A, Lecomte T, Leger J, Queiroz L, Adotevi O, Bonnetain F, Borg C. Prognostic Value of Angiopoietin-2 for Overall Survival in Patients with Metastatic Colorectal Carcinoma Treated By Chemotherapy and Bevacizumab. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu326.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Almeida M, Queiroz L, Domingues N, Espírito-Santo A, Oliveira I, Oliveira Â, Moreira I, Viterbo L, Mariz J. Aplastic Anemia: A Single Institution Experience. Ann Oncol 2012. [DOI: 10.1016/s0923-7534(20)33652-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Avansini S, Torres F, Rogerio F, Dogini D, Coan A, Secolin R, Rocha C, Costa A, Costa A, Piaza A, Reis L, Oliveira E, Tedeschi H, Queiroz L, Cendes F, Lopes-Cendes I. Investigating the Role of microRNAs Regulation in the Development of Focal Cortical Dysplasia (P05.081). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.p05.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Izar M, Helfenstein T, Fonseca M, Colovati M, Relvas W, Ihara S, Santos A, Queiroz L, Fonseca F. T01-P-012 The D9N polymorphism of lipoprotein lipase gene is a marker for myocardial infarction in diabetics. ATHEROSCLEROSIS SUPP 2005. [DOI: 10.1016/s1567-5688(05)80529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
We determined the antioxidant status of the aqueous humor after extracapsular lens extraction in 14 mongrel dogs weighing about 10 kg. The animals were examined by slit lamp biomicroscopy, applanation tonometry and indirect ophthalmoscopy. One eye was submitted to conventional extracapsular lens extraction and the other was used as control. Samples of aqueous humor were obtained by anterior chamber paracentesis before and at days 1, 2, 3, 7 and 15 after surgery. Total antioxidant status was determined as the capacity of aqueous humor to inhibit free radical generation by 2,2-azobis(2-amidopropane) chlorine. Ascorbic acid concentration was measured by HPLC with UV detection. Protein content was determined with the biuret reagent. Statistical analysis was performed by ANOVA followed by the Tukey-Kramer test. Protein concentration increased from 0.61 to 22 mg/ml 24 h after surgery. These levels were maintained and returned to normal at day 7. Total antioxidant capacity was reduced from 50 to about 30 min until day 3 and at day 7 it was equal to control. Ascorbic acid levels were reduced from 252 to about 110 microM and then returned to control values at day 15. Considering the importance of ascorbic acid concentration in aqueous humor for the maintenance of the antioxidant status of the anterior segment of the eye, the decrease of antioxidant defenses suggests that the surgical procedures promote an oxidative stress condition in the eye.
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Affiliation(s)
- P S M Barros
- Departamento de Cirurgia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil.
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Maciel Jr. JA, Queiroz L. Neuropatia pela amiodarona: estudo clínico-patológico de dois casos. Arq Neuro-Psiquiatr 1989. [DOI: 10.1590/s0004-282x1989000400016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dois pacientes, uma mulher de 40 anos e um homem de 75 anos, apresentavam polineurite sensítivo-motora, cujo único antecedente era o uso de amiodarona há 4 e 6 anos respectivamente. O ENMG revelou quadro neuropático tipo axonal. A biópsia do nervo sural mostrou rarefação axonal, mielínica e amielínica, bem como inclusões lamelares osmiofílicas nas células de Schwann e no endotélio venular. Com a retirada da amiodarona houve regressão da polineurite. À semelhança do que foi descrito na neuropatia pelo maleato de perhexiline e pela cloroquina, a amiodarona constitui importante fator de indução de neuro-lipidose medicamentosa.
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Maciel Júnior JA, Queiroz L. [Neuropathy caused by amiodarone: clinico-pathologic study of 2 cases]. Arq Neuropsiquiatr 1989; 47:474-8. [PMID: 2634390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Two patients, a 40-year-old woman and a 75-year-old man, were investigated due to a chronic polyneuritis. Amiodarone was used by them to treat refractory cardiac arrhythmia since 4 and 6 years before, respectively. The EMG study showed an axonal neuropathy. The light and electron-microscopical study of sural nerve displayed a loss of large myelinated fibers and a marked reduction of unmyelinated axons, associated with osmiophilic lamellated inclusions in Schwann cells and endothelial venulae. The interruption of amiodarone therapy improved neuropathy. Considered together with similar reports in perhexiline neuropathy and with chloroquine induced neuropathy this would stress the importance of these new drug-induced neurolipidosis.
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