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Alves Costa Silva C, Piccinno G, Suissa D, Bourgin M, Schreibelt G, Durand S, Birebent R, Fidelle M, Sow C, Aprahamian F, Manghi P, Punčochář M, Asnicar F, Pinto F, Armanini F, Terrisse S, Routy B, Drubay D, Eggermont AMM, Kroemer G, Segata N, Zitvogel L, Derosa L, Bol KF, de Vries IJM. Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial. Nat Commun 2024; 15:1633. [PMID: 38395948 PMCID: PMC10891084 DOI: 10.1038/s41467-024-45357-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Tumor immunosurveillance plays a major role in melanoma, prompting the development of immunotherapy strategies. The gut microbiota composition, influencing peripheral and tumoral immune tonus, earned its credentials among predictors of survival in melanoma. The MIND-DC phase III trial (NCT02993315) randomized (2:1 ratio) 148 patients with stage IIIB/C melanoma to adjuvant treatment with autologous natural dendritic cell (nDC) or placebo (PL). Overall, 144 patients collected serum and stool samples before and after 2 bimonthly injections to perform metabolomics (MB) and metagenomics (MG) as prespecified exploratory analysis. Clinical outcomes are reported separately. Here we show that different microbes were associated with prognosis, with the health-related Faecalibacterium prausnitzii standing out as the main beneficial taxon for no recurrence at 2 years (p = 0.008 at baseline, nDC arm). Therapy coincided with major MB perturbations (acylcarnitines, carboxylic and fatty acids). Despite randomization, nDC arm exhibited MG and MB bias at baseline: relative under-representation of F. prausnitzii, and perturbations of primary biliary acids (BA). F. prausnitzii anticorrelated with BA, medium- and long-chain acylcarnitines. Combined, these MG and MB biomarkers markedly determined prognosis. Altogether, the host-microbial interaction may play a role in localized melanoma. We value systematic MG and MB profiling in randomized trials to avoid baseline differences attributed to host-microbe interactions.
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Grants
- The MIND-DC trial was funded by ZonMw, Ministry of Health, Welfare and Sport (VWS), Stichting ATK, Miltenyi Biotec (in-kind). This work was supported by SEERAVE Foundation, European Union Horizon 2020:Project Number: 825410 and Project Acronym: ONCOBIOME, Institut National du Cancer (INCa), ANR Ileobiome - 19-CE15-0029-01, ANR RHU5 “ANR-21-RHUS-0017” IMMUNOLIFE”, MAdCAM INCA_ 16698, Ligue contre le cancer, LABEX OncoImmunology, la direction generale de l’offre de soins (DGOS), Universite Paris-Sud, SIRIC SOCRATE (INCa/DGOS/INSERM 6043), and PACRI network. G.K. is supported by the Ligue contre le Cancer (équipe labellisée); Agence National de la Recherche (ANR) – Projets blancs; AMMICa US23/CNRS UMS3655; Association pour la recherche sur le cancer (ARC); Cancéropôle Ile-de-France; Fondation pour la Recherche Médicale (FRM); a donation by Elior; Equipex Onco-Pheno-Screen; European Joint Programme on Rare Diseases (EJPRD); European Research Council Advanced Investigator Award (ERC-2021-ADG, ICD-Cancer, Grant No. 101052444), European Union Horizon 2020 Projects Oncobiome, Prevalung (grant No. 101095604) and Crimson; Fondation Carrefour; Institut National du Cancer (INCa); Institut Universitaire de France; LabEx Immuno-Oncology (ANR-18-IDEX-0001); a Cancer Research ASPIRE Award from the Mark Foundation; the RHU Immunolife; Seerave Foundation; SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE); and SIRIC Cancer Research and Personalized Medicine (CARPEM). This study contributes to the IdEx Université de Paris ANR-18-IDEX-0001. This work is supported by the Prism project funded by the Agence Nationale de la Recherche under grant number ANR-18-IBHU-0002. CACS was funded by MSD Avenir. MF is funded by SEERAVE Foundation and MERCK Foundation. LD and BR were supported by Philantropia at Gustave Roussy Foundation.
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Affiliation(s)
- Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Gianmarco Piccinno
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Déborah Suissa
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Mélanie Bourgin
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Gerty Schreibelt
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Roxanne Birebent
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Marine Fidelle
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Cissé Sow
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Fanny Aprahamian
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Paolo Manghi
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michal Punčochář
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Asnicar
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Safae Terrisse
- Oncology Department, Assistance Publique Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, Paris, France
| | - Bertrand Routy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, QC, Canada
| | - Damien Drubay
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Office of Biostatistics and Epidemiology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Inserm, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif, France
| | - Alexander M M Eggermont
- Princess Máxima Center and University Medical Center Utrecht, 3584 CS Utrecht, The Netherlands
- Comprehensive Cancer Center Munich, Technical University Munich & Ludwig Maximiliaan University, Munich, Germany
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France.
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France.
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France.
- Center of Clinical Investigations BIOTHERIS, INSERM CIC1428, Villejuif, France.
| | - Lisa Derosa
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Kalijn F Bol
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherlands
| | - I Jolanda M de Vries
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
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2
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Routy B, Lenehan JG, Miller WH, Jamal R, Messaoudene M, Daisley BA, Hes C, Al KF, Martinez-Gili L, Punčochář M, Ernst S, Logan D, Belanger K, Esfahani K, Richard C, Ninkov M, Piccinno G, Armanini F, Pinto F, Krishnamoorthy M, Figueredo R, Thebault P, Takis P, Magrill J, Ramsay L, Derosa L, Marchesi JR, Parvathy SN, Elkrief A, Watson IR, Lapointe R, Segata N, Haeryfar SMM, Mullish BH, Silverman MS, Burton JP, Maleki Vareki S. Author Correction: Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial. Nat Med 2024; 30:604. [PMID: 37923839 DOI: 10.1038/s41591-023-02650-8] [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: 11/06/2023]
Affiliation(s)
- Bertrand Routy
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - John G Lenehan
- Department of Oncology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
| | - Wilson H Miller
- Lady Davis Institute of the Jewish General Hospital, Segal Cancer Centre, Montreal, Quebec, Canada
- Departments of Oncology and Medicine, McGill University, Montreal, Quebec, Canada
| | - Rahima Jamal
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Meriem Messaoudene
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Brendan A Daisley
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Cecilia Hes
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Peter Brojde Lung Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
| | - Kait F Al
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Laura Martinez-Gili
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Michal Punčochář
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Scott Ernst
- Department of Oncology, Western University, London, Ontario, Canada
| | - Diane Logan
- Department of Oncology, Western University, London, Ontario, Canada
| | - Karl Belanger
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Khashayar Esfahani
- Lady Davis Institute of the Jewish General Hospital, Segal Cancer Centre, Montreal, Quebec, Canada
- Departments of Oncology and Medicine, McGill University, Montreal, Quebec, Canada
| | - Corentin Richard
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Marina Ninkov
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
| | - Gianmarco Piccinno
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Mithunah Krishnamoorthy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Rene Figueredo
- Department of Oncology, Western University, London, Ontario, Canada
| | - Pamela Thebault
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Panteleimon Takis
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, National Phenome Centre, Imperial College London, London, UK
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jamie Magrill
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Quebec, Canada
| | - LeeAnn Ramsay
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Quebec, Canada
| | - Lisa Derosa
- Gustave Roussy Cancer Campus, Villejuif, France
- Cancer Medicine Department, Gustave Roussy, Villejuif, France
- Institut National de la Santé Et et de la Recherche Médicale (INSERM) U1015, ClinicObiome, Equipe Labellisée-28 Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Ile-de-France, France
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Seema Nair Parvathy
- Department of Medicine, Division of Infectious Diseases, Western University, London, Ontario, Canada
- Division of Infectious Diseases, St Joseph's Health Care, London, Ontario, Canada
| | - Arielle Elkrief
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Ian R Watson
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Quebec, Canada
- Department of Biochemistry, McGill University, Montréal, Quebec, Canada
| | - Rejean Lapointe
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - S M Mansour Haeryfar
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Department of Medicine, Division of Clinical Immunology and Allergy, Western University, London, Ontario, Canada
- Department of Surgery, Division of General Surgery, Western University, London, Ontario, Canada
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Michael S Silverman
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, Western University, London, Ontario, Canada
- Division of Infectious Diseases, St Joseph's Health Care, London, Ontario, Canada
| | - Jeremy P Burton
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Saman Maleki Vareki
- Department of Oncology, Western University, London, Ontario, Canada.
- Lawson Health Research Institute, London, Ontario, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
- Department of Medical Biophysics, Western University, London, Ontario, Canada.
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada.
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3
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Sukeert, Pizzurro S, Esteban-Martín A, Gotti R, Carrà L, Piccinno G, Agnesi A, Pirzio F, Kumar SC, Ebrahim-Zadeh M. Efficient femtosecond optical parametric generation in group-velocity-matched MgO:PPLN at 10 MHz. Opt Lett 2023; 48:6008-6011. [PMID: 37966775 DOI: 10.1364/ol.507136] [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] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023]
Abstract
We report on efficient single-pass optical parametric generation (OPG) of broadband femtosecond pulses in the mid-infrared at 10 MHz by exploiting group-velocity-matched interaction in a 42-mm-long MgO:PPLN crystal. Using a microchip-started femtosecond amplified Mamyshev oscillator at 1064 nm as the pump, the OPG source can provide tunable femtosecond pulses across 1516-1566 nm in the signal and 3318-3568 nm in the idler, with slope efficiencies of ∼93% and ∼41%, respectively. For 650 mW of average input pump power, signal powers of up to 283 mW at 1524 nm are generated, with more than 200 mW over the entire tuning range. Idler average powers of up to 104 mW at 3450 nm, with more than 80 mW across the full range, are also obtained. For input pump pulses of ∼182 fs, the generated signal pulses have a duration of ∼460 fs at 1516 nm. The idler pulses have a typical bandwidth of ≥100 nm over the entire tuning range, and as wide as 181 nm at 3457 nm. The OPG source exhibits excellent passive power stability, better than 0.5% rms in the signal and 0.6% rms in the idler, over 1 h, both in Gaussian TEM00 spatial profile with M2 < 1.5.
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4
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Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Punčochář M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 2023; 41:1633-1644. [PMID: 36823356 PMCID: PMC10635831 DOI: 10.1038/s41587-023-01688-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.
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Affiliation(s)
| | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Lauren J McIver
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kelsey N Thompson
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | | | - William A Nickols
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | | | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | | | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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5
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Routy B, Lenehan JG, Miller WH, Jamal R, Messaoudene M, Daisley BA, Hes C, Al KF, Martinez-Gili L, Punčochář M, Ernst S, Logan D, Belanger K, Esfahani K, Richard C, Ninkov M, Piccinno G, Armanini F, Pinto F, Krishnamoorthy M, Figueredo R, Thebault P, Takis P, Magrill J, Ramsay L, Derosa L, Marchesi JR, Parvathy SN, Elkrief A, Watson IR, Lapointe R, Segata N, Haeryfar SMM, Mullish BH, Silverman MS, Burton JP, Maleki Vareki S. Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial. Nat Med 2023; 29:2121-2132. [PMID: 37414899 DOI: 10.1038/s41591-023-02453-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023]
Abstract
Fecal microbiota transplantation (FMT) represents a potential strategy to overcome resistance to immune checkpoint inhibitors in patients with refractory melanoma; however, the role of FMT in first-line treatment settings has not been evaluated. We conducted a multicenter phase I trial combining healthy donor FMT with the PD-1 inhibitors nivolumab or pembrolizumab in 20 previously untreated patients with advanced melanoma. The primary end point was safety. No grade 3 adverse events were reported from FMT alone. Five patients (25%) experienced grade 3 immune-related adverse events from combination therapy. Key secondary end points were objective response rate, changes in gut microbiome composition and systemic immune and metabolomics analyses. The objective response rate was 65% (13 of 20), including four (20%) complete responses. Longitudinal microbiome profiling revealed that all patients engrafted strains from their respective donors; however, the acquired similarity between donor and patient microbiomes only increased over time in responders. Responders experienced an enrichment of immunogenic and a loss of deleterious bacteria following FMT. Avatar mouse models confirmed the role of healthy donor feces in increasing anti-PD-1 efficacy. Our results show that FMT from healthy donors is safe in the first-line setting and warrants further investigation in combination with immune checkpoint inhibitors. ClinicalTrials.gov identifier NCT03772899 .
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Affiliation(s)
- Bertrand Routy
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - John G Lenehan
- Department of Oncology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
| | - Wilson H Miller
- Lady Davis Institute of the Jewish General Hospital, Segal Cancer Centre, Montreal, Quebec, Canada
- Departments of Oncology and Medicine, McGill University, Montreal, Quebec, Canada
| | - Rahima Jamal
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Meriem Messaoudene
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Brendan A Daisley
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Cecilia Hes
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Peter Brojde Lung Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
| | - Kait F Al
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Laura Martinez-Gili
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Michal Punčochář
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Scott Ernst
- Department of Oncology, Western University, London, Ontario, Canada
| | - Diane Logan
- Department of Oncology, Western University, London, Ontario, Canada
| | - Karl Belanger
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Khashayar Esfahani
- Lady Davis Institute of the Jewish General Hospital, Segal Cancer Centre, Montreal, Quebec, Canada
- Departments of Oncology and Medicine, McGill University, Montreal, Quebec, Canada
| | - Corentin Richard
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Marina Ninkov
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
| | - Gianmarco Piccinno
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Mithunah Krishnamoorthy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Rene Figueredo
- Department of Oncology, Western University, London, Ontario, Canada
| | - Pamela Thebault
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Panteleimon Takis
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, National Phenome Centre, Imperial College London, London, UK
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jamie Magrill
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Quebec, Canada
| | - LeeAnn Ramsay
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Quebec, Canada
| | - Lisa Derosa
- Gustave Roussy Cancer Campus, Villejuif, France
- Cancer Medicine Department, Gustave Roussy, Villejuif, France
- Institut National de la Santé Et et de la Recherche Médicale (INSERM) U1015, ClinicObiome, Equipe Labellisée-28 Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Ile-de-France, France
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Seema Nair Parvathy
- Department of Medicine, Division of Infectious Diseases, Western University, London, Ontario, Canada
- Division of Infectious Diseases, St Joseph's Health Care, London, Ontario, Canada
| | - Arielle Elkrief
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Ian R Watson
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, Quebec, Canada
- Department of Biochemistry, McGill University, Montréal, Quebec, Canada
| | - Rejean Lapointe
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montréal (CRCHUM), Montreal, Quebec, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - S M Mansour Haeryfar
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Department of Medicine, Division of Clinical Immunology and Allergy, Western University, London, Ontario, Canada
- Department of Surgery, Division of General Surgery, Western University, London, Ontario, Canada
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Michael S Silverman
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, Western University, London, Ontario, Canada
- Division of Infectious Diseases, St Joseph's Health Care, London, Ontario, Canada
| | - Jeremy P Burton
- Lawson Health Research Institute, London, Ontario, Canada
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Saman Maleki Vareki
- Department of Oncology, Western University, London, Ontario, Canada.
- Lawson Health Research Institute, London, Ontario, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
- Department of Medical Biophysics, Western University, London, Ontario, Canada.
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada.
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6
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Manghi P, Blanco-Míguez A, Manara S, NabiNejad A, Cumbo F, Beghini F, Armanini F, Golzato D, Huang KD, Thomas AM, Piccinno G, Punčochář M, Zolfo M, Lesker TR, Bredon M, Planchais J, Glodt J, Valles-Colomer M, Koren O, Pasolli E, Asnicar F, Strowig T, Sokol H, Segata N. MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice. Cell Rep 2023; 42:112464. [PMID: 37141097 DOI: 10.1016/j.celrep.2023.112464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/28/2022] [Revised: 03/10/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.
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Affiliation(s)
- Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | - Amir NabiNejad
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marius Bredon
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Julien Planchais
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | - Jeremy Glodt
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | | | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | | | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy.
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7
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Silva CAC, Zoppi S, Reni A, Piccinno G, Lahmar I, Cerbone L, Carril-Ajuria L, Colomba E, Flippot R, Sow C, Segata N, Escudier B, Zitvogel L, Albiges L, Derosa L. The Lung Immune Prognostic Index (LIPI) stratifies prognostic groups and correlates with gut microbiota (GM) in patients with advanced renal cell carcinoma (RCC). J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.6_suppl.719] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
719 Background: The LIPI score has been reported as an independent prognostic factor in RCC patients treated with immune checkpoint inhibitors (ICI) or tyrosine kinase inhibitors (TKI). Here, we aimed to correlate LIPI score and GM composition in patients with RCC. Methods: We prospectively collected fecal samples of all comers RCC patients who started a 1st or beyond line therapy (standard or clinical trial) in the NCT0457446 at Gustave Roussy. Neutrophil to lymphocyte ratio (dNLR) and lactate dehydrogenase (LDH) were obtained from routine blood tests. Shot gun metagenomic sequencing (MGS) data were analyzed by multivariate and pair-wise/fold ratio . Clinical benefit ratio (CBR, complete response + partial response + stable disease, RECIST1.1) and overall survival (OS, from treatment start) were evaluated. Multivariate analysis (MVA) for OS included age, gender, therapy line, IMDC, histology, hypoalbuminemia. Results: From February 2016 to July 2021, 160 patients were screened and 102 were included. Median age was 61 years (22-89), patients were mostly males (75%) and clear cell histology (90%). Patients were treated in 1st (15%), 2nd (53%) and beyond (32%) lines. Treated with ICI monotherapy (65%), followed by TKI or mTOR (20%) and ICI combination (19%). IMDC was 32% good (G), 54% intermediate (I) and 14% poor (P) and LIPI was 69% G, 25% I and 6% P. Median OS was 42.9, 17.7 and 8.3 months in patients with LIPI G, I and P, respectively (p<0.0001) . Among IMDC risk groups, IMDC G + LIPI G had better OS compared to other subgroups (p=0.017), and those with IMDC P + LIPI P had the worse OS. Overall, LIPI G had higher rates of CBR than I+P LIPI (74% vs 50%; p=0.0158). At MVA, LIPI was independently associated with OS (HR 6.25, 2.02-24.34; p=0.0187). Overall, Parabacteroides merdae and Veillonella parvula were enriched in LIPI I+P, while LIPI G harbored Faecalibacterium prausnitzii. In patients treated with ICI monotherapy, LIPI I+P were enriched with Bacteroides spp ( P. merdae, Phocaeicola vulgatus), and LIPI G had an overrepresentation of Ruminococcaceae unclass bacterium. Conclusions: We report the first MGS study correlating LIPI score and GM composition in RCC patients. LIPI score correlates with clinical outcomes (OS and CBR) and helped to better-stratified IMDC risk groups. Patients LIPI G harbor health-related commensals, while I and P groups are associated with harmful ones. LIPI score could represent a clinically relevant score to stratify mRCC patients. Clinical trial information: NCT04567446 .
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Affiliation(s)
- Carolina Alves Costa Silva
- Inserm U1015, Equipe Labellisée - Ligue Nationale Contre Le Cancer, Gustave Roussy Cancer Campus, Villejuif, France
| | - Silvia Zoppi
- Department of Medicine and Surgery, University of Parma, Parma, Italy, Parma, Italy
| | - Anna Reni
- Azienda Ospedaliera Universitaria Integrata, Verona, Verona, Italy
| | - Gianmarco Piccinno
- Department Of Cellular, Computational And Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | - Imran Lahmar
- Inserm U1015, Equipe Labellisée - Ligue Nationale Contre Le Cancer, Gustave Roussy Cancer Campus, Villejuif, France
| | - Luigi Cerbone
- Azienda Ospedaliera Ss Antonio E Biagio E Cesare Arrigo, SSD Mesotelioma, Alessandria, Italy
| | | | | | | | - Cissé Sow
- Inserm U1015, Equipe Labellisée - Ligue Nationale Contre Le Cancer, Gustave Roussy Cancer Campus, Villejuif, France
| | - Nicola Segata
- Department Of Cellular, Computational And Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | | | | | - Laurence Albiges
- Medical Oncology, Gustave Roussy, Université Paris Saclay, Paris, France
| | - Lisa Derosa
- Gustave Roussy Cancer Campus Grand Paris, Villejuif, France
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8
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Piccinno G, Mota D, Troiano G, Nante N, Niccolini F. A new alarm system to preserve Cryoconserved products from technical failures. Eur J Public Health 2018. [DOI: 10.1093/eurpub/cky218.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- G Piccinno
- Hygiene and Health Organization, Hospital “Careggi”, Florence, Italy
| | - D Mota
- Health Technologies, Estar, Florence, Italy
| | - G Troiano
- Post Graduate School of Public Health, Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - N Nante
- Post Graduate School of Public Health, Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - F Niccolini
- Hygiene and Health Organization, Hospital “Careggi”, Florence, Italy
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9
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Agnesi A, Carrà L, Dallocchio P, Pirzio F, Reali G, Lodo S, Piccinno G. 50-mJ macro-pulses at 1064 nm from a diode-pumped picosecond laser system. Opt Express 2011; 19:20316-20321. [PMID: 21997042 DOI: 10.1364/oe.19.020316] [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: 05/31/2023]
Abstract
Pulse-picking from a 100-mW cw mode-locked seeder, a hybrid master-oscillator power-amplifier (MOPA) system, based on Nd:YVO4 and Nd:YAG amplifier modules, has been developed, delivering single-pulses of 8.6 ps at 455-MHz repetition-rate, bunched into ~1-μs trains of 50 mJ ("macro-pulses"). The output beam is linearly polarized and nearly diffraction limited up to the maximum macro-pulse repetition-rate of 50 Hz. The single-pulse peak power and the macro-pulse duration and energy are quite suitable for high-energy nonlinear optical applications such as low-threshold synchronously-pumped parametric converters in the mid infrared. The impact on the overall efficiency of saturation distortion of the macro-pulse envelope as well as of amplified spontaneous emission (ASE) is considered. The managing of the envelope distortion compensation and of the ASE suppression by means of fast saturable absorbers is reported.
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Affiliation(s)
- A Agnesi
- INFN and Dipartimento di Elettronica dell’Università di Pavia, Via Ferrata 1 - 27100 Pavia, Italy.
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