Publications

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 (23/02/2023)

Blanco-Miguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, 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 

Gut microbiota composition in colorectal cancer patients is genetically regulated. Sci Rep. 12(1):11424 (2022). doi: 10.1038/s41598-022-15230-6

Colombo F, Illescas O, Noci S, Minnai F, Pintarelli G, Pettinicchio A, Vannelli A, Sorrentino L, Battaglia L, Cosimelli M, Dragani TA, Gariboldi M. 

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer. Nat Med. 2022 Feb;28(2):315-324. doi: 10.1038/s41591-021-01655-5.

Derosa L, Routy B, Thomas AM, Iebba V, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Moro-Sibilot D, Goldwasser F, Silva CAC, Terrisse S, Bonvalet M, Scherpereel A, Pegliasco H, Richard C, Ghiringhelli F, Elkrief A, Desilets A, Blanc-Durand F, Cumbo F, Blanco A, Boidot R, Chevrier S, Daillère R, Kroemer G, Alla L, Pons N, Le Chatelier E, Galleron N, Roume H, Dubuisson A, Bouchard N, Messaoudene M, Drubay D, Deutsch E, Barlesi F, Planchard D, Segata N, Martinez S, Zitvogel L, Soria JC, Besse B. 

The 8q24 region hosts miRNAs altered in biospecimens of colorectal and bladder cancer patients. Cancer Medicine 00, 1–15 (2022). doi: 10.1002/cam4.5375

Gagliardi A, Francescato G, Ferrero G, Birolo G, Tarallo S, Francavilla A, Piaggeschi G, Di Battista C, Gallo G, Realis Luc A, Sacerdote C, Matullo G, Vineis P, Naccarati A, Pardini B

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases (15/09/2022)

Ianiro G, Punčochář M, Karcher N, Porcari S, Armanini F, Asnicar F, Beghini F, Blanco-Míguez A, Cumbo F, Manghi P, Pinto F, Masucci L, Quaranta G, De Giorgi S, Sciumè GD, Bibbò S, Del Chierico F, Putignani L, Sanguinetti M, Gasbarrini A, Valles-Colomer M, Cammarota G, Segata N 

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma (28/02/2022)

Lee KA, Thomas AM, Bolte LA, Björk JR, Kist de Ruijter L, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Leeming ER, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Vijay A, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Bataille V, Hospers GAP, Spector TD, Weersma RK, Segata N 

FeatSEE: a new multi-omics integration framework for Feature Selection, Explainability and Evaluation, paper in preparation

Licheri N, Ferrero G, Rosso E, Pardini B, Naccarati A, Beccuti M, Cordero F. 

A Natural Polyphenol Exerts Antitumor Activity and Circumvents Anti-PD1 Resistance through Effects on the Gut Microbiota. Cancer Discov. 2022 Apr 1;12(4):1070-1087. doi: 10.1158/2159-8290.CD-21-0808

Messaoudene M, Pidgeon R, Richard C, Ponce M, Diop K, Benlaifaoui M, Nolin-Lapalme A, Cauchois F, Malo J, Belkaid W, Isnard S, Fradet Y, Dridi L, Velin D, Oster P, Raoult D, Ghiringhelli F, Boidot R, Chevrier S, Kysela DT, Brun YV, Falcone EL, Pilon G, Oñate FP, Gitton-Quent O, Le Chatelier E, Durand S, Kroemer G, Elkrief A, Marette A, Castagner B, Routy B. 

Using empirical biological knowledge to infer regulatory networks from multi-omics data (22/08/22)

Pačínková A, Popovici V. 

IntOMICS: a Bayesian framework for reconstructing regulatory networks using multi-omics data. Journal of computational biology in press

Pačínková, A., Popovici, V.

A fecal miRNA signature by small RNA sequencing in different populations distinguishes colorectal cancers and adenomas. Gastroenterology, under revision preparation

Pardini B,… Budinska E,…Cordero F, Naccarati A. 

CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinformatics, under revision preparation

Pernice S, Sirovich R, Grassi E, Viviani M, Ferri M, Sassi F, Alessandrì L, Tortarolo D, Calogero RA, Trusolino L, Bertotti A, Beccuti M, Olivero M, Cordero F. 

UnifiedGreatMod: a new modeling paradigm to study complete and harmonious whole biological systems. Plos Computational Biology, under revision preparation

Pernice S, Aucello R, Tortarolo D, Calogero RA, Herrera-Rincon C, Ronchi G, Geuna S, Cordero F, Beccuti M, Lio P.

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals. Gut. 2022 Jul;71(7):1302-1314. doi: 10.1136/gutjnl-2021-325168.

Tarallo S, Ferrero G, De Filippis F, Francavilla A, Pasolli E, Panero V, Cordero F, Segata N, Grioni S, Pensa RG, Pardini B, Ercolini D, Naccarati A. 

Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer. J Immunother Cancer. 10(3):e004191 (2022). doi: 10.1136/jitc-2021-004191

Terrisse S, Goubet AG, Ueda K, Thomas AM, Quiniou V, Thelemaque C, Dunsmore G, Clave E, Gamat-Huber M, Yonekura S, Ferrere G, Rauber C, Pham HP, Fahrner JE, Pizzato E, Ly P, Fidelle M, Mazzenga M, Costa Silva CA, Armanini F, Pinto F, Asnicar F, Daillère R, Derosa L, Richard C, Blanchard P, Routy B, Culine S, Opolon P, Silvin A, Ginhoux F, Toubert A, Segata N, McNeel DG, Fizazi K, Kroemer G, Zitvogel L 

Gut OncoMicrobiome Signatures as next gene ration biomarkers for cancer immunotherapy Nature Rev. Clin. Oncol in press

Thomas AM, Fidelle M, Kroemer G, Routy B, Wargo JA, Segata N, Zitvogel L. 

Cancer Induces a Stress Ileopathy Depending on β-Adrenergic Receptors and Promoting Dysbiosis that Contributes to Carcinogenesis. Cancer Discov. 2022 Apr 1;12(4):1128-1151. doi: 10.1158/2159-8290.CD-21-0999.

Yonekura S, Terrisse S, Alves Costa Silva C, Lafarge A, Iebba V, Ferrere G, Goubet AG, Fahrner JE, Lahmar I, Ueda K, Mansouri G, Pizzato E, Ly P, Mazzenga M, Thelemaque C, Fidelle M, Jaulin F, Cartry J, Deloger M, Aglave M, Droin N, Opolon P, Puget A, Mann F, Neunlist M, Bessard A, Aymeric L, Matysiak-Budnik T, Bosq J, Hofman P, Duong CPM, Ugolini S, Quiniou V, Berrard S, Ryffel B, Kepp O, Kroemer G, Routy B, Lordello L, Bani MA, Segata N, Yengej FY, Clevers H, Scoazec JY, Pasolli E, Derosa L, Zitvogel L.

Présentation et prix ASCO 21
https://www.pourquoidocteur.fr/Articles/Question-d-actu/36510-ASCO-bacteries-microbiote-boostent-l-immunotherapie

Le parisien ASCO 2021
Quand des bactéries de l’intestin aident à lutter contre le cancer

Oral administration of Akkermansia muciniphila elevates systemic antiaging and anticancer metabolites Claudia Grajeda-Iglesias Sylvère Durand,* Romain Daillère, Kristina Iribarren, Fabien Lemaitre, Lisa Derosa, Fanny Aprahamian, Noélie Bossut, Nitharsshini Nirmalathasan, Frank Madeo, Laurence Zitvogel, Guido Kroemer (2021). Aging (Albany NY). 13, Advance.

Physiologic colonic uptake of 18F-FDG on PET/CT is associated with clinical response and gut microbiome composition in patients with advanced non-small cell lung cancer treated with immune checkpoint inhibitors.
Cvetkovic L, Régis C, Richard C, Derosa L, Leblond A, Malo J, Messaoudene M, Desilets A, Belkaid W, Elkrief A, Routy B, Juneau D.Eur J Nucl Med Mol Imaging.
2020 Oct 31. doi: 10.1007/s00259-020-05081-6. Online ahead of print.PMID: 33128571

The Gut Microbiome Associates with Immune Checkpoint Inhibition Outcomes in Patients with Advanced Non-Small Cell Lung Cancer.
Hakozaki T, Richard C, Elkrief A, Hosomi Y, Benlaïfaoui M, Mimpen I, Terrisse S, Derosa L, Zitvogel L, Routy B, Okuma Y.Cancer Immunol Res.
2020 Oct;8(10):1243-1250. doi: 10.1158/2326-6066.CIR-20-0196. Epub 2020 Jul 27.PMID: 32847937

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples
Sonia Tarallo, Giulio Ferrero, Gaetano Gallo, Antonio Francavilla, Giuseppe Clerico, Alberto Realis Luc, Paolo Manghi, Andrew Maltez Thomas, Paolo Vineis, Nicola Segata, Barbara Pardini, Alessio Naccarati, Francesca Corderoa

A Holistic Perspective: Exosomes Shuttle between Nerves and Immune Cells in the Tumor Microenvironment
Mihnea P. Dragomir, Vlad Moisoiu, Roxana Manaila, Barbara Pardini, Erik Knutsen, Simone Anfossi, Moran Amit and George A. Calin

Trial watch : the gut microbiota as a tool to boost the clinical efficacy of anticancer immunotherapy
Romain Daillère, Lisa Derosa , Mélodie Bonvalet, Nicola Segata, Bertrand Routy, Manuela Gariboldi, Eva Budinská, I. Jolanda M. De Vries, Alessio Gordon Naccarati, Valérie Zitvogel, Carlos Caldas, Lars Engstrand, Sibylle Loilbl, Jacques Fieschi, Lucie Heinzerling, Guido Kroemer & Laurence Zitvogel

Intake of Natural Compounds and Circulating microRNA Expression Levels: Their Relationship Investigated in Healthy Subjects With Different Dietary Habits
Giulio Ferrero, Sara Carpi, Beatrice Polini, Barbara Pardini, Paola Nieri, Alessia Impeduglia, Sara Grioni, Sonia Tarallo and Alessio Naccarati

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.
Asnicar, F., Berry, S.E., Valdes, A.M. et al.
Nat Med 27, 321–332 (2021).

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.
Karcher, N., Pasolli, E., Asnicar, F. et al.
Genome Biol 21, 138 (2020).

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations,
Adrian Tett, Kun D. Huang, Francesco Asnicar, Hannah Fehlner-Peach, Edoardo Pasolli, Nicolai Karcher, Federica Armanini, Paolo Manghi, Kevin Bonham, Moreno Zolfo, Francesca De Filippis, Cara Magnabosco, Richard Bonneau, John Lusingu, John Amuasi, Karl Reinhard, Thomas Rattei, Fredrik Boulund, Lars Engstrand, Albert Zink, Maria Carmen Collado, Dan R. Littman, Daniel Eibach, Danilo Ercolini, Omar Rota-Stabelli, Curtis Huttenhower, Frank Maixner, Nicola Segata.
Cell Host & Microbe, Volume 26, Issue 5, 2019

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