Publications

  • CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. 

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.

Bioinformatics. 2023 May 4;39(5):btad201. doi: 10.1093/bioinformatics/btad201

  • A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers. Science.

Fidelle M, Rauber C, Alves Costa Silva C, Tian AL, Lahmar I, de La Varende AM, Zhao L, Thelemaque C, Lebhar I, Messaoudene M, Pizzato E, Birebent R, Mbogning Fonkou MD, Zoppi S, Reni A, Dalban C, Leduc M, Ferrere G, Durand S, Ly P, Silvin A, Mulder K, Dutertre CA, Ginhoux F, Yonekura S, Roberti MP, Tidjani-Alou M, Terrisse S, Chen J, Kepp O, Schippers A, Wagner N, Suárez-Gosálvez J, Kobold S, Fahrner JE, Richard C, Bosq J, Lordello L, Vitali G, Galleron N, Quinquis B, Le Chatelier E, Blanchard L, Girard JP, Jarry A, Gervois N, Godefroy E, Labarrière N, Koschny R, Daillère R, Besse B, Truntzer C, Ghiringhelli F, Coatnoan N, Mhanna V, Klatzmann D, Drubay D, Albiges L, Thomas AM, Segata N, Danlos FX, Marabelle A, Routy B, Derosa L, Kroemer G, Zitvogel L.

2023 Jun 9;380(6649):eabo2296. doi: 10.1126/science.abo2296.

  • Bile acids regulate MAdCAM-1 expression to link the gut microbiota to cancer immunosurveillance.

Fidelle M, Tian AL, Zitvogel L, Kroemer G.

2023 Jun 29;12(1):2224672. doi: 10.1080/2162402X.2023.2224672.

  • Formyl peptide receptor-1 (FPR1) represses intestinal oncogenesis.

Le Naour J, Montégut L, Pan Y, Scuderi SA, Cordier P, Joseph A, Sauvat A, Iebba V, Paillet J, Ferrere G, Brechard L, Mulot C, Dubourg G, Zitvogel L, Pol JG, Vacchelli E, Puig PL, Kroemer G.

2023 Jul 21;12(1):2237354. doi: 10.1080/2162402X.2023.2237354.

  • Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial.

Routy B, Lenehan JG, Miller WH Jr, 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

Nat Med. 2023 Aug;29(8):2121-2132. doi: 10.1038/s41591-023-02453-x. Epub 2023 Jul 6. Erratum in: Nat Med. 2024 Feb;30(2):604. doi: 10.1038/s41591-023-02650-8.

  • A Fecal MicroRNA Signature by Small RNA Sequencing Accurately Distinguishes Colorectal Cancers: Results From a Multicenter Study. Gastroenterology

Pardini B, Ferrero G, Tarallo S, Gallo G, Francavilla A, Licheri N, Trompetto M, Clerico G, Senore C, Peyre S, Vymetalkova V, Vodickova L, Liska V, Vycital O, Levy M, Macinga P, Hucl T, Budinska E, Vodicka P, Cordero F, Naccarati A.

2023 Sep;165(3):582-599.e8. doi: 10.1053/j.gastro.2023.05.037

  • Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy.

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

Nat Rev Clin Oncol. 2023 Sep;20(9):583-603. doi: 10.1038/s41571-023-00785-8.

  • Profiling small RNAs in fecal immunochemical tests: is it possible?

Birkeland E, Ferrero G, Pardini B, Umu SU, Tarallo S, Bulfamante S, Hoff G, Senore C, Rounge TB, Naccarati A.

Mol Cancer. 2023 Oct 3;22(1):161. doi: 10.1186/s12943-023-01869-w

  • Molecular portraits of colorectal cancer morphological regions.

Budinská E, Hrivňáková M, Ivkovic TC, Madrzyk M, Nenutil R, Bencsiková B, Al Tukmachi D, Ručková M, Zdražilová Dubská L, Slabý O, Feit J, Dragomir MP, Borilova Linhartova P, Tejpar S, Popovici V.

2023 Nov 13;12:RP86655. doi: 10.7554/eLife.86655.

  • TIGIT+ NK cells in combination with specific gut microbiota features predict response to checkpoint inhibitor therapy in melanoma patients.

Tsakmaklis A, Farowski F, Zenner R, Lesker TR, Strowig T, Schlößer H, Lehmann J, von Bergwelt-Baildon M, Mauch C, Schlaak M, Knuever J, Schweinsberg V, Heinzerling LM, Vehreschild MJGT.

BMC Cancer. 2023 Nov 28;23(1):1160. doi: 10.1186/s12885-023-11551-5.

  • Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial

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.

Nat Commun. 2024 Feb 23;15(1):1633. doi: 10.1038/s41467-024-45357-1.

  • SnoRNA profiling in colorectal cancer and assessment of non-invasive biomarker capacity by ddPCR in fecal samples.

Gómez-Matas J, Duran-Sanchon S, Lozano JJ, Ferrero G, Tarallo S, Pardini B, Naccarati A, Castells A, Gironella M.

2024 Feb 20;27(3):109283. doi: 10.1016/j.isci.2024.109283

  • Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study.

Istvan P, Birkeland E, Avershina E, Kværner AS, Bemanian V, Pardini B, Tarallo S, de Vos WM, Rognes T, Berstad P, Rounge TB.

Nat Commun. 2024 Feb 29;15(1):1791. doi: 10.1038/s41467-024-46033-0

  • Modulation of faecal miRNAs highlights the preventive effects of a Mediterranean low-inflammatory dietary intervention.

Illescas O, Ferrero G, Belfiore A, Pardini B, Tarallo S, Ciniselli CM, Noci S, Daveri E, Signoroni S, Cattaneo L, Mancini A, Morelli D, Milione M, Cordero F, Rivoltini L, Verderio P, Pasanisi P, Vitellaro M, Naccarati A, Gariboldi M.

Clin Nutr. 2024 Apr;43(4):951-959. doi: 10.1016/j.clnu.2024.02.023

  • Fecal miRNA profiles in colorectal cancers with mucinous morphology.

Naccarati A, Dragomir MP, Tarallo S, Gagliardi A, Alberini V, Buchler T, Liska V, Gallo G, Vymetalkova V, Vodickova L, Vodicka P, Pardini B, Ferrero G.

Mutagenesis. 2024 Jun 6:geae015. doi: 10.1093/mutage/geae015

  • Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome.

Derosa L, Iebba V, Silva CAC, Piccinno G, Wu G, Lordello L, Routy B, Zhao N, Thelemaque C, Birebent R, Marmorino F, Fidelle M, Messaoudene M, Thomas AM, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Sibilot DM, Goldwasser F, Scherpereel A, Pegliasco H, Ghiringhelli F, Bouchard N, Sow C, Darik I, Zoppi S, Ly P, Reni A, Daillère R, Deutsch E, Lee KA, Bolte LA, Björk JR, Weersma RK, Barlesi F, Padilha L, Finzel A, Isaksen ML, Escudier B, Albiges L, Planchard D, André F, Cremolini C, Martinez S, Besse B, Zhao L, Segata N, Wojcik J, Kroemer G, Zitvogel L.

2024 Jun 20;187(13):3373-3389.e16. doi: 10.1016/j.cell.2024.05.029.

  • Navigating beyond associations: Opportunities to establish causal relationships between the gut microbiome and colorectal carcinogenesis.

Baas FS, Brusselaers N, Nagtegaal ID, Engstrand L, Boleij A.

Cell Host Microbe. 2024 Aug 14;32(8):1235-1247. doi: 10.1016/j.chom.2024.07.008.

  • The gut microbiome in colorectal cancer: a cross-stage strain-level pooled analysis of 3,512 individuals from 16 cohorts.

Piccinno G, Thompson KN, Manghi P, Ghazi AR, Thomas AM, Blanco-Miguez A, Asnicar F, Mladenovic K, Pinto F, Armanini F, Ferrero G, Tarallo S, Nguyen LH, Yan Y, Vymetalkova V, Trompetto M, Liska V, Hucl T, Vodicka P, Bencsiková B, Čarnogurská M, Popovici V., Marmorino F, Cremolini C, Pardini B, Cordero F, Song M, Chan AT, Derosa L, Zitvogel L, Huttenhower C, Naccarati A, Budinska E, Segata N.

In revision, Nat. Med

  • Surrogate markers of intestinal dysfunction associated with survival in advanced cancers.

Birebent R, Drubay D, Alves Costa Silva C, Marmorino F, Vitali G, Piccinno G, Hurtado Y, Bonato A, Belluomini L, Messaoudene M, Routy B, Fidelle M, Zalcman G, Mazieres J, Audigier-Valette C, Moro-Sibilot D, Goldwasser F, Scherpereel A, Pegliasco H, Ghiringhelli F, Reni A, Barlesi F, Albiges L, Planchard D, Martinez S, Besse B, Segata N, Cremolini C, Zitvogel L, Iebba V, Derosa L.

2025 Dec;14(1):2484880. PMID: 40189749.

  • A quantitative tumor-wide analysis of morphological heterogeneity of colorectal adenocarcinoma.

Dragomir MP, Popovici V, Schallenberg S, Čarnogurská M, Horst D, Nenutil R, Bosman F, Budinská E.

J Pathol Clin Res. 2025 Jul;11(4):e70034. doi: 10.1002/2056-4538.70034. PMID: 40511583; PMCID: PMC12163513.

  • Gut microbiota modulation through Akkermansia spp. supplementation increases CAR-T cell potency.

Marcos-Kovandzic L, Avagliano M, Ben Khelil M, Srikanthan J, Abdallah R, Petrocelli V, Rengassamy J, Alfaro A, Bied M, Fidelle M, Ferrere G, Daillere R, Arbab A, Amine-Hneineh R, Pages A, Dartigues P, Ly P, Simon S, Durand S, Gottschlich A, Ginhoux F, Bleriot C, Liu P, Zhao L, Creusot L, Rolhion N, Kroemer G, Menger L, Kobold S, Castilla-Llorente C, Sokol H, Casola S, Pasolli E, Zitvogel L, Bigenwald C.

Cancer Discov. 2025 Jun 11. doi: 10.1158/2159-8290.CD-24-1230. Epub ahead of print. PMID: 40498998.

  • Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer.

Piccinno G, Thompson KN, Manghi P, Ghazi AR, Thomas AM, Blanco-Míguez A, Asnicar F, Mladenovic K, Pinto F, Armanini F, Punčochář M, Piperni E, Heidrich V, Fackelmann G, Ferrero G, Tarallo S, Nguyen LH, Yan Y, Keles NA, Tuna BG, Vymetalkova V, Trompetto M, Liska V, Hucl T, Vodicka P, Bencsiková B, Čarnogurská M, Popovici V, Marmorino F, Cremolini C, Pardini B, Cordero F, Song M, Chan AT, Derosa L, Zitvogel L, Huttenhower C, Naccarati A, Budinska E, Segata N.

Nat Med. 2025 Jun 3. doi: 10.1038/s41591-025-03693-9. Epub ahead of print. PMID: 40461820.

  • Gut Microbiota in Immuno-Oncology: A Practical Guide for Medical Oncologists With a Focus on Antibiotics Stewardship.

Elkrief A, Routy B, Derosa L, Bolte L, Wargo JA, McQuade JL, Zitvogel L.

Am Soc Clin Oncol Educ Book. 2025 Jun;45(3):e472902. PMID: 40262063

  • Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai.

Ricci L, Selma-Royo M, Golzato D, Servais C, Nabinejad A, Marchi P, Punčochář M, Trenti F, Garcia-Aloy M, Armanini F, Marconi R, Asnicar F, Pinto F, Guella G, Tamburin S, Segata N.

Int J Syst Evol Microbiol. 2025 May;75(5):006798. doi: 10.1099/ijsem.0.006798. PMID: 40445840; PMCID: PMC12125477.

  • Search for Mutations Connected With Non-Response to Anti-EGFR Therapy in mCRC in the Morphologically Defined Regions of Primary Tumours.

Čarnogurská M, Vasylieva VS, Macháčková T, Boudná M, Pifková L, Orlíčková J, Ivkovic TC, Slabý O, Bencsiková B, Popovici V, Budinská E.

Cancer Med. 2025 May;14(9):e70910. doi: 10.1002/cam4.70910. PMID: 40302146; PMCID: PMC12040724.

  • Oncobiomics: Leveraging Microbiome Translational Research in Immuno-Oncology for Clinical-Practice Changes.

Alves Costa Silva C, Almonte AA, Zitvogel L.

Biomolecules. 2025 Mar 31;15(4):504. doi: 10.3390/biom15040504. PMID: 40305219; PMCID: PMC12024955.

  • Low-dose irradiation of the gut improves the efficacy of PD-L1 blockade in metastatic cancer patients.

Chen J, Levy A, Tian AL, Huang X, Cai G, Fidelle M, Rauber C, Ly P, Pizzato E, Sitterle L, Piccinno G, Liu P, Durand S, Mao M, Zhao L, Iebba V, Felchle H, Mallard de La Varende AL, Fischer JC, Thomas S, Greten TF, Jones JC, Monge C, Demaria S, Formenti S, Belluomini L, Dionisi V, Massard C, Blanchard P, Robert C, Quevrin C, Lopes E, Clémenson C, Mondini M, Meziani L, Zhan Y, Zeng C, Cai Q, Morel D, Sun R, Laurent PA, Mangoni M, Di Cataldo V, Arilli C, Trommer M, Wegen S, Neppl S, Riechelmann RP, Camandaroba MP, Neto ES, Fournier PE, Segata N, Holicek P, Galluzzi L, Buqué A, Alves Costa Silva C, Derosa L, Kroemer G, Chen C, Zitvogel L, Deutsch E.

Cancer Cell. 2025 Mar 10;43(3):361-379.e10. PMID: 40068595

  • Multiple regulatory events contribute to a widespread circular RNA downregulation in precancer and early stage of colorectal cancer development.

Camandona A, Gagliardi A, Licheri N, Tarallo S, Francescato G, Budinska E, Carnogurska M, Zwinsová B, Martinoglio B, Franchitti L, Gallo G, Cutrupi S, De Bortoli M, Pardini B, Naccarati A, Ferrero G.

Biomark Res. 2025 Feb 20;13(1):30. doi: 10.1186/s40364-025-00744-8. PMID: 39980011; PMCID: PMC11844049.

  • Gut Microbiota-Related Biomarkers in Immuno-Oncology.

Silva CAC, Fidelle M, Almonte AA, Derosa L, Zitvogel L.

Annu Rev Pharmacol Toxicol. 2025 Jan;65(1):333-354. PMID: 39259979

  • The danger theory of immunity revisited. 

Kroemer G, Montégut L, Kepp O, Zitvogel L.

Nat Rev Immunol. 2024 Dec;24(12):912-928. PMID: 39511426

  • AI-based classification of anticancer drugs reveals nucleolar condensation as a predictor of immunogenicity.

Cerrato G, Liu P, Zhao L, Petrazzuolo A, Humeau J, Schmid ST, Abdellatif M, Sauvat A, Kroemer G.

Mol Cancer. 2024 Dec 20;23(1):275. doi: 10.1186/s12943-024-02189-3. PMID: 39702289; PMCID: PMC11660623.

  • Benzodiazepines compromise the outcome of cancer immunotherapy.

Montégut L, Derosa L, Messaoudene M, Chen H, Lambertucci F, Routy B, Zitvogel L, Martins I, Kroemer G.

Oncoimmunology. 2024 Oct 7;13(1):2413719. PMID: 39381589

  • Long-distance microbial mechanisms impacting cancer immunosurveillance.

Zitvogel L, Fidelle M, Kroemer G.

Immunity. 2024 Sep 10;57(9):2013-2029. PMID: 39151425

  • Acyl-CoA binding protein for the experimental treatment of anorexia.

Chen H, Moriceau S, Joseph A, Mailliet F, Li S, Tolle V, Duriez P, Dardennes R, Durand S, Carbonnier V, Stoll G, Sauvat A, Lachkar S, Aprahamian F, Alves Costa Silva C, Pan H, Montégut L, Anagnostopoulos G, Lambertucci F, Motiño O, Nogueira-Recalde U, Bourgin M, Mao M, Pan Y, Cerone A, Boedec E, Gouveia ZL, Marmorino F, Cremolini C, Derosa L, Zitvogel L, Kepp O, López-Otín C, Maiuri MC, Perez F, Gorwood P, Ramoz N, Oury F, Martins I, Kroemer G.

Sci Transl Med. 2024 Aug 14;16(760):eadl0715. doi: 10.1126/scitranslmed.adl0715. Epub 2024 Aug 14. PMID: 39141698

  • Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries.

Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, Giordano F, Hadjigeorgiou G, Leeming ER, Lobina M, Masala M, Maschio A, McIver LJ, Pala M, Pitzalis M, Wolf J, Fu J, Zhernakova A, Cacciò SM, Cucca F, Berry SE, Ercolini D, Chan AT, Huttenhower C, Spector TD, Segata N, Asnicar F.

2024 Aug 22;187(17):4554-4570.e18. doi: 10.1016/j.cell.2024.06.018. Epub 2024 Jul 8. PMID: 38981480.

  • Navigating beyond associations: Opportunities to establish causal relationships between the gut microbiome and colorectal carcinogenesis.

Baas FS, Brusselaers N, Nagtegaal ID, Engstrand L, Boleij A.

Cell Host Microbe. 2024 Aug 14;32(8):1235-1247. doi: 10.1016/j.chom.2024.07.008. PMID: 39146796.

  • Impact of the ONCOBIOME network in cancer microbiome research.

Zitvogel L, Derosa L, Routy B, Loibl S, Heinzerling L, de Vries IJM, Engstrand L; ONCOBIOME Network; Segata N, Kroemer G.

Nat Med. 2025 Apr;31(4):1085-1098. doi: 10.1038/s41591-025-03608-8. Epub 2025 Apr 11. PMID: 40217075.

 

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