RESEARCH ARTICLE
◥CANCER IMMUNOLOGY
Cross-reactivity between tumor MHC
class I–restricted antigens and an
enterococcal bacteriophage
Aurélie Fluckiger1,2, Romain Daillère1,2,3, Mohamed Sassi^4 , Barbara Susanne Sixt5,6,7,8,9,10,
Peng Liu6,7,8,9,10, Friedemann Loos6,7,8,9,10, Corentin Richard11,12,13, Catherine Rabu14,15,
Maryam Tidjani Alou1,2,16,Anne-GaëlleGoubet1,2, Fabien Lemaitre1,3,GladysFerrere1,2, Lisa Derosa1,2,17,
Connie P. M. Duong1,2, Meriem Messaoudene^18 ,AndréanneGagné^18 , Philippe Joubert^18 ,
Luisa De Sordi19,20, Laurent Debarbieux^19 , Sylvain Simon14,15, Clara-Maria Scarlata^21 , Maha Ayyoub^21 ,
Belinda Palermo^22 , Francesco Facciolo^23 , Romain Boidot^24 , Richard Wheeler^25 ,
Ivo Gomperts Boneca^25 , Zsofia Sztupinszki^26 , Krisztian Papp^27 , Istvan Csabai^27 , Edoardo Pasolli^28 ,
Nicola Segata^29 , Carlos Lopez-Otin7,8,9,10,30, Zoltan Szallasi26,31,32,33, Fabrice Andre34,35,
Valerio Iebba1,2,36, Valentin Quiniou37,38, David Klatzmann37,38, Jacques Boukhalil^16 , Saber Khelaifia^16 ,
Didier Raoult^16 , Laurence Albiges1,39, Bernard Escudier1,39,40, Alexander Eggermont1,41,
Fathia Mami-Chouaib^42 , Paola Nistico22,23, François Ghiringhelli^43 , Bertrand Routy18,44,
Nathalie Labarrière14,15,VincentCattoir4,45,46, Guido Kroemer6,7,8,9,10,47,48,49,50,LaurenceZitvogel1,2,17,49
Intestinal microbiota have been proposed to induce commensal-specific memory T cells that cross-react
with tumor-associated antigens. We identified major histocompatibility complex (MHC) class I–binding
epitopes in the tail length tape measure protein (TMP) of a prophage found in the genome of the
bacteriophageEnterococcus hirae. Mice bearingE. hiraeharboring this prophage mounted a TMP-specific
H-2Kb–restricted CD8+T lymphocyte response upon immunotherapy with cyclophosphamide or
anti–PD-1 antibodies. Administration of bacterial strains engineered to express the TMP epitope
improved immunotherapy in mice. In renal and lung cancer patients, the presence of the enterococcal
prophage in stools and expression of a TMP–cross-reactive antigen by tumors correlated with long-term
benefit of PD-1 blockade therapy. In melanoma patients, T cell clones recognizing naturally processed
cancer antigens that are cross-reactive with microbial peptides were detected.
U
nleashing immune responses against
tumor-associated antigens through chemo-
therapy, radiotherapy, targeted thera-
pies, or immune checkpoint inhibitors
has formed the basis of successful can-
cer treatments ( 1 , 2 ). The recent discovery that
the gut microbiota affects the cancer-immune
set point, thus influencing the clinical out-
come of cancer therapies, has rekindled the
concept that microbes or their products mod-
ulate not only intestinal but also systemic im-
munity ( 3 , 4 ). Indeed, memory responses byinterferon-g(IFNg)–secreting CD4+and CD8+
T cells specific forEnterococcus hirae,Bacteroides
fragilis,andAkkermansia muciniphilaare
associated with favorable clinical outcome in
cancer patients ( 5 – 8 ), suggesting that microbe-
specific T lymphocytes may contribute to anti-
tumor immune responses. The mechanisms
through which microbes trigger chronic in-
testinal inflammation and systemic auto-
immune disease have not been resolved ( 9 ).
The theory of“molecular mimicry”( 10 – 15 )
posits that T cells elicited by bacteria or viruses
accidentally recognize autoantigens as they
“escape”from self-tolerance–inducing mecha-
nisms (such as clonal deletion or inactivation).
Although major histocompatibility complex
(MHC) class I–and class II–binding epitopes
encoded by bacterial genomes may be immu-
nogenic ( 10 – 14 ), very few reports have dem-
onstrated that microbe-specific CD4+or CD8+
T lymphocytes attack normal or neoplastic
tissues ( 16 – 18 ).
Cyclophosphamide (CTX) is a chemothera-
peutic drug that can induce the translocation
ofE. hiraefrom the gut lumen to the mesen-
teric and splenic immunetissues. This results
in CD4+and CD8+T lymphocytes producing
interleukin-17 (IL-17) and IFNgand correlates
with improved anticancer immune responses
in mice ( 6 , 19 ). Broad-spectrum antibiotics
abolished the therapeutic efficacy of CTX
unlessE. hiraewas supplied by oral gavage
( 6 ). When comparing a panel of distinct
E. hiraestrains (table S1 and fig. S1A) for their
capacity to restore the antibiotic-perturbed
anticancer effects of CTX, we found that only a
fewE. hiraeisolates (such as 13144 and IGR11)
were efficient to reduce MCA205 tumor size
(Fig.1,AandB)( 6 ). Given that the therapeutic
efficacy of the combination of CTX andE. hirae
13144 is abrogated by the depletion of CD8+
T cells or the neutralization of IFNg( 6 ), weRESEARCH
Fluckigeret al.,Science 369 , 936–942 (2020) 21 August 2020 1of7
(^1) Gustave Roussy Cancer Campus (GRCC), Villejuif, France. (^2) Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France. (^3) everImmune, Gustave
Roussy Cancer Center, Villejuif, France.^4 Université Rennes 1, Laboratoire de Biochimie Pharmaceutique, Inserm U1230 - UPRES EA 2311, Rennes, France.^5 Laboratory for Molecular Infection
Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, 90187, Umeå, Sweden.^6 Cell Biology and Metabolomics Platforms, Gustave Roussy
Cancer Campus, Villejuif, France.^7 Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.^8 INSERM U1138, Paris, France.^9 Université de Paris, Paris,
France.^10 Sorbonne Université, Paris, France.^11 Research Platform in Biological Oncology, Dijon, France.^12 GIMI Genetic and Immunology Medical Institute, Dijon, France.^13 University of Burgundy-
Franche Comté, Dijon, France.^14 CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.^15 LabEx IGO“Immunotherapy, Graft, Oncology,”Nantes, France.^16 UMR MEPHI, Aix-
Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.^17 Université Paris-Saclay, Villejuif,
F-94805, France.^18 Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada.
(^19) Bacteriophage, Bacterium, Host Laboratory, Institut Pasteur, F-75015 Paris, France. (^20) Sorbonne Université, Centre de Recherche Saint Antoine, INSERM UMRS_938, Paris, France. (^21) Cancer
Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole,
31100 Toulouse, France.^22 Unit of Tumor Immunology and Immunotherapy, Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS Regina Elena National Cancer
Institute, Rome, Italy.^23 Thoracic Surgery Unit, Department of Surgical Oncology, IRCCS Regina Elena National Cancer Institute, Rome, Italy.^24 Unit of Molecular Biology, Department of Biology
and Pathology of Tumors, Georges-François Leclerc Anticancer Center, UNICANCER, Dijon, France.^25 Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France.
(^26) Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA. (^27) Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest,
Hungary.^28 Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy.^29 Department CIBIO, University of Trento, Trento, Italy.^30 Departamento de Bioquímica y Biología
Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain.^31 Harvard Medical School, Boston, MA, USA.^32 Danish Cancer Society Research Center,
Copenhagen, Denmark.^33 MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary.^34 Department of Cancer Medicine, Breast
Cancer Committee, Gustave Roussy, Villejuif, France.^35 INSERM Unit 981, Gustave Roussy, Villejuif, France.^36 Department of Medical Sciences, University of Trieste, 34137 Trieste, Italy.^37 AP-HP,
Hôpital Pitié-Salpêtrière, Clinical Investigation Center in Biotherapy (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), F-75651, Paris, France.^38 Sorbonne
Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), F-75651, Paris, France.^39 Department of Medical Oncology, Gustave Roussy, Villejuif, France.^40 INSERM U981, GRCC,
Villejuif, France.^41 Princess Maxima Center, CS 3584 Utrecht, the Netherlands.^42 INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Fac. de Médecine -
Univ. Paris-Sud, Université Paris-Saclay, 94805, Villejuif, France.^43 Department of Medical Oncology, Center GF Leclerc, Dijon, France.^44 Division d'Hémato-Oncologie, Département de Médicine,
Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.^45 CHU de Rennes - Hôpital Ponchaillou, Service de Bactériologie-Hygiène Hospitalière, Rennes, France.^46 CNR
de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France.^47 Pôle de Biologie, Hôpital Européen Georges Pompidou, Assistance Publique–Hôpitaux de Paris, Paris,
France.^48 Department of Women's and Children's Health, Karolinska University Hospital, 1 Stockholm, Sweden.^49 Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences,
Suzhou, China.^50 Institut Universitaire de France, Paris, France.
*Corresponding author. Email: [email protected] (L.Z.); [email protected] (G.K.)