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Bosch TCG, Wigley M, Colomina B, Bohannan B, Meggers F, Amato KR, Azad MB, Blaser MJ, Brown K, Dominguez-Bello MG, Ehrlich SD, Elinav E, Finlay BB, Geddie K, Geva-Zatorsky N, Giles-Vernick T, Gros P, Guillemin K, Haraoui LP, Johnson E, Keck F, Lorimer J, McFall-Ngai MJ, Nichter M, Pettersson S, Poinar H, Rees T, Tropini C, Undurraga EA, Zhao L, Melby MK. The potential importance of the built-environment microbiome and its impact on human health. Proc Natl Acad Sci U S A 2024; 121:e2313971121. [PMID: 38662573 PMCID: PMC11098107 DOI: 10.1073/pnas.2313971121] [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] [Indexed: 05/18/2024] Open
Abstract
There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments.
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Affiliation(s)
- Thomas C. G. Bosch
- Zoological Institute, University of Kiel, Kiel24118, Germany
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
| | - Mark Wigley
- Graduate School of Architecture, Planning and Preservation, Columbia University, New York, NY10027
| | - Beatriz Colomina
- School of Architecture, Princeton University, Princeton, NJ08544
| | - Brendan Bohannan
- The Institute of Ecology and Evolution, University of Oregon, Eugene, OR97403-5289
| | - Forrest Meggers
- Princeton University School of Architecture & Andlinger Center for Energy and the Environment, Princeton, NJ08540
| | - Katherine R. Amato
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, Northwestern University, Evanston, IL60208
| | - Meghan B. Azad
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3E 0Z3, Canada
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Martin J. Blaser
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MBR3E 3P4, Canada
- Center for Advanced Biotechnology and Medicine at Rutgers Biomedical and Health Sciences, Rutgers University, Piscataway, NJ08854-8021
| | - Kate Brown
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Program in Science, Technology and Society, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Maria Gloria Dominguez-Bello
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ08901
- Department of Anthropology, Rutgers University, New Brunswick, NJ08901
| | - Stanislav Dusko Ehrlich
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Institute of Neurology, University College London, LondonWC1N 3RX, United Kingdom
| | - Eran Elinav
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Systems Immunology Department, Weizmann Institute of Science, Rehovot761000, Israel
- Division of Microbiome & Cancer, Deutsches Krebsforschungszentrum, 69120Heidelberg, Germany
| | - B. Brett Finlay
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Kate Geddie
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Medical and Related Sciences Centre, The Canadian Institute for Advanced Research, Toronto, ONM5G 1L7, Canada
| | - Naama Geva-Zatorsky
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Technion Integrated Cancer Center, Technion-Israel Institute of Technology, Haifa3525433, Israel
- Department of Cell Biology and Cancer Science, Technion-Israel Institute of Technology, Haifa3525433, Israel
| | - Tamara Giles-Vernick
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Anthropology & Ecology of Disease Emergence, Institut Pasteur, Université Paris Cité, Paris75015, France
| | - Philippe Gros
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry, McGill University, Montreal, QCH3G 1Y6, Canada
| | - Karen Guillemin
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Institute of Molecular Biology, University of Oregon, Eugene, OR97403
| | - Louis-Patrick Haraoui
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, CanadaJ1E 4K8
| | - Elizabeth Johnson
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- College of Human Ecology, Cornell University, IthakaNY14853
| | - Frédéric Keck
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Laboratoire d’Anthropologie Sociale, Collège de France, Paris75005, France
| | - Jamie Lorimer
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- School of Geography and the Environment, University of Oxford, OX1 3QY, United Kingdom
| | - Margaret J. McFall-Ngai
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA91125
| | - Mark Nichter
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- School of Anthropology, University of Arizona, Tucson, AZ85721
| | - Sven Pettersson
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Nanyang Technological University, Singapore637715, Singapore
| | - Hendrik Poinar
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4M4, Canada
| | - Tobias Rees
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- LIMN, Berkeley, CA94708
| | - Carolina Tropini
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Microbiology and Immunology and School of Biomedical Engineering, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Eduardo A. Undurraga
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago7820436, Chile
| | - Liping Zhao
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ08901
| | - Melissa K. Melby
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, University of Delaware, Newark, DE19716
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2
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Braun T, Feng R, Amir A, Levhar N, Shacham H, Mao R, Hadar R, Toren I, Algavi Y, Abu-Saad K, Zhuo S, Efroni G, Malik A, Picard O, Yavzori M, Agranovich B, Liu TC, Stappenbeck TS, Denson L, Kalter-Leibovici O, Gottlieb E, Borenstein E, Elinav E, Chen M, Ben-Horin S, Haberman Y. Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort. Nat Commun 2024; 15:3764. [PMID: 38704361 PMCID: PMC11069498 DOI: 10.1038/s41467-024-48106-6] [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: 10/11/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n = 380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene expression modules, that are directly linked to potential protective dietary exposures (coffee, manganese, vitamin D), fecal metabolites, and the microbiome. Bacteria-associated metabolites are primarily linked with host immune modules, whereas diet-linked metabolites are associated with host epithelial metabolic functions.
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Affiliation(s)
- Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Rui Feng
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-Sen University, Nanning, Guangxi, China
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Nina Levhar
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hila Shacham
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ren Mao
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Rotem Hadar
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Itamar Toren
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Department of Military Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yadid Algavi
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Kathleen Abu-Saad
- Gertner Institute for Epidemiology and Health Policy Research, Tel Hashomer, Israel
| | - Shuoyu Zhuo
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Gilat Efroni
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Alona Malik
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Orit Picard
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Miri Yavzori
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Bella Agranovich
- Laura and Isaac Perlmutter Metabolomics Center, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St. Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ofra Kalter-Leibovici
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Gertner Institute for Epidemiology and Health Policy Research, Tel Hashomer, Israel
| | - Eyal Gottlieb
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Elhanan Borenstein
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, NM, USA
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Microbiome & Cancer Division, German National Cancer Center (DKFZ), Heidelberg, Germany
| | - Minhu Chen
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shomron Ben-Horin
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel.
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Nobs SP, Elinav E. A microbial iron fist to fight tumors. Nat Immunol 2024; 25:720-721. [PMID: 38664584 DOI: 10.1038/s41590-024-01806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Affiliation(s)
- Samuel P Nobs
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
- Microbiome & Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Ratiner K, Ciocan D, Abdeen SK, Elinav E. Utilization of the microbiome in personalized medicine. Nat Rev Microbiol 2024; 22:291-308. [PMID: 38110694 DOI: 10.1038/s41579-023-00998-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Inter-individual human variability, driven by various genetic and environmental factors, complicates the ability to develop effective population-based early disease detection, treatment and prognostic assessment. The microbiome, consisting of diverse microorganism communities including viruses, bacteria, fungi and eukaryotes colonizing human body surfaces, has recently been identified as a contributor to inter-individual variation, through its person-specific signatures. As such, the microbiome may modulate disease manifestations, even among individuals with similar genetic disease susceptibility risks. Information stored within microbiomes may therefore enable early detection and prognostic assessment of disease in at-risk populations, whereas microbiome modulation may constitute an effective and safe treatment tailored to the individual. In this Review, we explore recent advances in the application of microbiome data in precision medicine across a growing number of human diseases. We also discuss the challenges, limitations and prospects of analysing microbiome data for personalized patient care.
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Affiliation(s)
- Karina Ratiner
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Dragos Ciocan
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany.
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Porcari S, Fusco W, Spivak I, Fiorani M, Gasbarrini A, Elinav E, Cammarota G, Ianiro G. Fine-tuning the gut ecosystem: the current landscape and outlook of artificial microbiome therapeutics. Lancet Gastroenterol Hepatol 2024; 9:460-475. [PMID: 38604200 DOI: 10.1016/s2468-1253(23)00357-6] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 04/13/2024]
Abstract
The gut microbiome is acknowledged as a key determinant of human health, and technological progress in the past two decades has enabled the deciphering of its composition and functions and its role in human disorders. Therefore, manipulation of the gut microbiome has emerged as a promising therapeutic option for communicable and non-communicable disorders. Full exploitation of current therapeutic microbiome modulators (including probiotics, prebiotics, and faecal microbiota transplantation) is hindered by several factors, including poor precision, regulatory and safety issues, and the impossibility of providing reproducible and targeted treatments. Artificial microbiota therapeutics (which include a wide range of products, such as microbiota consortia, bacteriophages, bacterial metabolites, and engineered probiotics) have appeared as an evolution of current microbiota modulators, as they promise safe and reproducible effects, with variable levels of precision via different pathways. We describe the landscape of artificial microbiome therapeutics, from those already on the market to those still in the pipeline, and outline the major challenges for positioning these therapeutics in clinical practice.
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Affiliation(s)
- Serena Porcari
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - William Fusco
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Igor Spivak
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Medical Clinic III, University Hospital Aachen, Aachen, Germany
| | - Marcello Fiorani
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Microbiome and Cancer Division, DKFZ, Heidelberg, Germany
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
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Bar Ziv O, Cahn A, Jansen T, Istomin V, Kedem E, Olshtain-Pops K, Israel S, Oster Y, Orenbuch-Harroch E, Korem M, Strahilevitz J, Levy I, Valdés-Mas R, Ivanova V, Elinav E, Shahar E, Elinav H. Diagnosis and Risk Factors of Prediabetes and Diabetes in People Living with HIV- Evaluation of Clinical and Microbiome Parameters. J Infect Dis 2024:jiae167. [PMID: 38557867 DOI: 10.1093/infdis/jiae167] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 03/08/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Diabetes is more common among people living with HIV (PLWH), as compared with healthy individuals. In a prospective multicenter study (N = 248), we identified normoglycemic (48.7%), prediabetic (44.4%) and diabetic (6.9%) PLWH. HbA1c and fasting blood glucose (FBG) sensitivity in defining dysglycemia was 96.8%, while addition of oral glucose tolerance test led to reclassification of only 4 patients. Inclusion of 93 additional PLWH with known DM enabled identification of multiple independent predictors of dysglycemia or diabetes: older age, higher BMI, Ethiopian origin, HIV duration, lower integrase inhibitor exposure and advanced disease at diagnosis. Shotgun metagenomic microbiome analysis revealed 4 species that were significantly expanded with hyperglycemia/hyperinsulinemia, and 2 species that were differentially more prevalent in prediabetic/diabetic PLWH. Collectively, we uncover multiple potential host and microbiome predictors of altered glycemic status in PLWH, while demonstrating that FBG and HbA1C likely suffice for diabetes screening. These potential diabetic predictors merit future prospective validation.
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Affiliation(s)
- Omer Bar Ziv
- Department of military Medicine and "Zameret", Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel and Medical Corps, Israel Defense forces, Israel
| | - Avivit Cahn
- Diabetes Unit, Department of Endocrinology and Metabolism, Hadassah Medical Center, Jerusalem, 9112102, Israel
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
| | - Tallulah Jansen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7632706, Israel
| | - Valery Istomin
- HIV Service, Hillel-Yafe Medical Center, Hadera, 3842401, Israel
| | - Eynat Kedem
- Allergy, Immunology and AIDS unit, Rambam Medical Center, Haifa, 35254908, Israel
| | - Karen Olshtain-Pops
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center. Jerusalem, 9112102, Israel
| | - Sarah Israel
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center. Jerusalem, 9112102, Israel
| | - Yonatan Oster
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center. Jerusalem, 9112102, Israel
| | - Efrat Orenbuch-Harroch
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center. Jerusalem, 9112102, Israel
| | - Maya Korem
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center. Jerusalem, 9112102, Israel
| | - Jacob Strahilevitz
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center. Jerusalem, 9112102, Israel
| | - Itzchak Levy
- Infectious diseases unit, Sheba Medical Center, Tel Hashomer, 5262000, Israel
| | - Rafael Valdés-Mas
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7632706, Israel
| | - Valeria Ivanova
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7632706, Israel
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7632706, Israel
- Division of Microbiome & Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, 280 69120, Germany
| | - Eduardo Shahar
- Allergy, Immunology and AIDS unit, Rambam Medical Center, Haifa, 35254908, Israel
| | - Hila Elinav
- Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
- Hadassah AIDS Center, Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Center. Jerusalem, 9112102, Israel
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7
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Nobs SP, Elinav E. Complement(ing) the microbiome in infants through breastmilk. Cell Res 2024:10.1038/s41422-024-00944-1. [PMID: 38443564 DOI: 10.1038/s41422-024-00944-1] [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: 03/07/2024] Open
Affiliation(s)
- Samuel P Nobs
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
- Microbiome & Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Reiter O, Leshem A, Alexander-Shani R, Brandwein M, Cohen Y, Yeshurun A, Ziv M, Elinav E, Hodak E, Dodiuk-Gad RP. Bacterial Skin Dysbiosis in Darier Disease. Dermatology 2024:000537714. [PMID: 38330926 DOI: 10.1159/000537714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/05/2024] [Indexed: 02/10/2024] Open
Abstract
INTRODUCTION Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection of skin lesions is common and Staphylococcus aureus commonly colonizes these lesions. The aim of the study was to characterize the bacterial microbiome of cutaneous Darier lesions compared to normal-looking skin and to disease severity. METHODS All patients with a history of Darier followed-up at Emek Medical Center were invited to participate in the study. Patients that did not use antibiotics in the past month and signed informed consent had four skin sites sampled with swabs: scalp, chest, axilla and palm. All samples were analyzed for bacterial microbiome using 16S rDNA sequencing. RESULTS Two-hundred and eighty microbiome samples obtained from lesional and non-lesional skin of the scalp, chest, axilla, and palm of 42 Darier patients were included in the analysis. The most abundant bacterial genera across all skin sites were Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, and Anearococcus. Scalp and chest lesions featured a distinct microbiome configuration that was mainly driven by an overabundance of Staphylococci species. Patients with more severe disease exhibited microbiome alterations in the chest, axilla, and palm compared with patients with only mild disease, driven by Peptoniphilus and Moryella genera in scalp and palmar lesions, respectively. CONCLUSION Staphylococci were significantly associated with Darier lesions and drive Darier-associated dysbiosis. Severity of the disease was associated with two other bacterial genera. Whether these associations also hold a causative role and may serve as a therapeutic target remains to be determined and requires further investigation.
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9
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Nobs SP, Kolodziejczyk AA, Adler L, Horesh N, Botscharnikow C, Herzog E, Mohapatra G, Hejndorf S, Hodgetts RJ, Spivak I, Schorr L, Fluhr L, Kviatcovsky D, Zacharia A, Njuki S, Barasch D, Stettner N, Dori-Bachash M, Harmelin A, Brandis A, Mehlman T, Erez A, He Y, Ferrini S, Puschhof J, Shapiro H, Kopf M, Moussaieff A, Abdeen SK, Elinav E. Lung dendritic-cell metabolism underlies susceptibility to viral infection in diabetes. Nature 2023; 624:645-652. [PMID: 38093014 PMCID: PMC10733144 DOI: 10.1038/s41586-023-06803-0] [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: 11/08/2022] [Accepted: 10/31/2023] [Indexed: 12/22/2023]
Abstract
People with diabetes feature a life-risking susceptibility to respiratory viral infection, including influenza and SARS-CoV-2 (ref. 1), whose mechanism remains unknown. In acquired and genetic mouse models of diabetes, induced with an acute pulmonary viral infection, we demonstrate that hyperglycaemia leads to impaired costimulatory molecule expression, antigen transport and T cell priming in distinct lung dendritic cell (DC) subsets, driving a defective antiviral adaptive immune response, delayed viral clearance and enhanced mortality. Mechanistically, hyperglycaemia induces an altered metabolic DC circuitry characterized by increased glucose-to-acetyl-CoA shunting and downstream histone acetylation, leading to global chromatin alterations. These, in turn, drive impaired expression of key DC effectors including central antigen presentation-related genes. Either glucose-lowering treatment or pharmacological modulation of histone acetylation rescues DC function and antiviral immunity. Collectively, we highlight a hyperglycaemia-driven metabolic-immune axis orchestrating DC dysfunction during pulmonary viral infection and identify metabolic checkpoints that may be therapeutically exploited in mitigating exacerbated disease in infected diabetics.
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Affiliation(s)
- Samuel Philip Nobs
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Aleksandra A Kolodziejczyk
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- International Institute of Molecular and Cellular Biology, Warsaw, Poland
| | - Lital Adler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Horesh
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of General Surgery and Transplantations, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Ella Herzog
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Gayatree Mohapatra
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sophia Hejndorf
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Ryan-James Hodgetts
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Spivak
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Lena Schorr
- Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Leviel Fluhr
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Denise Kviatcovsky
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Anish Zacharia
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suzanne Njuki
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dinorah Barasch
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Mally Dori-Bachash
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Mehlman
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yiming He
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sara Ferrini
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jens Puschhof
- Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany
| | - Hagit Shapiro
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Arieh Moussaieff
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany.
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10
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Kviatcovsky D, Valdés-Mas R, Federici S, Elinav E. Phage therapy in noncommunicable diseases. Science 2023; 382:266-267. [PMID: 37856612 DOI: 10.1126/science.adh2718] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Bacteriophages have potential as suppressors of disease-contributing commensal bacteria.
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Affiliation(s)
- Denise Kviatcovsky
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sara Federici
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Microbiome and Cancer Division, DKFZ, Heidelberg, Germany
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11
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Abstract
Recent evidence suggests that some human cancers may harbor low-biomass microbial ecosystems, spanning bacteria, viruses, and fungi. Bacteria, the most-studied kingdom in this context, are suggested by these studies to localize within cancer cells, immune cells and other tumor microenvironment cell types, where they are postulated to impact multiple cancer-related functions. Herein, we provide an overview of intratumoral bacteria, while focusing on intracellular bacteria, their suggested molecular activities, communication networks, host invasion and evasion strategies, and long-term colonization capacity. We highlight how the integration of sequencing-based and spatial techniques may enable the recognition of bacterial tumor niches. We discuss pitfalls, debates and challenges in decisively proving the existence and function of intratumoral microbes, while reaching a mechanistic elucidation of their impacts on tumor behavior and treatment responses. Together, a causative understanding of possible roles played by intracellular bacteria in cancer may enable their future utilization in diagnosis, patient stratification, and treatment.
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Affiliation(s)
- Lena Schorr
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Marius Mathies
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany.
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany.
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12
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Jaber Y, Netanely Y, Naamneh R, Saar O, Zubeidat K, Saba Y, Georgiev O, Kles P, Barel O, Horev Y, Yosef O, Eli-Berchoer L, Nadler C, Betser-Cohen G, Shapiro H, Elinav E, Wilensky A, Hovav AH. Langerhans cells shape postnatal oral homeostasis in a mechanical-force-dependent but microbiota and IL17-independent manner. Nat Commun 2023; 14:5628. [PMID: 37699897 PMCID: PMC10497507 DOI: 10.1038/s41467-023-41409-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/06/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023] Open
Abstract
The postnatal interaction between microbiota and the immune system establishes lifelong homeostasis at mucosal epithelial barriers, however, the barrier-specific physiological activities that drive the equilibrium are hardly known. During weaning, the oral epithelium, which is monitored by Langerhans cells (LC), is challenged by the development of a microbial plaque and the initiation of masticatory forces capable of damaging the epithelium. Here we show that microbial colonization following birth facilitates the differentiation of oral LCs, setting the stage for the weaning period, in which adaptive immunity develops. Despite the presence of the challenging microbial plaque, LCs mainly respond to masticatory mechanical forces, inducing adaptive immunity, to maintain epithelial integrity that is also associated with naturally occurring alveolar bone loss. Mechanistically, masticatory forces induce the migration of LCs to the lymph nodes, and in return, LCs support the development of immunity to maintain epithelial integrity in a microbiota-independent manner. Unlike in adult life, this bone loss is IL-17-independent, suggesting that the establishment of oral mucosal homeostasis after birth and its maintenance in adult life involve distinct mechanisms.
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Affiliation(s)
- Yasmin Jaber
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Yasmine Netanely
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Reem Naamneh
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Or Saar
- Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel; Department of Periodontology, Hadassah Medical Center, Jerusalem, Israel
| | - Khaled Zubeidat
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Yasmin Saba
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Olga Georgiev
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Paz Kles
- Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel; Department of Periodontology, Hadassah Medical Center, Jerusalem, Israel
| | - Or Barel
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Yael Horev
- Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel; Department of Periodontology, Hadassah Medical Center, Jerusalem, Israel
| | - Omri Yosef
- The Lautenberg Center for Immunology and Cancer Research, Israel-Canada Medical Research Institute, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Luba Eli-Berchoer
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
| | - Chen Nadler
- Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel
- Department of Oral Medicine, Sedation & Maxillofacial Imaging, Hadassah Medical Center, Jerusalem, Israel
| | - Gili Betser-Cohen
- Division of Identification and Forensic Science, Police National HQ, Jerusalem, Israel
| | - Hagit Shapiro
- System Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- System Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Microbe & Cancer Division, DKFZ, Heidelberg, Germany
| | - Asaf Wilensky
- Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel; Department of Periodontology, Hadassah Medical Center, Jerusalem, Israel
| | - Avi-Hai Hovav
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Jerusalem, Israel.
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13
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Dougherty MW, Valdés-Mas R, Wernke KM, Gharaibeh RZ, Yang Y, Brant JO, Riva A, Muehlbauer M, Elinav E, Puschhof J, Herzon SB, Jobin C. The microbial genotoxin colibactin exacerbates mismatch repair mutations in colorectal tumors. Neoplasia 2023; 43:100918. [PMID: 37499275 PMCID: PMC10413156 DOI: 10.1016/j.neo.2023.100918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/26/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
Certain Enterobacteriaceae strains contain a 54-kb biosynthetic gene cluster referred to as "pks" encoding the biosynthesis of a secondary metabolite, colibactin. Colibactin-producing E. coli promote colorectal cancer (CRC) in preclinical models, and in vitro induce a specific mutational signature that is also detected in human CRC genomes. Yet, how colibactin exposure affects the mutational landscape of CRC in vivo remains unclear. Here we show that colibactin-producing E. coli-driven colonic tumors in mice have a significantly higher SBS burden and a larger percentage of these mutations can be attributed to a signature associated with mismatch repair deficiency (MMRd; SBS15), compared to tumors developed in the presence of colibactin-deficient E. coli. We found that the synthetic colibactin 742 but not an inactive analog 746 causes DNA damage and induces transcriptional activation of p53 and senescence signaling pathways in non-transformed human colonic epithelial cells. In MMRd colon cancer cells (HCT 116), chronic exposure to 742 resulted in the upregulation of BRCA1, Fanconi anemia, and MMR signaling pathways as revealed by global transcriptomic analysis. This was accompanied by increased T>N single-base substitutions (SBS) attributed to the proposed pks+E. coli signature (SBS88), reactive oxygen species (SBS17), and mismatch-repair deficiency (SBS44). A significant co-occurrence between MMRd SBS44 and pks-associated SBS88 signature was observed in a large cohort of human CRC patients (n=2,945), and significantly more SBS44 mutations were found when SBS88 was also detected. Collectively, these findings reveal the host response mechanisms underlying colibactin genotoxic activity and suggest that colibactin may exacerbate MMRd-associated mutations.
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Affiliation(s)
- Michael W Dougherty
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, IL, Israel
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Ye Yang
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jason O Brant
- Department of Biostatistics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Marcus Muehlbauer
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, IL, Israel; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, DE, Germany
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, DE, Germany
| | - Seth B Herzon
- Department of Biostatistics, University of Florida College of Medicine, Gainesville, FL, USA; Departments of Pharmacology and Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA; Department of Infectious Diseases and Immunology, University of Florida College of Medicine, Gainesville, FL, USA; Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA.
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14
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Siracusa F, Schaltenberg N, Kumar Y, Lesker TR, Steglich B, Liwinski T, Cortesi F, Frommann L, Diercks BP, Bönisch F, Fischer AW, Scognamiglio P, Pauly MJ, Casar C, Cohen Y, Pelczar P, Agalioti T, Delfs F, Worthmann A, Wahib R, Jagemann B, Mittrücker HW, Kretz O, Guse AH, Izbicki JR, Lassen KG, Strowig T, Schweizer M, Villablanca EJ, Elinav E, Huber S, Heeren J, Gagliani N. Short-term dietary changes can result in mucosal and systemic immune depression. Nat Immunol 2023; 24:1473-1486. [PMID: 37580603 PMCID: PMC10457203 DOI: 10.1038/s41590-023-01587-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 10/05/2022] [Accepted: 07/13/2023] [Indexed: 08/16/2023]
Abstract
Omnivorous animals, including mice and humans, tend to prefer energy-dense nutrients rich in fat over plant-based diets, especially for short periods of time, but the health consequences of this short-term consumption of energy-dense nutrients are unclear. Here, we show that short-term reiterative switching to 'feast diets', mimicking our social eating behavior, breaches the potential buffering effect of the intestinal microbiota and reorganizes the immunological architecture of mucosa-associated lymphoid tissues. The first dietary switch was sufficient to induce transient mucosal immune depression and suppress systemic immunity, leading to higher susceptibility to Salmonella enterica serovar Typhimurium and Listeria monocytogenes infections. The ability to respond to antigenic challenges with a model antigen was also impaired. These observations could be explained by a reduction of CD4+ T cell metabolic fitness and cytokine production due to impaired mTOR activity in response to reduced microbial provision of fiber metabolites. Reintroducing dietary fiber rewired T cell metabolism and restored mucosal and systemic CD4+ T cell functions and immunity. Finally, dietary intervention with human volunteers confirmed the effect of short-term dietary switches on human CD4+ T cell functionality. Therefore, short-term nutritional changes cause a transient depression of mucosal and systemic immunity, creating a window of opportunity for pathogenic infection.
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Affiliation(s)
- Francesco Siracusa
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Nicola Schaltenberg
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yogesh Kumar
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Babett Steglich
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timur Liwinski
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- University Psychiatric Clinics, University of Basel, Basel, Switzerland
| | - Filippo Cortesi
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Frommann
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Björn-Phillip Diercks
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedericke Bönisch
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander W Fischer
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pasquale Scognamiglio
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mira J Pauly
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Casar
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yotam Cohen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Penelope Pelczar
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Theodora Agalioti
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Flemming Delfs
- Core Facility of Electron Microscopy, Center for Molecular Neurobiology ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Worthmann
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ramez Wahib
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bettina Jagemann
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute for Health Service Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hans-Willi Mittrücker
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas H Guse
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kara G Lassen
- Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center, Basel, Switzerland
| | - 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
| | - Michaela Schweizer
- Core Facility of Electron Microscopy, Center for Molecular Neurobiology ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eduardo J Villablanca
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Gagliani
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden.
- Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany.
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15
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Cohen Y, Valdés-Mas R, Elinav E. The Role of Artificial Intelligence in Deciphering Diet-Disease Relationships: Case Studies. Annu Rev Nutr 2023; 43:225-250. [PMID: 37207358 DOI: 10.1146/annurev-nutr-061121-090535] [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] [Indexed: 05/21/2023]
Abstract
Modernization of society from a rural, hunter-gatherer setting into an urban and industrial habitat, with the associated dietary changes, has led to an increased prevalence of cardiometabolic and additional noncommunicable diseases, such as cancer, inflammatory bowel disease, and neurodegenerative and autoimmune disorders. However, while dietary sciences have been rapidly evolving to meet these challenges, validation and translation of experimental results into clinical practice remain limited for multiple reasons, including inherent ethnic, gender, and cultural interindividual variability, among other methodological, dietary reporting-related, and analytical issues. Recently, large clinical cohorts with artificial intelligence analytics have introduced new precision and personalized nutrition concepts that enable one to successfully bridge these gaps in a real-life setting. In this review, we highlight selected examples of case studies at the intersection between diet-disease research and artificial intelligence. We discuss their potential and challenges and offer an outlook toward the transformation of dietary sciences into individualized clinical translation.
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Affiliation(s)
- Yotam Cohen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel;
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel;
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel;
- Division of Microbiome & Cancer, National German Cancer Research Center (DKFZ), Heidelberg, Germany;
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16
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Kotsiliti E, Leone V, Schuehle S, Govaere O, Li H, Wolf MJ, Horvatic H, Bierwirth S, Hundertmark J, Inverso D, Zizmare L, Sarusi-Portuguez A, Gupta R, O'Connor T, Giannou AD, Shiri AM, Schlesinger Y, Beccaria MG, Rennert C, Pfister D, Öllinger R, Gadjalova I, Ramadori P, Rahbari M, Rahbari N, Healy ME, Fernández-Vaquero M, Yahoo N, Janzen J, Singh I, Fan C, Liu X, Rau M, Feuchtenberger M, Schwaneck E, Wallace SJ, Cockell S, Wilson-Kanamori J, Ramachandran P, Kho C, Kendall TJ, Leblond AL, Keppler SJ, Bielecki P, Steiger K, Hofmann M, Rippe K, Zitzelsberger H, Weber A, Malek N, Luedde T, Vucur M, Augustin HG, Flavell R, Parnas O, Rad R, Pabst O, Henderson NC, Huber S, Macpherson A, Knolle P, Claassen M, Geier A, Trautwein C, Unger K, Elinav E, Waisman A, Abdullah Z, Haller D, Tacke F, Anstee QM, Heikenwalder M. Intestinal B cells license metabolic T-cell activation in NASH microbiota/antigen-independently and contribute to fibrosis by IgA-FcR signalling. J Hepatol 2023; 79:296-313. [PMID: 37224925 PMCID: PMC10360918 DOI: 10.1016/j.jhep.2023.04.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/26/2023]
Abstract
BACKGROUND & AIMS The progression of non-alcoholic steatohepatitis (NASH) to fibrosis and hepatocellular carcinoma (HCC) is aggravated by auto-aggressive T cells. The gut-liver axis contributes to NASH, but the mechanisms involved and the consequences for NASH-induced fibrosis and liver cancer remain unknown. We investigated the role of gastrointestinal B cells in the development of NASH, fibrosis and NASH-induced HCC. METHODS C57BL/6J wild-type (WT), B cell-deficient and different immunoglobulin-deficient or transgenic mice were fed distinct NASH-inducing diets or standard chow for 6 or 12 months, whereafter NASH, fibrosis, and NASH-induced HCC were assessed and analysed. Specific pathogen-free/germ-free WT and μMT mice (containing B cells only in the gastrointestinal tract) were fed a choline-deficient high-fat diet, and treated with an anti-CD20 antibody, whereafter NASH and fibrosis were assessed. Tissue biopsy samples from patients with simple steatosis, NASH and cirrhosis were analysed to correlate the secretion of immunoglobulins to clinicopathological features. Flow cytometry, immunohistochemistry and single-cell RNA-sequencing analysis were performed in liver and gastrointestinal tissue to characterise immune cells in mice and humans. RESULTS Activated intestinal B cells were increased in mouse and human NASH samples and licensed metabolic T-cell activation to induce NASH independently of antigen specificity and gut microbiota. Genetic or therapeutic depletion of systemic or gastrointestinal B cells prevented or reverted NASH and liver fibrosis. IgA secretion was necessary for fibrosis induction by activating CD11b+CCR2+F4/80+CD11c-FCGR1+ hepatic myeloid cells through an IgA-FcR signalling axis. Similarly, patients with NASH had increased numbers of activated intestinal B cells; additionally, we observed a positive correlation between IgA levels and activated FcRg+ hepatic myeloid cells, as well the extent of liver fibrosis. CONCLUSIONS Intestinal B cells and the IgA-FcR signalling axis represent potential therapeutic targets for the treatment of NASH. IMPACT AND IMPLICATIONS There is currently no effective treatment for non-alcoholic steatohepatitis (NASH), which is associated with a substantial healthcare burden and is a growing risk factor for hepatocellular carcinoma (HCC). We have previously shown that NASH is an auto-aggressive condition aggravated, amongst others, by T cells. Therefore, we hypothesized that B cells might have a role in disease induction and progression. Our present work highlights that B cells have a dual role in NASH pathogenesis, being implicated in the activation of auto-aggressive T cells and the development of fibrosis via activation of monocyte-derived macrophages by secreted immunoglobulins (e.g., IgA). Furthermore, we show that the absence of B cells prevented HCC development. B cell-intrinsic signalling pathways, secreted immunoglobulins, and interactions of B cells with other immune cells are potential targets for combinatorial NASH therapies against inflammation and fibrosis.
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Affiliation(s)
- Elena Kotsiliti
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Valentina Leone
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; Research Unit of Radiation Cytogenetics (ZYTO), Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Oncology and Functional Genomics, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany; Translational Pancreatic Cancer Research Center, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany
| | - Svenja Schuehle
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Hai Li
- Maurice Müller Laboratories (DBMR), University Department of Visceral Surgery and Medicine Inselspital, University of Bern, Bern, Switzerland
| | - Monika J Wolf
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Helena Horvatic
- Institute of Molecular Medicine and Experimental Immunology, University Hospital, Bonn, Germany
| | - Sandra Bierwirth
- Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany; ZIEL - Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Jana Hundertmark
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Donato Inverso
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany; European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Laimdota Zizmare
- Department of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center (WSIC), Tübingen University, Tübingen, Germany
| | - Avital Sarusi-Portuguez
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Revant Gupta
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Tracy O'Connor
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; North Park University, Chicago, IL, USA
| | - Anastasios D Giannou
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Medicine II, University Hospital Freiburg - Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ahmad Mustafa Shiri
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yehuda Schlesinger
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maria Garcia Beccaria
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Charlotte Rennert
- Department of Medicine II, University Hospital Freiburg - Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominik Pfister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany
| | - Iana Gadjalova
- Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Munich, Germany
| | - Pierluigi Ramadori
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Mohammad Rahbari
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Nuh Rahbari
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Marc E Healy
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mirian Fernández-Vaquero
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Neda Yahoo
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Jakob Janzen
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Indrabahadur Singh
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chaofan Fan
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Xinyuan Liu
- Research Center for Immunotherapy (FZI), University Medical Center at the Johannes Gutenberg University, Mainz, Germany; Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Monika Rau
- Division of Hepatology, University-Hospital Würzburg, Würzburg, Germany
| | - Martin Feuchtenberger
- Rheumatology/Clinical Immunology, Kreiskliniken Altötting-Burghausen, Burghausen, Germany
| | - Eva Schwaneck
- Rheumatology, Medical Clinic II, Julius-Maximilians-University Würzburg, Germany
| | - Sebastian J Wallace
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Simon Cockell
- School of Biomedical, Nutrition and Sports Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John Wilson-Kanamori
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Prakash Ramachandran
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Celia Kho
- Institute of Molecular Medicine and Experimental Immunology, University Hospital, Bonn, Germany
| | - Timothy J Kendall
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Anne-Laure Leblond
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Selina J Keppler
- Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Munich, Germany
| | - Piotr Bielecki
- Department of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich (TUM), Munich, Germany; Comparative Experimental Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Maike Hofmann
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Horst Zitzelsberger
- Research Unit of Radiation Cytogenetics (ZYTO), Helmholtz Zentrum München, Neuherberg, Germany
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Nisar Malek
- Department Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Mihael Vucur
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Hellmut G Augustin
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany; European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Richard Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - Oren Parnas
- European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar of the Technical University of Munich (TUM), Munich, Germany; Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Munich, Germany
| | - Olivier Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Samuel Huber
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrew Macpherson
- Maurice Müller Laboratories (DBMR), University Department of Visceral Surgery and Medicine Inselspital, University of Bern, Bern, Switzerland
| | - Percy Knolle
- Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Manfred Claassen
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany; Department Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Andreas Geier
- Division of Hepatology, University-Hospital Würzburg, Würzburg, Germany
| | - Christoph Trautwein
- Department of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center (WSIC), Tübingen University, Tübingen, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics (ZYTO), Helmholtz Zentrum München, Neuherberg, Germany
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Cancer-Microbiome Research Division, DKFZ, Heidelberg, Germany
| | - Ari Waisman
- Research Center for Immunotherapy (FZI), University Medical Center at the Johannes Gutenberg University, Mainz, Germany; Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital, Bonn, Germany
| | - Dirk Haller
- Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany; ZIEL - Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; Newcastle NIHR Biomedical Research Center, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, United Kingdom
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany; M3 Research Institute, Eberhard Karls University Tübingen, Tübingen, Germany.
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17
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Ansari I, Solé-Boldo L, Ridnik M, Gutekunst J, Gilliam O, Korshko M, Liwinski T, Jickeli B, Weinberg-Corem N, Shoshkes-Carmel M, Pikarsky E, Elinav E, Lyko F, Bergman Y. TET2 and TET3 loss disrupts small intestine differentiation and homeostasis. Nat Commun 2023; 14:4005. [PMID: 37414790 PMCID: PMC10326054 DOI: 10.1038/s41467-023-39512-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/04/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
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Affiliation(s)
- Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Meshi Ridnik
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Gilliam
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Maria Korshko
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Timur Liwinski
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- University Psychiatric Clinics Basel, Clinic for Adults, University of Basel, Basel, Switzerland
| | - Birgit Jickeli
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Noa Weinberg-Corem
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Michal Shoshkes-Carmel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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18
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Bootz-Maoz H, Simon A, Del Mare-Roumani S, Bennet Y, Toister E, Romano H, Zheng D, Amidror S, Elinav E, Yissachar N. Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics. NPJ Biofilms Microbiomes 2023; 9:44. [PMID: 37400593 DOI: 10.1038/s41522-023-00409-0] [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] [Received: 11/22/2022] [Accepted: 06/09/2023] [Indexed: 07/05/2023] Open
Abstract
The intestinal epithelial barrier facilitates homeostatic host-microbiota interactions and immunological tolerance. However, mechanistic dissections of barrier dynamics following luminal stimulation pose a substantial challenge. Here, we describe an ex vivo intestinal permeability assay, X-IPA, for quantitative analysis of gut permeability dynamics at the whole-tissue level. We demonstrate that specific gut microbes and metabolites induce rapid, dose-dependent increases to gut permeability, thus providing a powerful approach for precise investigation of barrier functions.
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Affiliation(s)
- Hadar Bootz-Maoz
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Ariel Simon
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Sara Del Mare-Roumani
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yifat Bennet
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Einat Toister
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Hadar Romano
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Danping Zheng
- Systems Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Sivan Amidror
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
- Microbiome & Cancer Division, Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Nissan Yissachar
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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19
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Ciocan D, Elinav E. Engineering bacteria to modulate host metabolism. Acta Physiol (Oxf) 2023; 238:e14001. [PMID: 37222395 PMCID: PMC10909415 DOI: 10.1111/apha.14001] [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: 12/06/2022] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 05/25/2023]
Abstract
The microbial community of the gut, collectively termed the gut microbiota, modulates both host metabolism and disease development in a variety of clinical contexts. The microbiota can have detrimental effects and be involved in disease development and progression, but it can also offer benefits to the host. This has led in the last years to the development of different therapeutic strategies targeting the microbiota. In this review, we will focus on one of these strategies that involve the use of engineered bacteria to modulate gut microbiota in the treatment of metabolic disorders. We will discuss the recent developments and challenges in the use of these bacterial strains with an emphasis on their use for the treatment of metabolic diseases.
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Affiliation(s)
- Dragos Ciocan
- Systems Immunology DepartmentWeisman Institute of ScienceRehovotIsrael
- School of MedicineParis‐Saclay UniversityLe Kremlin‐BicêtreFrance
| | - Eran Elinav
- Systems Immunology DepartmentWeisman Institute of ScienceRehovotIsrael
- Microbiota & Cancer DivisionDKFZHeidelbergGermany
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20
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Cohen Y, Elinav E. Dietary fibers & immunity-more than meets the eye. Cell Res 2023; 33:411-412. [PMID: 36646763 PMCID: PMC10235049 DOI: 10.1038/s41422-022-00770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yotam Cohen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany.
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21
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Affiliation(s)
- Samuel Philip Nobs
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
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22
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Abstract
The microbiome may impact cancer development, progression and treatment responsiveness, but its fungal components remain insufficiently studied in this context. In this review, we highlight accumulating evidence suggesting a possible involvement of commensal and pathogenic fungi in modulation of cancer-related processes. We discuss the mechanisms by which fungi can influence tumour biology, locally by activity exerted within the tumour microenvironment, or remotely through secretion of bioactive metabolites, modulation of host immunity and communications with neighbouring bacterial commensals. We examine prospects of utilising fungi-related molecular signatures in cancer diagnosis, patient stratification and assessment of treatment responsiveness, while highlighting challenges and limitations faced in performing such research. In all, we demonstrate that fungi likely constitute important members of mucosal and tumour-residing microbiomes. Exploration of fungal inter-kingdom interactions with the bacterial microbiome and the host and decoding of their causal impacts on tumour biology may enable their harnessing into cancer diagnosis and treatment.
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Affiliation(s)
- Aurelia Saftien
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
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23
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Javitt A, Shmueli MD, Kramer MP, Kolodziejczyk AA, Cohen IJ, Radomir L, Sheban D, Kamer I, Litchfield K, Bab-Dinitz E, Zadok O, Neiens V, Ulman A, Wolf-Levy H, Eisenberg-Lerner A, Kacen A, Alon M, Rêgo AT, Stacher-Priehse E, Lindner M, Koch I, Bar J, Swanton C, Samuels Y, Levin Y, da Fonseca PCA, Elinav E, Friedman N, Meiners S, Merbl Y. The proteasome regulator PSME4 modulates proteasome activity and antigen diversity to abrogate antitumor immunity in NSCLC. Nat Cancer 2023; 4:629-647. [PMID: 37217651 DOI: 10.1038/s43018-023-00557-4] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 04/10/2023] [Indexed: 05/24/2023]
Abstract
Immunotherapy revolutionized treatment options in cancer, yet the mechanisms underlying resistance in many patients remain poorly understood. Cellular proteasomes have been implicated in modulating antitumor immunity by regulating antigen processing, antigen presentation, inflammatory signaling and immune cell activation. However, whether and how proteasome complex heterogeneity may affect tumor progression and the response to immunotherapy has not been systematically examined. Here, we show that proteasome complex composition varies substantially across cancers and impacts tumor-immune interactions and the tumor microenvironment. Through profiling of the degradation landscape of patient-derived non-small-cell lung carcinoma samples, we find that the proteasome regulator PSME4 is upregulated in tumors, alters proteasome activity, attenuates presented antigenic diversity and associates with lack of response to immunotherapy. Collectively, our approach affords a paradigm by which proteasome composition heterogeneity and function should be examined across cancer types and targeted in the context of precision oncology.
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Affiliation(s)
- Aaron Javitt
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav D Shmueli
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Matthias P Kramer
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ivan J Cohen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lihi Radomir
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daoud Sheban
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Kamer
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Kevin Litchfield
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Oranit Zadok
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Vanessa Neiens
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum Muenchen, Munich, Germany
- Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Adi Ulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Wolf-Levy
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Assaf Kacen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Alon
- Department of Molecular and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Ina Koch
- Member of the German Center for Lung Research (DZL), Munich, Germany
- Asklepios Lung Clinic Munich-Gauting, Gauting, Germany
| | - Jair Bar
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Charles Swanton
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Yardena Samuels
- Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Paula C A da Fonseca
- Department of Molecular and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany
| | - Nir Friedman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum Muenchen, Munich, Germany
- Member of the German Center for Lung Research (DZL), Munich, Germany
- Research Center Borstel, Borstel, Germany
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, Kiel, Germany
| | - Yifat Merbl
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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24
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Stein-Thoeringer CK, Saini NY, Zamir E, Blumenberg V, Schubert ML, Mor U, Fante MA, Schmidt S, Hayase E, Hayase T, Rohrbach R, Chang CC, McDaniel L, Flores I, Gaiser R, Edinger M, Wolff D, Heidenreich M, Strati P, Nair R, Chihara D, Fayad LE, Ahmed S, Iyer SP, Steiner RE, Jain P, Nastoupil LJ, Westin J, Arora R, Wang ML, Turner J, Menges M, Hidalgo-Vargas M, Reid K, Dreger P, Schmitt A, Müller-Tidow C, Locke FL, Davila ML, Champlin RE, Flowers CR, Shpall EJ, Poeck H, Neelapu SS, Schmitt M, Subklewe M, Jain MD, Jenq RR, Elinav E. A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy. Nat Med 2023; 29:906-916. [PMID: 36914893 PMCID: PMC10121864 DOI: 10.1038/s41591-023-02234-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [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: 10/11/2022] [Accepted: 01/25/2023] [Indexed: 03/14/2023]
Abstract
Increasing evidence suggests that the gut microbiome may modulate the efficacy of cancer immunotherapy. In a B cell lymphoma patient cohort from five centers in Germany and the United States (Germany, n = 66; United States, n = 106; total, n = 172), we demonstrate that wide-spectrum antibiotics treatment ('high-risk antibiotics') prior to CD19-targeted chimeric antigen receptor (CAR)-T cell therapy is associated with adverse outcomes, but this effect is likely to be confounded by an increased pretreatment tumor burden and systemic inflammation in patients pretreated with high-risk antibiotics. To resolve this confounding effect and gain insights into antibiotics-masked microbiome signals impacting CAR-T efficacy, we focused on the high-risk antibiotics non-exposed patient population. Indeed, in these patients, significant correlations were noted between pre-CAR-T infusion Bifidobacterium longum and microbiome-encoded peptidoglycan biosynthesis, and CAR-T treatment-associated 6-month survival or lymphoma progression. Furthermore, predictive pre-CAR-T treatment microbiome-based machine learning algorithms trained on the high-risk antibiotics non-exposed German cohort and validated by the respective US cohort robustly segregated long-term responders from non-responders. Bacteroides, Ruminococcus, Eubacterium and Akkermansia were most important in determining CAR-T responsiveness, with Akkermansia also being associated with pre-infusion peripheral T cell levels in these patients. Collectively, we identify conserved microbiome features across clinical and geographical variations, which may enable cross-cohort microbiome-based predictions of outcomes in CAR-T cell immunotherapy.
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Affiliation(s)
- Christoph K Stein-Thoeringer
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Internal Medicine I, University Clinic Tuebingen, Tuebingen, Germany
| | - Neeraj Y Saini
- Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center, Houston, TX, USA.
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA.
| | - Eli Zamir
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Viktoria Blumenberg
- Medizinische Klinik III, LMU Klinikum, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center of the LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK) and Bavarian Center for Cancer Research (BZKF), partner site Munich, Munich, Germany
| | - Maria-Luisa Schubert
- Department of Hematology, Oncology and Rheumatology, University Clinic Heidelberg, Heidelberg, Germany
| | - Uria Mor
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias A Fante
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Sabine Schmidt
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eiko Hayase
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Tomo Hayase
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Roman Rohrbach
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chia-Chi Chang
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren McDaniel
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Ivonne Flores
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Rogier Gaiser
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Edinger
- German Cancer Consortium (DKTK) and Bavarian Center for Cancer Research (BZKF), partner site Munich, Munich, Germany
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
- Leibnitz Institut für Immuntherapie (LIT), Regensburg, Germany
| | - Daniel Wolff
- German Cancer Consortium (DKTK) and Bavarian Center for Cancer Research (BZKF), partner site Munich, Munich, Germany
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
- Leibnitz Institut für Immuntherapie (LIT), Regensburg, Germany
| | - Martin Heidenreich
- German Cancer Consortium (DKTK) and Bavarian Center for Cancer Research (BZKF), partner site Munich, Munich, Germany
- Leibnitz Institut für Immuntherapie (LIT), Regensburg, Germany
| | - Paolo Strati
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Ranjit Nair
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Dai Chihara
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Luis E Fayad
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Swaminathan P Iyer
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Raphael E Steiner
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Preetesh Jain
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Loretta J Nastoupil
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Westin
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Reetakshi Arora
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Michael L Wang
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Joel Turner
- Department of Clinical Science, Moffitt Cancer Center, Tampa, FL, USA
| | - Meghan Menges
- Department of Clinical Science, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Kayla Reid
- Department of Clinical Science, Moffitt Cancer Center, Tampa, FL, USA
| | - Peter Dreger
- Department of Hematology, Oncology and Rheumatology, University Clinic Heidelberg, Heidelberg, Germany
| | - Anita Schmitt
- Department of Hematology, Oncology and Rheumatology, University Clinic Heidelberg, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Hematology, Oncology and Rheumatology, University Clinic Heidelberg, Heidelberg, Germany
| | - Frederick L Locke
- Blood and Marrow Transplant and Cellular Immunotherapy, Moffitt Cancer Center and Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Marco L Davila
- Blood and Marrow Transplant and Cellular Immunotherapy, Moffitt Cancer Center and Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Richard E Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Hendrik Poeck
- German Cancer Consortium (DKTK) and Bavarian Center for Cancer Research (BZKF), partner site Munich, Munich, Germany
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
- Leibnitz Institut für Immuntherapie (LIT), Regensburg, Germany
| | - Sattva S Neelapu
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Schmitt
- Department of Hematology, Oncology and Rheumatology, University Clinic Heidelberg, Heidelberg, Germany
| | - Marion Subklewe
- Medizinische Klinik III, LMU Klinikum, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center of the LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK) and Bavarian Center for Cancer Research (BZKF), partner site Munich, Munich, Germany
| | - Michael D Jain
- Blood and Marrow Transplant and Cellular Immunotherapy, Moffitt Cancer Center and Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Robert R Jenq
- Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA.
- CPRIT Scholar in Cancer Research, University of Texas, Houston, USA.
| | - Eran Elinav
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
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25
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Zheng D, Mohapatra G, Kern L, He Y, Shmueli MD, Valdés-Mas R, Kolodziejczyk AA, Próchnicki T, Vasconcelos MB, Schorr L, Hertel F, Lee YS, Rufino MC, Ceddaha E, Shimshy S, Hodgetts RJ, Dori-Bachash M, Kleimeyer C, Goldenberg K, Heinemann M, Stettner N, Harmelin A, Shapiro H, Puschhof J, Chen M, Flavell RA, Latz E, Merbl Y, Abdeen SK, Elinav E. Epithelial Nlrp10 inflammasome mediates protection against intestinal autoinflammation. Nat Immunol 2023; 24:585-594. [PMID: 36941399 DOI: 10.1038/s41590-023-01450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/06/2023] [Indexed: 03/23/2023]
Abstract
Unlike other nucleotide oligomerization domain-like receptors, Nlrp10 lacks a canonical leucine-rich repeat domain, suggesting that it is incapable of signal sensing and inflammasome formation. Here we show that mouse Nlrp10 is expressed in distal colonic intestinal epithelial cells (IECs) and modulated by the intestinal microbiome. In vitro, Nlrp10 forms an Apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC)-dependent, m-3M3FBS-activated, polyinosinic:polycytidylic acid-modulated inflammasome driving interleukin-1β and interleukin-18 secretion. In vivo, Nlrp10 signaling is dispensable during steady state but becomes functional during autoinflammation in antagonizing mucosal damage. Importantly, whole-body or conditional IEC Nlrp10 depletion leads to reduced IEC caspase-1 activation, coupled with enhanced susceptibility to dextran sodium sulfate-induced colitis, mediated by altered inflammatory and healing programs. Collectively, understanding Nlrp10 inflammasome-dependent and independent activity, regulation and possible human relevance might facilitate the development of new innate immune anti-inflammatory interventions.
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Affiliation(s)
- Danping Zheng
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Gayatree Mohapatra
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Lara Kern
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Yiming He
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Merav D Shmueli
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Tomasz Próchnicki
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | | | - Lena Schorr
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Franziska Hertel
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | - Ye Seul Lee
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | | | - Emmanuelle Ceddaha
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sandy Shimshy
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Ryan James Hodgetts
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Mally Dori-Bachash
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Christian Kleimeyer
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Kim Goldenberg
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Melina Heinemann
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Shapiro
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jens Puschhof
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Eicke Latz
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Yifat Merbl
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany.
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26
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Leshem A, Elinav E. Diversifying nutritional sciences-dietary practices and gut bacteria in individuals of Latino and Hispanic ancestry. Am J Clin Nutr 2023; 117:451-452. [PMID: 36872014 DOI: 10.1016/j.ajcnut.2022.12.010] [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] [Received: 12/15/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 03/06/2023] Open
Affiliation(s)
- Avner Leshem
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Microbiome & Cancer Division, DKFZ, Heidelberg, Germany.
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27
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Kviatcovsky D, Elinav E. A microbial workout. Cell Host Microbe 2023; 31:159-160. [PMID: 36758512 DOI: 10.1016/j.chom.2023.01.007] [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: 02/11/2023]
Abstract
In a recent report in Nature, Dohnalová et al., describe a gut-brain axis mechanism in highlighting the importance of the gut microbiota and its derived metabolites in long-term exercise engagement and performance.
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Affiliation(s)
- Denise Kviatcovsky
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Microbiome & Cancer Division, DKFZ, Heidelberg, Germany.
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28
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Asokan S, Cullin N, Stein-Thoeringer CK, Elinav E. CAR-T Cell Therapy and the Gut Microbiota. Cancers (Basel) 2023; 15:cancers15030794. [PMID: 36765752 PMCID: PMC9913364 DOI: 10.3390/cancers15030794] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
Chimeric antigen receptor (CAR) - T cell cancer therapy has yielded promising results in treating hematologic malignancies in clinical studies, and a growing number of CAR-T regimens are approved for clinical usage. While the therapy is considered of great potential in expanding the cancer immunotherapy arsenal, more than half of patients receiving CAR-T infusions do not respond, while others develop significant adverse effects, collectively indicating a need for optimization of CAR-T treatment to the individual. The microbiota is increasingly suggested as a major modulator of immunotherapy responsiveness. Studying causal microbiota roles possibly contributing to CAR-T therapy efficacy, adverse effects reduction, and prediction of patient responsiveness constitutes an exciting area of active research. Herein, we discuss the latest developments implicating human microbiota involvement in CAR-T therapy, while highlighting challenges and promises in harnessing the microbiota as a predictor and modifier of CAR-T treatment towards optimized efficacy and minimization of treatment-related adverse effects.
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Affiliation(s)
- Sahana Asokan
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Nyssa Cullin
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christoph K. Stein-Thoeringer
- Department of Internal Medicine I, Laboratory of Translational Microbiome Science, University Clinic Tuebingen, Otfried-Mueller-Strasse 10, 72076 Tuebingen, Germany
- Correspondence: (C.K.S-T.); (E.E.); Tel.: +972-8-9344014 (E.E.)
| | - Eran Elinav
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Systems Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
- Correspondence: (C.K.S-T.); (E.E.); Tel.: +972-8-9344014 (E.E.)
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29
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Ratiner K, Fachler-Sharp T, Elinav E. Small Intestinal Microbiota Oscillations, Host Effects and Regulation-A Zoom into Three Key Effector Molecules. Biology (Basel) 2023; 12:biology12010142. [PMID: 36671834 PMCID: PMC9855434 DOI: 10.3390/biology12010142] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
The gut microbiota features a unique diurnal rhythmicity which contributes to modulation of host physiology and homeostasis. The composition and activity of the microbiota and its secreted molecules influence the intestinal milieu and neighboring organs, such as the liver. Multiple immune-related molecules have been linked to the diurnal microbiota-host interaction, including Reg3γ, IgA, and MHCII, which are secreted or expressed on the gut surface and directly interact with intestinal bacteria. These molecules are also strongly influenced by dietary patterns, such as high-fat diet and time-restricted feeding, which are already known to modulate microbial rhythms and peripheral clocks. Herein, we use Reg3γ, IgA, and MHCII as test cases to highlight the divergent effects mediated by the diurnal activity of the gut microbiota and their downstream host effects. We further highlight current challenges and conflicts, remaining questions, and perspectives toward a holistic understanding of the microbiome's impacts on circadian human behavior.
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Affiliation(s)
- Karina Ratiner
- Systems Immunology Department, Weisman Institute of Science, Rehovot 7610001, Israel
| | - Tahel Fachler-Sharp
- Systems Immunology Department, Weisman Institute of Science, Rehovot 7610001, Israel
- Department of Dermatology, Hadassah-Hebrew University Medical Center, Jerusalem 9987500, Israel
| | - Eran Elinav
- Systems Immunology Department, Weisman Institute of Science, Rehovot 7610001, Israel
- Microbiota & Cancer Division, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Correspondence: or
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30
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Shapiro H, Leshem A, Elinav E. Trimming Trem2 and possible impacts on the metabolic syndrome. J Physiol 2022; 600:4387-4388. [PMID: 36114613 PMCID: PMC9828464 DOI: 10.1113/jp283781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Hagit Shapiro
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Avner Leshem
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael,Department of SurgeryTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - Eran Elinav
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael,Microbiome & Cancer DivisionDKFZHeidelbergGermany
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31
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Suez J, Cohen Y, Valdés-Mas R, Mor U, Dori-Bachash M, Federici S, Zmora N, Leshem A, Heinemann M, Linevsky R, Zur M, Ben-Zeev Brik R, Bukimer A, Eliyahu-Miller S, Metz A, Fischbein R, Sharov O, Malitsky S, Itkin M, Stettner N, Harmelin A, Shapiro H, Stein-Thoeringer CK, Segal E, Elinav E. Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance. Cell 2022; 185:3307-3328.e19. [PMID: 35987213 DOI: 10.1016/j.cell.2022.07.016] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [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: 01/03/2022] [Revised: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 02/06/2023]
Abstract
Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses. We causally assessed NNS impacts in humans and their microbiomes in a randomized-controlled trial encompassing 120 healthy adults, administered saccharin, sucralose, aspartame, and stevia sachets for 2 weeks in doses lower than the acceptable daily intake, compared with controls receiving sachet-contained vehicle glucose or no supplement. As groups, each administered NNS distinctly altered stool and oral microbiome and plasma metabolome, whereas saccharin and sucralose significantly impaired glycemic responses. Importantly, gnotobiotic mice conventionalized with microbiomes from multiple top and bottom responders of each of the four NNS-supplemented groups featured glycemic responses largely reflecting those noted in respective human donors, which were preempted by distinct microbial signals, as exemplified by sucralose. Collectively, human NNS consumption may induce person-specific, microbiome-dependent glycemic alterations, necessitating future assessment of clinical implications.
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Affiliation(s)
- Jotham Suez
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Yotam Cohen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rafael Valdés-Mas
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uria Mor
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mally Dori-Bachash
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sara Federici
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Niv Zmora
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel; Internal Medicine Department, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Avner Leshem
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Melina Heinemann
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raquel Linevsky
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Zur
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Ben-Zeev Brik
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aurelie Bukimer
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shimrit Eliyahu-Miller
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alona Metz
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ruthy Fischbein
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Olga Sharov
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagit Shapiro
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Christoph K Stein-Thoeringer
- Microbiome & Cancer Division, DKFZ, Heidelberg, Germany; National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Microbiome & Cancer Division, DKFZ, Heidelberg, Germany.
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32
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Spivak I, Fluhr L, Elinav E. Local and systemic effects of microbiome‐derived metabolites. EMBO Rep 2022; 23:e55664. [PMID: 36031866 PMCID: PMC9535759 DOI: 10.15252/embr.202255664] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 06/28/2022] [Revised: 08/10/2022] [Accepted: 08/16/2022] [Indexed: 12/12/2022] Open
Abstract
Commensal microbes form distinct ecosystems within their mammalian hosts, collectively termed microbiomes. These indigenous microbial communities broadly expand the genomic and functional repertoire of their host and contribute to the formation of a “meta‐organism.” Importantly, microbiomes exert numerous biochemical reactions synthesizing or modifying multiple bioactive small molecules termed metabolites, which impact their host's physiology in a variety of contexts. Identifying and understanding molecular mechanisms of metabolite–host interactions, and how their disrupted signaling can contribute to diseases, may enable their therapeutic application, a modality termed “postbiotic” therapy. In this review, we highlight key examples of effects of bioactive microbe‐associated metabolites on local, systemic, and immune environments, and discuss how these may impact mammalian physiology and associated disorders. We outline the challenges and perspectives in understanding the potential activity and function of this plethora of microbially associated small molecules as well as possibilities to harness them toward the promotion of personalized precision therapeutic interventions.
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Affiliation(s)
- Igor Spivak
- Systems Immunology Department Weizmann Institute of Science Rehovot Israel
- Medical Clinic III University Hospital Aachen Aachen Germany
| | - Leviel Fluhr
- Systems Immunology Department Weizmann Institute of Science Rehovot Israel
| | - Eran Elinav
- Systems Immunology Department Weizmann Institute of Science Rehovot Israel
- Microbiome & Cancer Division, DKFZ Heidelberg Germany
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33
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Ratiner K, Shapiro H, Goldenberg K, Elinav E. Time-limited diets and the gut microbiota in cardiometabolic disease. J Diabetes 2022; 14:377-393. [PMID: 35698246 PMCID: PMC9366560 DOI: 10.1111/1753-0407.13288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/11/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, intermittent fasting (IF), including periodic fasting and time-restricted feeding (TRF), has been increasingly suggested to constitute a promising treatment for cardiometabolic diseases (CMD). A deliberate daily pause in food consumption influences the gut microbiome and the host circadian clock, resulting in improved cardiometabolic health. Understanding the molecular mechanisms by which circadian host-microbiome interactions affect host metabolism and immunity may add a potentially important dimension to effective implementation of IF diets. In this review, we discuss emerging evidence potentially linking compositional and functional alterations of the gut microbiome with IF impacts on mammalian metabolism and risk of development of hypertension, type 2 diabetes (T2D), obesity, and their long-term micro- and macrovascular complications. We highlight the challenges and unknowns in causally linking diurnal bacterial signals with dietary cues and downstream metabolic consequences and means of harnessing these signals toward future microbiome integration into precision medicine.
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Affiliation(s)
- Karina Ratiner
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Hagit Shapiro
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Kim Goldenberg
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Eran Elinav
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
- Microbiome & Cancer Division, DKFZHeidelbergGermany
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34
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Spivak I, Elinav E. Risk factors for non-alcoholic fatty liver disease delineate the battlegrounds in optimizing disease prevention. Hepatobiliary Surg Nutr 2022; 11:492-494. [DOI: 10.21037/hbsn-22-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/14/2022] [Indexed: 11/06/2022]
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35
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Ben-Moshe S, Veg T, Manco R, Dan S, Papinutti D, Lifshitz A, Kolodziejczyk AA, Bahar Halpern K, Elinav E, Itzkovitz S. The spatiotemporal program of zonal liver regeneration following acute injury. Cell Stem Cell 2022; 29:973-989.e10. [DOI: 10.1016/j.stem.2022.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/28/2022] [Accepted: 04/12/2022] [Indexed: 12/19/2022]
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36
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de Castilhos J, Zamir E, Hippchen T, Rohrbach R, Schmidt S, Hengler S, Schumacher H, Neubauer M, Kunz S, Müller-Esch T, Hiergeist A, Gessner A, Khalid D, Gaiser R, Cullin N, Papagiannarou SM, Beuthien-Baumann B, Krämer A, Bartenschlager R, Jäger D, Müller M, Herth F, Duerschmied D, Schneider J, Schmid RM, Eberhardt JF, Khodamoradi Y, Vehreschild MJGT, Teufel A, Ebert MP, Hau P, Salzberger B, Schnitzler P, Poeck H, Elinav E, Merle U, Stein-Thoeringer CK. Correction to: Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients. Clin Infect Dis 2022; 75:185. [PMID: 35536665 PMCID: PMC9383973 DOI: 10.1093/cid/ciac254] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Juliana de Castilhos
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany.,Vale do Rio dos Sinos University (UNISINOS), Sao Leopoldo, Brazil
| | - Eli Zamir
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Theresa Hippchen
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Roman Rohrbach
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Sabine Schmidt
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Silvana Hengler
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Hanna Schumacher
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Melanie Neubauer
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sabrina Kunz
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Tonia Müller-Esch
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - Dina Khalid
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Rogier Gaiser
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Nyssa Cullin
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Stamatia M Papagiannarou
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | | | - Alwin Krämer
- German Cancer Research Center (DKFZ), Research Division Molecular Hematology/Oncology, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg
| | - Dirk Jäger
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Müller
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Daniel Duerschmied
- Department of Internal Medicine III, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Johann F Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Andreas Teufel
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Hau
- Wilhelm Sander-NeuroOncology Unit and Department of Neurology, University Clinic Regensburg, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infectious Disease, University Clinic Regensburg, Regensburg, Germany
| | - Paul Schnitzler
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany.,National Center for Tumor Diseases (NCT) WERA
| | - Eran Elinav
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany.,Weizmann Institute of Science, Rehovot, Israel
| | - Uta Merle
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Christoph K Stein-Thoeringer
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
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Ratiner K, Abdeen SK, Goldenberg K, Elinav E. Utilization of Host and Microbiome Features in Determination of Biological Aging. Microorganisms 2022; 10:microorganisms10030668. [PMID: 35336242 PMCID: PMC8950177 DOI: 10.3390/microorganisms10030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
The term ‘old age’ generally refers to a period characterized by profound changes in human physiological functions and susceptibility to disease that accompanies the final years of a person’s life. Despite the conventional definition of old age as exceeding the age of 65 years old, quantifying aging as a function of life years does not necessarily reflect how the human body ages. In contrast, characterizing biological (or physiological) aging based on functional parameters may better reflect a person’s temporal physiological status and associated disease susceptibility state. As such, differentiating ‘chronological aging’ from ‘biological aging’ holds the key to identifying individuals featuring accelerated aging processes despite having a young chronological age and stratifying them to tailored surveillance, diagnosis, prevention, and treatment. Emerging evidence suggests that the gut microbiome changes along with physiological aging and may play a pivotal role in a variety of age-related diseases, in a manner that does not necessarily correlate with chronological age. Harnessing of individualized gut microbiome data and integration of host and microbiome parameters using artificial intelligence and machine learning pipelines may enable us to more accurately define aging clocks. Such holobiont-based estimates of a person’s physiological age may facilitate prediction of age-related physiological status and risk of development of age-associated diseases.
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Affiliation(s)
- Karina Ratiner
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel; (K.R.); (S.K.A.); (K.G.)
| | - Suhaib K. Abdeen
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel; (K.R.); (S.K.A.); (K.G.)
| | - Kim Goldenberg
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel; (K.R.); (S.K.A.); (K.G.)
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel; (K.R.); (S.K.A.); (K.G.)
- Division of Cancer-Microbiome Research, Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Correspondence:
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Rein M, Ben-Yacov O, Godneva A, Shilo S, Zmora N, Kolobkov D, Cohen-Dolev N, Wolf BC, Kosower N, Lotan-Pompan M, Weinberger A, Halpern Z, Zelber-Sagi S, Elinav E, Segal E. Effects of personalized diets by prediction of glycemic responses on glycemic control and metabolic health in newly diagnosed T2DM: a randomized dietary intervention pilot trial. BMC Med 2022; 20:56. [PMID: 35135549 PMCID: PMC8826661 DOI: 10.1186/s12916-022-02254-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/12/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Dietary modifications are crucial for managing newly diagnosed type 2 diabetes mellitus (T2DM) and preventing its health complications, but many patients fail to achieve clinical goals with diet alone. We sought to evaluate the clinical effects of a personalized postprandial-targeting (PPT) diet on glycemic control and metabolic health in individuals with newly diagnosed T2DM as compared to the commonly recommended Mediterranean-style (MED) diet. METHODS We enrolled 23 adults with newly diagnosed T2DM (aged 53.5 ± 8.9 years, 48% males) for a randomized crossover trial of two 2-week-long dietary interventions. Participants were blinded to their assignment to one of the two sequence groups: either PPT-MED or MED-PPT diets. The PPT diet relies on a machine learning algorithm that integrates clinical and microbiome features to predict personal postprandial glucose responses (PPGR). We further evaluated the long-term effects of PPT diet on glycemic control and metabolic health by an additional 6-month PPT intervention (n = 16). Participants were connected to continuous glucose monitoring (CGM) throughout the study and self-recorded dietary intake using a smartphone application. RESULTS In the crossover intervention, the PPT diet lead to significant lower levels of CGM-based measures as compared to the MED diet, including average PPGR (mean difference between diets, - 19.8 ± 16.3 mg/dl × h, p < 0.001), mean glucose (mean difference between diets, - 7.8 ± 5.5 mg/dl, p < 0.001), and daily time of glucose levels > 140 mg/dl (mean difference between diets, - 2.42 ± 1.7 h/day, p < 0.001). Blood fructosamine also decreased significantly more during PPT compared to MED intervention (mean change difference between diets, - 16.4 ± 37 μmol/dl, p < 0.0001). At the end of 6 months, the PPT intervention leads to significant improvements in multiple metabolic health parameters, among them HbA1c (mean ± SD, - 0.39 ± 0.48%, p < 0.001), fasting glucose (- 16.4 ± 24.2 mg/dl, p = 0.02) and triglycerides (- 49 ± 46 mg/dl, p < 0.001). Importantly, 61% of the participants exhibited diabetes remission, as measured by HbA1c < 6.5%. Finally, some clinical improvements were significantly associated with gut microbiome changes per person. CONCLUSION In this crossover trial in subjects with newly diagnosed T2DM, a PPT diet improved CGM-based glycemic measures significantly more than a Mediterranean-style MED diet. Additional 6-month PPT intervention further improved glycemic control and metabolic health parameters, supporting the clinical efficacy of this approach. TRIAL REGISTRATION ClinicalTrials.gov number, NCT01892956.
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Affiliation(s)
- Michal Rein
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel.,School of Public Health, University of Haifa, 3498838, Haifa, Israel
| | - Orly Ben-Yacov
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Smadar Shilo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Pediatric Diabetes Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, Haifa, Israel
| | - Niv Zmora
- Immunology Department, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Digestive Center, Tel Aviv Sourasky Medical Center, 6423906, Tel Aviv, Israel.,Internal Medicine Department, Tel Aviv Sourasky Medical Center, 6423906, Tel Aviv, Israel
| | - Dmitry Kolobkov
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noa Cohen-Dolev
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Bat-Chen Wolf
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noa Kosower
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Zamir Halpern
- Digestive Center, Tel Aviv Sourasky Medical Center, 6423906, Tel Aviv, Israel.,Internal Medicine Department, Tel Aviv Sourasky Medical Center, 6423906, Tel Aviv, Israel
| | - Shira Zelber-Sagi
- School of Public Health, University of Haifa, 3498838, Haifa, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 7610001, Rehovot, Israel.
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001, Rehovot, Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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Deczkowska A, David E, Ramadori P, Pfister D, Safran M, Li B, Giladi A, Jaitin DA, Barboy O, Cohen M, Yofe I, Gur C, Shlomi-Loubaton S, Henri S, Suhail Y, Qiu M, Kam S, Hermon H, Lahat E, Ben Yakov G, Cohen-Ezra O, Davidov Y, Likhter M, Goitein D, Roth S, Weber A, Malissen B, Weiner A, Ben-Ari Z, Heikenwälder M, Elinav E, Amit I. Publisher Correction: XCR1 + type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis. Nat Med 2022; 28:214. [PMID: 35022579 DOI: 10.1038/s41591-021-01668-0] [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: 11/09/2022]
Affiliation(s)
- Aleksandra Deczkowska
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. .,Departments of Immunology and Neuroscience, Institut Pasteur, Paris, France.
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Pierluigi Ramadori
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Dominik Pfister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Michal Safran
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Baoguo Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Oren Barboy
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Cohen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Yofe
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Chamutal Gur
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.,Department of Medicine, Hadassah-Hebrew University Hospital, Jerusalem, Israel
| | | | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Yousuf Suhail
- Chirurgische Klinik, Allgemein, Viszeral und Transplantationschirurgie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Mengjie Qiu
- Chirurgische Klinik, Allgemein, Viszeral und Transplantationschirurgie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Shing Kam
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Hila Hermon
- Department of Surgery C, Sheba Medical Center, Tel Hashomer, Israel
| | - Eylon Lahat
- Department of Surgery B, Sheba Medical Center, Tel Hashomer, Israel
| | - Gil Ben Yakov
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Yana Davidov
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Mariya Likhter
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | - David Goitein
- Department of Surgery C, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Susanne Roth
- Chirurgische Klinik, Allgemein, Viszeral und Transplantationschirurgie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Ben-Ari
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany.
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. .,Division of Microbiome and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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40
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Fluhr L, Mor U, Kolodziejczyk AA, Dori-Bachash M, Leshem A, Itav S, Cohen Y, Suez J, Zmora N, Moresi C, Molina S, Ayalon N, Valdés-Mas R, Hornstein S, Karbi H, Kviatcovsky D, Livne A, Bukimer A, Eliyahu-Miller S, Metz A, Brandis A, Mehlman T, Kuperman Y, Tsoory M, Stettner N, Harmelin A, Shapiro H, Elinav E. Gut microbiota modulates weight gain in mice after discontinued smoke exposure. Nature 2021; 600:713-719. [PMID: 34880502 DOI: 10.1038/s41586-021-04194-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/28/2021] [Indexed: 12/20/2022]
Abstract
Cigarette smoking constitutes a leading global cause of morbidity and preventable death1, and most active smokers report a desire or recent attempt to quit2. Smoking-cessation-induced weight gain (SCWG; 4.5 kg reported to be gained on average per 6-12 months, >10 kg year-1 in 13% of those who stopped smoking3) constitutes a major obstacle to smoking abstinence4, even under stable5,6 or restricted7 caloric intake. Here we use a mouse model to demonstrate that smoking and cessation induce a dysbiotic state that is driven by an intestinal influx of cigarette-smoke-related metabolites. Microbiome depletion induced by treatment with antibiotics prevents SCWG. Conversely, fecal microbiome transplantation from mice previously exposed to cigarette smoke into germ-free mice naive to smoke exposure induces excessive weight gain across diets and mouse strains. Metabolically, microbiome-induced SCWG involves a concerted host and microbiome shunting of dietary choline to dimethylglycine driving increased gut energy harvest, coupled with the depletion of a cross-regulated weight-lowering metabolite, N-acetylglycine, and possibly by the effects of other differentially abundant cigarette-smoke-related metabolites. Dimethylglycine and N-acetylglycine may also modulate weight and associated adipose-tissue immunity under non-smoking conditions. Preliminary observations in a small cross-sectional human cohort support these findings, which calls for larger human trials to establish the relevance of this mechanism in active smokers. Collectively, we uncover a microbiome-dependent orchestration of SCWG that may be exploitable to improve smoking-cessation success and to correct metabolic perturbations even in non-smoking settings.
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Affiliation(s)
- Leviel Fluhr
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Mor
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Avner Leshem
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Shlomik Itav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Yotam Cohen
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jotham Suez
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Niv Zmora
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Internal Medicine Department, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Claudia Moresi
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Shahar Molina
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Niv Ayalon
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Valdés-Mas
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Shanni Hornstein
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Hodaya Karbi
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adi Livne
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Aurelie Bukimer
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Alona Metz
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Mehlman
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Kuperman
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Tsoory
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Shapiro
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel. .,Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany.
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Beyaz S, Chung C, Mou H, Bauer-Rowe KE, Xifaras ME, Ergin I, Dohnalova L, Biton M, Shekhar K, Eskiocak O, Papciak K, Ozler K, Almeqdadi M, Yueh B, Fein M, Annamalai D, Valle-Encinas E, Erdemir A, Dogum K, Shah V, Alici-Garipcan A, Meyer HV, Özata DM, Elinav E, Kucukural A, Kumar P, McAleer JP, Fox JG, Thaiss CA, Regev A, Roper J, Orkin SH, Yilmaz ÖH. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell 2021; 28:1922-1935.e5. [PMID: 34529935 DOI: 10.1016/j.stem.2021.08.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 10/19/2020] [Revised: 05/25/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022]
Abstract
Little is known about how interactions of diet, intestinal stem cells (ISCs), and immune cells affect early-stage intestinal tumorigenesis. We show that a high-fat diet (HFD) reduces the expression of the major histocompatibility complex class II (MHC class II) genes in intestinal epithelial cells, including ISCs. This decline in epithelial MHC class II expression in a HFD correlates with reduced intestinal microbiome diversity. Microbial community transfer experiments suggest that epithelial MHC class II expression is regulated by intestinal flora. Mechanistically, pattern recognition receptor (PRR) and interferon-gamma (IFNγ) signaling regulates epithelial MHC class II expression. MHC class II-negative (MHC-II-) ISCs exhibit greater tumor-initiating capacity than their MHC class II-positive (MHC-II+) counterparts upon loss of the tumor suppressor Apc coupled with a HFD, suggesting a role for epithelial MHC class II-mediated immune surveillance in suppressing tumorigenesis. ISC-specific genetic ablation of MHC class II increases tumor burden cell autonomously. Thus, HFD perturbs a microbiome-stem cell-immune cell interaction that contributes to tumor initiation in the intestine.
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Affiliation(s)
- Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA.
| | - Charlie Chung
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Haiwei Mou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Khristian E Bauer-Rowe
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Michael E Xifaras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Ilgin Ergin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Lenka Dohnalova
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Moshe Biton
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; The Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Karthik Shekhar
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemical and Biomolecular Engineering, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
| | - Onur Eskiocak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Kadir Ozler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Mohammad Almeqdadi
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Brian Yueh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Miriam Fein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damodaran Annamalai
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eider Valle-Encinas
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Aysegul Erdemir
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Karoline Dogum
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Vyom Shah
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Hannah V Meyer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Deniz M Özata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pawan Kumar
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jeremy P McAleer
- Department of Pharmaceutical Science and Research, Marshall University School of Pharmacy, Huntington, WV 25701, USA
| | - James G Fox
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aviv Regev
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Jatin Roper
- Department of Medicine, Division of Gastroenterology, Duke University, Durham, NC 27710, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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de Castilhos J, Zamir E, Hippchen T, Rohrbach R, Schmidt S, Hengler S, Schumacher H, Neubauer M, Kunz S, Müller-Esch T, Hiergeist A, Gessner A, Khalid D, Gaiser R, Cullin N, Papagiannarou SM, Beuthien-Baumann B, Krämer A, Bartenschlager R, Jäger D, Müller M, Herth F, Duerschmied D, Schneider J, Schmid RM, Eberhardt JF, Khodamoradi Y, Vehreschild MJGT, Teufel A, Ebert MP, Hau P, Salzberger B, Schnitzler P, Poeck H, Elinav E, Merle U, Stein-Thoeringer CK. Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients. Clin Infect Dis 2021; 75:e1063-e1071. [PMID: 34694375 PMCID: PMC8586732 DOI: 10.1093/cid/ciab902] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND At the entry site of respiratory virus infections, the oropharyngeal microbiome has been proposed as a major hub integrating viral and host immune signals. Early studies suggested that infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are associated with changes of the upper and lower airway microbiome, and that specific microbial signatures may predict coronavirus disease 2019 (COVID-19) illness. However, the results are not conclusive, as critical illness can drastically alter a patient's microbiome through multiple confounders. METHODS To study oropharyngeal microbiome profiles in SARS-CoV-2 infection, clinical confounders, and prediction models in COVID-19, we performed a multicenter, cross-sectional clinical study analyzing oropharyngeal microbial metagenomes in healthy adults, patients with non-SARS-CoV-2 infections, or with mild, moderate, and severe COVID-19 (n = 322 participants). RESULTS In contrast to mild infections, patients admitted to a hospital with moderate or severe COVID-19 showed dysbiotic microbial configurations, which were significantly pronounced in patients treated with broad-spectrum antibiotics, receiving invasive mechanical ventilation, or when sampling was performed during prolonged hospitalization. In contrast, specimens collected early after admission allowed us to segregate microbiome features predictive of hospital COVID-19 mortality utilizing machine learning models. Taxonomic signatures were found to perform better than models utilizing clinical variables with Neisseria and Haemophilus species abundances as most important features. CONCLUSIONS In addition to the infection per se, several factors shape the oropharyngeal microbiome of severely affected COVID-19 patients and deserve consideration in the interpretation of the role of the microbiome in severe COVID-19. Nevertheless, we were able to extract microbial features that can help to predict clinical outcomes.
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Affiliation(s)
- Juliana de Castilhos
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Vale do Rio dos Sinos University (UNISINOS), Sao Leopoldo, Brazil
| | - Eli Zamir
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Theresa Hippchen
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Roman Rohrbach
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Sabine Schmidt
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Silvana Hengler
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Hanna Schumacher
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Melanie Neubauer
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sabrina Kunz
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Tonia Müller-Esch
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - Dina Khalid
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Rogier Gaiser
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Nyssa Cullin
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Stamatia M Papagiannarou
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | | | - Alwin Krämer
- German Cancer Research Center (DKFZ), Research Division Molecular Hematology/Oncology, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany,German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg
| | - Dirk Jäger
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Müller
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Daniel Duerschmied
- Department of Internal Medicine III, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Johann F Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Andreas Teufel
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Hau
- Wilhelm Sander-NeuroOncology Unit and Department of Neurology, University Clinic Regensburg, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infectious Disease, University Clinic Regensburg, Regensburg, Germany
| | - Paul Schnitzler
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany,National Center for Tumor Diseases (NCT) WERA
| | - Eran Elinav
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Weizmann Institute of Science, Rehovot, Israel
| | - Uta Merle
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Christoph K Stein-Thoeringer
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany,Corresponding author: Christoph K. Stein-Thoeringer, MD, Microbiome and Cancer Research Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany,
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Abstract
The human microbiome constitutes a complex multikingdom community that symbiotically interacts with the host across multiple body sites. Host-microbiome interactions impact multiple physiological processes and a variety of multifactorial disease conditions. In the past decade, microbiome communities have been suggested to influence the development, progression, metastasis formation, and treatment response of multiple cancer types. While causal evidence of microbial impacts on cancer biology is only beginning to be unraveled, enhanced molecular understanding of such cancer-modulating interactions and impacts on cancer treatment are considered of major scientific importance and clinical relevance. In this review, we describe the molecular pathogenic mechanisms shared throughout microbial niches that contribute to the initiation and progression of cancer. We highlight advances, limitations, challenges, and prospects in understanding how the microbiome may causally impact cancer and its treatment responsiveness, and how microorganisms or their secreted bioactive metabolites may be potentially harnessed and targeted as precision cancer therapeutics.
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Affiliation(s)
- Nyssa Cullin
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Camila Azevedo Antunes
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, 234 Herzl Street, 7610001 Rehovot, Israel
| | - Christoph K Stein-Thoeringer
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 7610001 Rehovot, Israel.
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44
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Ben-Yacov O, Godneva A, Rein M, Shilo S, Kolobkov D, Koren N, Cohen Dolev N, Travinsky Shmul T, Wolf BC, Kosower N, Sagiv K, Lotan-Pompan M, Zmora N, Weinberger A, Elinav E, Segal E. Personalized Postprandial Glucose Response-Targeting Diet Versus Mediterranean Diet for Glycemic Control in Prediabetes. Diabetes Care 2021; 44:1980-1991. [PMID: 34301736 DOI: 10.2337/dc21-0162] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To compare the clinical effects of a personalized postprandial-targeting (PPT) diet versus a Mediterranean (MED) diet on glycemic control and metabolic health in prediabetes. RESEARCH DESIGN AND METHODS We randomly assigned adults with prediabetes (n = 225) to follow a MED diet or a PPT diet for a 6-month dietary intervention and additional 6-month follow-up. The PPT diet relies on a machine learning algorithm that integrates clinical and microbiome features to predict personal postprandial glucose responses. During the intervention, all participants were connected to continuous glucose monitoring (CGM) and self-reported dietary intake using a smartphone application. RESULTS Among 225 participants randomized (58.7% women, mean ± SD age 50 ± 7 years, BMI 31.3 ± 5.8 kg/m2, HbA1c, 5.9 ± 0.2% [41 ± 2.4 mmol/mol], fasting plasma glucose 114 ± 12 mg/dL [6.33 ± 0.67 mmol/L]), 200 (89%) completed the 6-month intervention. A total of 177 participants also contributed 12-month follow-up data. Both interventions reduced the daily time with glucose levels >140 mg/dL (7.8 mmol/L) and HbA1c levels, but reductions were significantly greater in PPT compared with MED. The mean 6-month change in "time above 140" was -0.3 ± 0.8 h/day and -1.3 ± 1.5 h/day for MED and PPT, respectively (95% CI between-group difference -1.29 to -0.66, P < 0.001). The mean 6-month change in HbA1c was -0.08 ± 0.19% (-0.9 ± 2.1 mmol/mol) and -0.16 ± 0.24% (-1.7 ± 2.6 mmol/mol) for MED and PPT, respectively (95% CI between-group difference -0.14 to -0.02, P = 0.007). The significant between-group differences were maintained at 12-month follow-up. No significant differences were noted between the groups in a CGM-measured oral glucose tolerance test. CONCLUSIONS In this clinical trial in prediabetes, a PPT diet improved glycemic control significantly more than a MED diet as measured by daily time of glucose levels >140 mg/dL (7.8 mmol/L) and HbA1c. These findings may have implications for dietary advice in clinical practice.
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Affiliation(s)
- Orly Ben-Yacov
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Rein
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,School of Public Health, University of Haifa, Haifa, Israel
| | - Smadar Shilo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Pediatric Diabetes Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, Haifa, Israel
| | - Dmitry Kolobkov
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Netta Koren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Cohen Dolev
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tamara Travinsky Shmul
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bat Chen Wolf
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Kosower
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Sagiv
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Niv Zmora
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Digestive Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Internal Medicine Department, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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45
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Kern L, Abdeen SK, Kolodziejczyk AA, Elinav E. Commensal inter-bacterial interactions shaping the microbiota. Curr Opin Microbiol 2021; 63:158-171. [PMID: 34365152 DOI: 10.1016/j.mib.2021.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiota, a complex ecosystem of microorganisms of different kingdoms, impacts host physiology and disease. Within this ecosystem, inter-bacterial interactions and their impacts on microbiota community structure and the eukaryotic host remain insufficiently explored. Microbiota-related inter-bacterial interactions range from symbiotic interactions, involving exchange of nutrients, enzymes, and genetic material; competition for nutrients and space, mediated by biophysical alterations and secretion of toxins and anti-microbials; to predation of overpopulating bacteria. Collectively, these understudied interactions hold important clues as to forces shaping microbiota diversity, niche formation, and responses to signals perceived from the host, incoming pathogens and the environment. In this review, we highlight the roles and mechanisms of selected inter-bacterial interactions in the microbiota, and their potential impacts on the host and pathogenic infection. We discuss challenges in mechanistically decoding these complex interactions, and prospects of harnessing them as future targets for rational microbiota modification in a variety of diseases.
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Affiliation(s)
- Lara Kern
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Suhaib K Abdeen
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel; Cancer-Microbiota Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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46
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Deczkowska A, David E, Ramadori P, Pfister D, Safran M, Li B, Giladi A, Jaitin DA, Barboy O, Cohen M, Yofe I, Gur C, Shlomi-Loubaton S, Henri S, Suhail Y, Qiu M, Kam S, Hermon H, Lahat E, Ben Yakov G, Cohen-Ezra O, Davidov Y, Likhter M, Goitein D, Roth S, Weber A, Malissen B, Weiner A, Ben-Ari Z, Heikenwälder M, Elinav E, Amit I. XCR1 + type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis. Nat Med 2021; 27:1043-1054. [PMID: 34017133 DOI: 10.1038/s41591-021-01344-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) are prevalent liver conditions that underlie the development of life-threatening cirrhosis, liver failure and liver cancer. Chronic necro-inflammation is a critical factor in development of NASH, yet the cellular and molecular mechanisms of immune dysregulation in this disease are poorly understood. Here, using single-cell transcriptomic analysis, we comprehensively profiled the immune composition of the mouse liver during NASH. We identified a significant pathology-associated increase in hepatic conventional dendritic cells (cDCs) and further defined their source as NASH-induced boost in cycling of cDC progenitors in the bone marrow. Analysis of blood and liver from patients on the NAFLD/NASH spectrum showed that type 1 cDCs (cDC1) were more abundant and activated in disease. Sequencing of physically interacting cDC-T cell pairs from liver-draining lymph nodes revealed that cDCs in NASH promote inflammatory T cell reprogramming, previously associated with NASH worsening. Finally, depletion of cDC1 in XCR1DTA mice or using anti-XCL1-blocking antibody attenuated liver pathology in NASH mouse models. Overall, our study provides a comprehensive characterization of cDC biology in NASH and identifies XCR1+ cDC1 as an important driver of liver pathology.
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Affiliation(s)
- Aleksandra Deczkowska
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. .,Departments of Immunology and Neuroscience, Institut Pasteur, Paris, France.
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Pierluigi Ramadori
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Dominik Pfister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Michal Safran
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Baoguo Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Oren Barboy
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Cohen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Yofe
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Chamutal Gur
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.,Department of Medicine, Hadassah-Hebrew University Hospital, Jerusalem, Israel
| | | | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Yousuf Suhail
- Chirurgische Klinik, Allgemein, Viszeral und Transplantationschirurgie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Mengjie Qiu
- Chirurgische Klinik, Allgemein, Viszeral und Transplantationschirurgie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Shing Kam
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Hila Hermon
- Department of Surgery C, Sheba Medical Center, Tel Hashomer, Israel
| | - Eylon Lahat
- Department of Surgery B, Sheba Medical Center, Tel Hashomer, Israel
| | - Gil Ben Yakov
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Yana Davidov
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Mariya Likhter
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel
| | - David Goitein
- Department of Surgery C, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Susanne Roth
- Chirurgische Klinik, Allgemein, Viszeral und Transplantationschirurgie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Ben-Ari
- Liver Disease Center, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany.
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. .,Division of Microbiome and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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47
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Adlung L, Cohen Y, Mor U, Elinav E. Machine learning in clinical decision making. Med 2021; 2:642-665. [DOI: 10.1016/j.medj.2021.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/24/2022]
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48
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Affiliation(s)
- Suhaib K Abdeen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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49
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Finlay BB, Amato KR, Azad M, Blaser MJ, Bosch TCG, Chu H, Dominguez-Bello MG, Ehrlich SD, Elinav E, Geva-Zatorsky N, Gros P, Guillemin K, Keck F, Korem T, McFall-Ngai MJ, Melby MK, Nichter M, Pettersson S, Poinar H, Rees T, Tropini C, Zhao L, Giles-Vernick T. The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome. Proc Natl Acad Sci U S A 2021; 118:e2010217118. [PMID: 33472859 PMCID: PMC8017729 DOI: 10.1073/pnas.2010217118] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [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: 08/03/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has the potential to affect the human microbiome in infected and uninfected individuals, having a substantial impact on human health over the long term. This pandemic intersects with a decades-long decline in microbial diversity and ancestral microbes due to hygiene, antibiotics, and urban living (the hygiene hypothesis). High-risk groups succumbing to COVID-19 include those with preexisting conditions, such as diabetes and obesity, which are also associated with microbiome abnormalities. Current pandemic control measures and practices will have broad, uneven, and potentially long-term effects for the human microbiome across the planet, given the implementation of physical separation, extensive hygiene, travel barriers, and other measures that influence overall microbial loss and inability for reinoculation. Although much remains uncertain or unknown about the virus and its consequences, implementing pandemic control practices could significantly affect the microbiome. In this Perspective, we explore many facets of COVID-19-induced societal changes and their possible effects on the microbiome, and discuss current and future challenges regarding the interplay between this pandemic and the microbiome. Recent recognition of the microbiome's influence on human health makes it critical to consider both how the microbiome, shaped by biosocial processes, affects susceptibility to the coronavirus and, conversely, how COVID-19 disease and prevention measures may affect the microbiome. This knowledge may prove key in prevention and treatment, and long-term biological and social outcomes of this pandemic.
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Affiliation(s)
- B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Katherine R Amato
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Anthropology, Northwestern University, Evanston, IL 60208
| | - Meghan Azad
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Manitoba Interdisciplinary Lactation Centre, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Martin J Blaser
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Center for Advanced Biotechnology and Medicine at Rutgers Biomedical and Health Sciences, Rutgers University, Piscataway, NJ 08854-8021
| | - Thomas C G Bosch
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Zoologisches Institut, University of Kiel, 24118 Kiel, Germany
| | - Hiutung Chu
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Maria Gloria Dominguez-Bello
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901
| | - Stanislav Dusko Ehrlich
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Metagenopolis Unit, French National Institute for Agricultural Research, 78350 Jouy-en-Josas, France
| | - Eran Elinav
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Immunology, Weizmann Institute of Science, Rehovot 761000, Israel
- Cancer-Microbiome Division, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
| | - Naama Geva-Zatorsky
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Technion Integrated Cancer Center, Department of Cell Biology and Cancer Science, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Philippe Gros
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Karen Guillemin
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Frédéric Keck
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Centre National de la Recherche Scientifique, 75016 Paris, France
- Laboratoire d'Anthropologie Sociale, Collège de France, 75005 Paris, France
| | - Tal Korem
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Systems Biology, Irving Cancer Research Center, Columbia University, New York, NY 10032
- Department of Obstetrics and Gynecology, Irving Cancer Research Center, Columbia University, New York, NY 10032
| | - Margaret J McFall-Ngai
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI 96822
| | - Melissa K Melby
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Anthropology, University of Delaware, Newark, DE 19711
| | - Mark Nichter
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Anthropology, University of Arizona, Tucson, AZ 85721
| | - Sven Pettersson
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Lee Kong Chian School of Medicine, Nanyang Technological University, 637715 Singapore
| | - Hendrik Poinar
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Anthropology, McMaster University, Hamilton, ON L8S 4M4, Canada
| | - Tobias Rees
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Transformations of the Human Program, Berggruen Institute, Los Angeles, CA 90013
| | - Carolina Tropini
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Liping Zhao
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901
| | - Tamara Giles-Vernick
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada;
- Anthropology & Ecology of Disease Emergence, Institut Pasteur, 75015 Paris, France
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50
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Liwinski T, Leshem A, Elinav E. Breakthroughs and Bottlenecks in Microbiome Research. Trends Mol Med 2021; 27:298-301. [PMID: 33563544 DOI: 10.1016/j.molmed.2021.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 01/01/2023]
Abstract
Over the past 15 years, the research community has witnessed unprecedented progress in microbiome research. We review this increasing knowledge and first attempts of its clinical application, and also limitations and challenges faced by the research community, in mechanistically understanding host-microbiome interactions and integrating these insights into clinical practice.
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Affiliation(s)
- Timur Liwinski
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel; 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Avner Leshem
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel; Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel; Cancer-Microbiome Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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