1
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Özçam M, Lynch SV. The gut-airway microbiome axis in health and respiratory diseases. Nat Rev Microbiol 2024; 22:492-506. [PMID: 38778224 DOI: 10.1038/s41579-024-01048-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Communication between the gut and remote organs, such as the brain or the cardiovascular system, has been well established and recent studies provide evidence for a potential bidirectional gut-airway axis. Observations from animal and human studies indicate that respiratory insults influence the activity of the gut microbiome and that microbial ligands and metabolic products generated by the gut microbiome shape respiratory immunity. Information exchange between these two large mucosal surface areas regulates microorganism-immune interactions, with significant implications for the clinical and treatment outcomes of a range of respiratory conditions, including asthma, chronic obstructive pulmonary disease and lung cancer. In this Review, we summarize the most recent data in this field, offering insights into mechanisms of gut-airway crosstalk across spatial and temporal gradients and their relevance for respiratory health.
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Affiliation(s)
- Mustafa Özçam
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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2
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Zhang Y, Li Z, Huang Y, Xu Y, Zou B. Advancements in immunotherapy for advanced esophageal squamous cell carcinoma: a comprehensive review of current strategies and future directions. Expert Rev Clin Immunol 2024; 20:971-984. [PMID: 38884604 DOI: 10.1080/1744666x.2024.2368194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
INTRODUCTION Esophageal cancer (EC), particularly esophageal squamous cell carcinoma (ESCC), is characterized by high incidence and poor prognosis worldwide, necessitating novel therapeutic approaches like immunotherapy. This review explores the impact of immune checkpoint inhibitors (ICIs) on ESCC, especially focusing on PD-1/PD-L1 and CTLA-4 inhibitors. Our literature search, conducted across databases including PubMed, Web of Science, and EMBASE, from January 2010 to December 2023, aimed at identifying advancements, challenges, and future directions in the use of immunotherapy for ESCC. AREAS COVERED We provide a detailed analysis of clinical trials evaluating the efficacy of ICIs as monotherapy and in combination with chemotherapy, radiotherapy, and targeted therapy for locally advanced ESCC. Our findings highlight the significant survival benefits offered by ICIs, albeit with varying efficacy across patient populations, emphasizing the need for precise biomarkers to tailor treatment strategies. EXPERT OPINION The integration of immunotherapy into the ESCC treatment paradigm represents a significant shift, improving survival outcomes. Future research should focus on optimizing combination therapies and novel immunotherapeutic agents, incorporating genetic and tumor microenvironment analyses to enhance patient selection and treatment efficacy.
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Affiliation(s)
- Yi Zhang
- Department of Radiation Oncology, Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Zheng Li
- Department of Radiation Oncology, Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Ying Huang
- College of Management, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yong Xu
- Department of Radiation Oncology, Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Bingwen Zou
- Department of Radiation Oncology, Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, P.R. China
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3
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Espelage L, Wagner N, Placke JM, Ugurel S, Tasdogan A. The Interplay between Metabolic Adaptations and Diet in Cancer Immunotherapy. Clin Cancer Res 2024; 30:3117-3127. [PMID: 38771898 DOI: 10.1158/1078-0432.ccr-22-3468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/07/2023] [Accepted: 04/15/2024] [Indexed: 05/23/2024]
Abstract
Over the past decade, cancer immunotherapy has significantly advanced through the introduction of immune checkpoint inhibitors and the augmentation of adoptive cell transfer to enhance the innate cancer defense mechanisms. Despite these remarkable achievements, some cancers exhibit resistance to immunotherapy, with limited patient responsiveness and development of therapy resistance. Metabolic adaptations in both immune cells and cancer cells have emerged as central contributors to immunotherapy resistance. In the last few years, new insights emphasized the critical role of cancer and immune cell metabolism in animal models and patients. During therapy, immune cells undergo important metabolic shifts crucial for their acquired effector function against cancer cells. However, cancer cell metabolic rewiring and nutrient competition within tumor microenvironment (TME) alters many immune functions, affecting their fitness, polarization, recruitment, and survival. These interactions have initiated the development of novel therapies targeting tumor cell metabolism and favoring antitumor immunity within the TME. Furthermore, there has been increasing interest in comprehending how diet impacts the response to immunotherapy, given the demonstrated immunomodulatory and antitumor activity of various nutrients. In conclusion, recent advances in preclinical and clinical studies have highlighted the capacity of immune-based cancer therapies. Therefore, further exploration into the metabolic requirements of immune cells within the TME holds significant promise for the development of innovative therapeutic approaches that can effectively combat cancer in patients.
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Affiliation(s)
- Lena Espelage
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Essen, Germany
| | - Natalie Wagner
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Essen, Germany
| | - Jan-Malte Placke
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Essen, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Essen, Germany
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Essen, Germany
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4
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Adolph TE, Tilg H. Western diets and chronic diseases. Nat Med 2024:10.1038/s41591-024-03165-6. [PMID: 39085420 DOI: 10.1038/s41591-024-03165-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024]
Abstract
'Westernization', which incorporates industrial, cultural and dietary trends, has paralleled the rise of noncommunicable diseases across the globe. Today, the Western-style diet emerges as a key stimulus for gut microbial vulnerability, chronic inflammation and chronic diseases, affecting mainly the cardiovascular system, systemic metabolism and the gut. Here we review the diet of modern times and evaluate the threat it poses for human health by summarizing recent epidemiological, translational and clinical studies. We discuss the links between diet and disease in the context of obesity and type 2 diabetes, cardiovascular diseases, gut and liver diseases and solid malignancies. We collectively interpret the evidence and its limitations and discuss future challenges and strategies to overcome these. We argue that healthcare professionals and societies must react today to the detrimental effects of the Western diet to bring about sustainable change and improved outcomes in the future.
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Affiliation(s)
- Timon E Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria.
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria.
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5
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Dzutsev AK, Goldszmid RS. Towards enhancing the predictive value of the microbiota for cancer immunotherapy. Trends Cancer 2024:S2405-8033(24)00147-X. [PMID: 39089931 DOI: 10.1016/j.trecan.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
The gut microbiota has emerged as a potential determinant of immune checkpoint inhibitor (ICI) response, yet using it as a biomarker remains challenging. A recent study in Cell by Derosa et al. describes a two-tier model based on gut microbiota composition to discriminate responder from non-responder patients with cancer, offering new ideas that could be leveraged in the clinic.
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Affiliation(s)
- Amiran K Dzutsev
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Romina S Goldszmid
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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6
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Verhaert MAM, Aspeslagh S. Immunotherapy efficacy and toxicity: Reviewing the evidence behind patient implementable strategies. Eur J Cancer 2024; 209:114235. [PMID: 39059186 DOI: 10.1016/j.ejca.2024.114235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
The use of immune checkpoint inhibitors (ICI) in cancer treatment is expanding, offering promising outcomes but with an important risk of immune-related adverse events (irAEs). These events, stemming from an overstimulated immune system attacking healthy cells, can necessitate immunosuppressant treatment, disrupt treatment courses, and impact patients' quality of life. The analysis of ICI efficacy data has led to a better understanding of the characteristics of responders. Similarly, we are gaining clearer insights into the characteristics of patients who develop irAEs, prompting an increasing emphasis on modifiable factors associated with irAE risk. These factors include lifestyle choices and the composition of the gut microbiome. Despite comprehensive reviews exploring the microbiome's role in therapy efficacy, understanding its connection with immune-related toxicity remains incomplete. While endeavours to identify predictive biomarkers continue, lifestyle modifications emerge as a promising avenue for enhancing treatment outcomes. This review consolidates the current evidence regarding the impact of the gut microbiome on irAE occurrence. Furthermore, it focuses on actionable strategies for mitigating these adverse events, elucidating the evidence supporting dietary adjustments, supplementation, medication management, and physical activity. With the expanding range of indications for ICI therapy, a significant proportion of oncology patients, including those in early disease stages, are now exposed to these treatments. Acknowledging the importance of averting irAEs in this context, our review offers timely insights crucial for addressing the evolving challenges associated with immunotherapy across diverse oncological settings.
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Affiliation(s)
- Marthe August Marianne Verhaert
- Department of Medical Oncology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium.
| | - Sandrine Aspeslagh
- Department of Medical Oncology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium; Department of Internal Medicine, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
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7
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Xia L, Zhu X, Wang Y, Lu S. The gut microbiota improves the efficacy of immune-checkpoint inhibitor immunotherapy against tumors: From association to cause and effect. Cancer Lett 2024; 598:217123. [PMID: 39033797 DOI: 10.1016/j.canlet.2024.217123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/20/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Immune-checkpoint inhibitors (ICIs), including anti-PD-1/PD-L1 therapeutic antibodies, have markedly enhanced survival across numerous cancer types. However, the limited number of patients with durable benefits creates an urgent need to identify response biomarkers and to develop novel strategies so as to improve response. It is widely recognized that the gut microbiome is a key mediator in shaping immunity. Additionally, the gut microbiome shows significant potential in predicting the response to and enhancing the efficacy of ICI immunotherapy against cancer. Recent studies encompassing mechanistic analyses and clinical trials of microbiome-based therapy have shown a cause-and-effect relationship between the gut microbiome and the modulation of the ICI immunotherapeutic response, greatly contributing to the establishment of novel strategies that will improve response and overcome resistance to ICI treatment. In this review, we outline the current state of research advances and discuss the future directions of utilizing the gut microbiome to enhance the efficacy of ICI immunotherapy against tumors.
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Affiliation(s)
- Liliang Xia
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Xiaokuan Zhu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Ying Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, PR China.
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China.
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8
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Yamaguchi H, Hsu JM, Sun L, Wang SC, Hung MC. Advances and prospects of biomarkers for immune checkpoint inhibitors. Cell Rep Med 2024; 5:101621. [PMID: 38906149 PMCID: PMC11293349 DOI: 10.1016/j.xcrm.2024.101621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/22/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Immune checkpoint inhibitors (ICIs) activate anti-cancer immunity by blocking T cell checkpoint molecules such as programmed death 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4). Although ICIs induce some durable responses in various cancer patients, they also have disadvantages, including low response rates, the potential for severe side effects, and high treatment costs. Therefore, selection of patients who can benefit from ICI treatment is critical, and identification of biomarkers is essential to improve the efficiency of ICIs. In this review, we provide updated information on established predictive biomarkers (tumor programmed death-ligand 1 [PD-L1] expression, DNA mismatch repair deficiency, microsatellite instability high, and tumor mutational burden) and potential biomarkers currently under investigation such as tumor-infiltrated and peripheral lymphocytes, gut microbiome, and signaling pathways related to DNA damage and antigen presentation. In particular, this review aims to summarize the current knowledge of biomarkers, discuss issues, and further explore future biomarkers.
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Affiliation(s)
- Hirohito Yamaguchi
- Graduate Institute of Cell Biology, China Medical University, Taichung City 406040, Taiwan; Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan
| | - Jung-Mao Hsu
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan
| | - Linlin Sun
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung City 40402, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences and Institute of Biochemistry and Molecular Biology, China Medical University, Taichung City 406040, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung City 40402, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung City 40402, Taiwan.
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9
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Drew L. Faecal transplants can treat some cancers - but probably won't ever be widely used. Nature 2024:10.1038/d41586-024-02212-z. [PMID: 38965449 DOI: 10.1038/d41586-024-02212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
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10
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Cho YS, Han K, Xu J, Moon JJ. Novel strategies for modulating the gut microbiome for cancer therapy. Adv Drug Deliv Rev 2024; 210:115332. [PMID: 38759702 PMCID: PMC11268941 DOI: 10.1016/j.addr.2024.115332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Recent advancements in genomics, transcriptomics, and metabolomics have significantly advanced our understanding of the human gut microbiome and its impact on the efficacy and toxicity of anti-cancer therapeutics, including chemotherapy, immunotherapy, and radiotherapy. In particular, prebiotics, probiotics, and postbiotics are recognized for their unique properties in modulating the gut microbiota, maintaining the intestinal barrier, and regulating immune cells, thus emerging as new cancer treatment modalities. However, clinical translation of microbiome-based therapy is still in its early stages, facing challenges to overcome physicochemical and biological barriers of the gastrointestinal tract, enhance target-specific delivery, and improve drug bioavailability. This review aims to highlight the impact of prebiotics, probiotics, and postbiotics on the gut microbiome and their efficacy as cancer treatment modalities. Additionally, we summarize recent innovative engineering strategies designed to overcome challenges associated with oral administration of anti-cancer treatments. Moreover, we will explore the potential benefits of engineered gut microbiome-modulating approaches in ameliorating the side effects of immunotherapy and chemotherapy.
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Affiliation(s)
- Young Seok Cho
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kai Han
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 21009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 21009, China
| | - Jin Xu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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11
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Nakatsu G, Andreeva N, MacDonald MH, Garrett WS. Interactions between diet and gut microbiota in cancer. Nat Microbiol 2024; 9:1644-1654. [PMID: 38907007 DOI: 10.1038/s41564-024-01736-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/20/2024] [Indexed: 06/23/2024]
Abstract
Dietary patterns and specific dietary components, in concert with the gut microbiota, can jointly shape susceptibility, resistance and therapeutic response to cancer. Which diet-microbial interactions contribute to or mitigate carcinogenesis and how they work are important questions in this growing field. Here we interpret studies of diet-microbial interactions to assess dietary determinants of intestinal colonization by opportunistic and oncogenic bacteria. We explore how diet-induced expansion of specific gut bacteria might drive colonic epithelial tumorigenesis or create immuno-permissive tumour milieus and introduce recent findings that provide insight into these processes. Additionally, we describe available preclinical models that are widely used to study diet, microbiome and cancer interactions. Given the rising clinical interest in dietary modulations in cancer treatment, we highlight promising clinical trials that describe the effects of different dietary alterations on the microbiome and cancer outcomes.
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Affiliation(s)
- Geicho Nakatsu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Natalia Andreeva
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Meghan H MacDonald
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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12
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Bredon M, Danne C, Pham HP, Ruffié P, Bessede A, Rolhion N, Creusot L, Brot L, Alonso I, Langella P, Derosa L, Cortot AB, Routy B, Zitvogel L, Segata N, Sokol H. Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors. Oncoimmunology 2024; 13:2374954. [PMID: 38957477 PMCID: PMC11218805 DOI: 10.1080/2162402x.2024.2374954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Gut microbiota impacts responses to immune checkpoint inhibitors (ICI). A high level of Faecalibacterium prausnitzii have been associated with a positive response to ICI in multiple cancer types. Here, based on fecal shotgun metagenomics data, we show in two independent cohorts of patients with non-small cell lung cancer and advanced melanoma that a high level of F. prausnitzii at baseline is positively associated with a better clinical response to ICI. In MCA205 tumor-bearing mice, administration of F. prausnitzii strain EXL01, already in clinical development for Inflammatory Bowel Disease, restores the anti-tumor response to ICI in the context of antibiotic-induced microbiota perturbation at clinical and tumor transcriptomics level. In vitro, EXL01 strain enhances T cell activation in the presence of ICI. Interestingly, oral administration of EXL01 strain did not induce any change in fecal microbiota diversity or composition, suggesting a direct effect on immune cells in the small intestine. F. prausnitzii strain EXL01 will be evaluated as an adjuvant to ICI in multiple cancers in the near future.
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Affiliation(s)
- Marius Bredon
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Camille Danne
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | | | | | | | - Nathalie Rolhion
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Laura Creusot
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Loic Brot
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Iria Alonso
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Philippe Langella
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Lisa Derosa
- UMR1015 Gustave Roussy Cancer Campus, Villejuif, France
- Département de Médecine Oncologique, Gustave Roussy Cancer Campus, Villejuif, France
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicetre, France
| | - Alexis B. Cortot
- Université de Lille, CHU Lille, Thoracic Oncology Department, Centre National de la Recherche Scientifique, INSERM, Institut Pasteur de Lille, UMR9020-UMR-S 1277-Canther, Lille, France
| | - Bertrand Routy
- Department of Medicine, Hematology-Oncology Division, University of Montreal Healthcare Centre (CHUM), Montreal, QC, Canada
- University of Montreal Research Center (CRCHUM), Montreal, QC, Canada
| | - Laurence Zitvogel
- UMR1015 Gustave Roussy Cancer Campus, Villejuif, France
- Département de Médecine Oncologique, Gustave Roussy Cancer Campus, Villejuif, France
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicetre, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Villejuif, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
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13
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Raoul JL, Hansten PD. Proton pump inhibitors and cancer treatments: Emerging evidence against coadministration. Cancer Treat Rev 2024; 129:102794. [PMID: 38968741 DOI: 10.1016/j.ctrv.2024.102794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Proton pump inhibitors (PPIs) are widely used in cancer patients despite accumulating data showing that they can impact the efficacy of major anticancer drugs. This is particularly important with tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (CPIs). RESULTS Most TKIs require gastric acidity for their absorption and some retrospective series demonstrated that coprescription decreases the survival benefit of some TKI use (erlotinib, gefitinib and pazopanib). Relations between microbiota, the immune system, and the efficacy of immunotherapy are now obvious, just as modifications to gut flora after PPIs use are well-known. Many retrospective articles, including articles based on individual-participant data from randomized studies, demonstrated that patients treated with CPIs have a poorer outcome (overall survival, progression-free survival and response rate) when they received PPIs concomitantly, while there was no impact of such coprescription among patients in control arms, not treated with immunotherapies. Similar data were also observed in patients treated with palbociclib. CONCLUSION For these interactions, it is very important to use the precautionary principle and warn patients and physicians about this. In patients who require acid suppression because of severe symptoms, using antacids or H2 blockers could be recommended.
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Affiliation(s)
- Jean-Luc Raoul
- Department of Clinical Research, Institut de Cancérologie de l'Ouest, Saint-Herblain, France.
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14
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Holder AM, Dedeilia A, Sierra-Davidson K, Cohen S, Liu D, Parikh A, Boland GM. Defining clinically useful biomarkers of immune checkpoint inhibitors in solid tumours. Nat Rev Cancer 2024; 24:498-512. [PMID: 38867074 DOI: 10.1038/s41568-024-00705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Although more than a decade has passed since the approval of immune checkpoint inhibitors (ICIs) for the treatment of melanoma and non-small-cell lung, breast and gastrointestinal cancers, many patients still show limited response. US Food and Drug Administration (FDA)-approved biomarkers include programmed cell death 1 ligand 1 (PDL1) expression, microsatellite status (that is, microsatellite instability-high (MSI-H)) and tumour mutational burden (TMB), but these have limited utility and/or lack standardized testing approaches for pan-cancer applications. Tissue-based analytes (such as tumour gene signatures, tumour antigen presentation or tumour microenvironment profiles) show a correlation with immune response, but equally, these demonstrate limited efficacy, as they represent a single time point and a single spatial assessment. Patient heterogeneity as well as inter- and intra-tumoural differences across different tissue sites and time points represent substantial challenges for static biomarkers. However, dynamic biomarkers such as longitudinal biopsies or novel, less-invasive markers such as blood-based biomarkers, radiomics and the gut microbiome show increasing potential for the dynamic identification of ICI response, and patient-tailored predictors identified through neoadjuvant trials or novel ex vivo tumour models can help to personalize treatment. In this Perspective, we critically assess the multiple new static, dynamic and patient-specific biomarkers, highlight the newest consortia and trial efforts, and provide recommendations for future clinical trials to make meaningful steps forwards in the field.
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Affiliation(s)
- Ashley M Holder
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - David Liu
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Aparna Parikh
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
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15
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Glitza IC, Seo YD, Spencer CN, Wortman JR, Burton EM, Alayli FA, Loo CP, Gautam S, Damania A, Densmore J, Fairchild J, Cabanski CR, Wong MC, Peterson CB, Weiner B, Hicks N, Aunins J, McChalicher C, Walsh E, Tetzlaff MT, Hamid O, Ott PA, Boland GM, Sullivan RJ, Grossmann KF, Ajami NJ, LaVallee T, Henn MR, Tawbi HA, Wargo JA. Randomized Placebo-Controlled, Biomarker-Stratified Phase Ib Microbiome Modulation in Melanoma: Impact of Antibiotic Preconditioning on Microbiome and Immunity. Cancer Discov 2024; 14:1161-1175. [PMID: 38588588 PMCID: PMC11215408 DOI: 10.1158/2159-8290.cd-24-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/10/2024]
Abstract
Gut-microbiota modulation shows promise in improving immune-checkpoint blockade (ICB) response; however, precision biomarker-driven, placebo-controlled trials are lacking. We performed a multicenter, randomized placebo-controlled, biomarker-stratified phase I trial in patients with ICB-naïve metastatic melanoma using SER-401, an orally delivered Firmicutesenriched spore formulation. Fecal microbiota signatures were characterized at baseline; patients were stratified by high versus low Ruminococcaceae abundance prior to randomization to the SER-401 arm (oral vancomycin-preconditioning/SER-401 alone/nivolumab + SER-401), versus the placebo arm [placebo antibiotic/placebo microbiome modulation (PMM)/nivolumab + PMM (NCT03817125)]. Analysis of 14 accrued patients demonstrated that treatment with SER-401 + nivolumab was safe, with an overall response rate of 25% in the SER-401 arm and 67% in the placebo arm (though the study was underpowered related to poor accrual during the COVID-19 pandemic). Translational analyses demonstrated that vancomycin preconditioning was associated with the disruption of the gut microbiota and impaired immunity, with incomplete recovery at ICB administration (particularly in patients with high baseline Ruminococcaceae). These results have important implications for future microbiome modulation trials. Significance: This first-of-its-kind, placebo-controlled, randomized biomarker-driven microbiome modulation trial demonstrated that vancomycin + SER-401 and anti-PD-1 are safe in melanoma patients. Although limited by poor accrual during the pandemic, important insights were gained via translational analyses, suggesting that antibiotic preconditioning and interventional drug dosing regimens should be carefully considered when designing such trials.
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Affiliation(s)
- Isabella C. Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Yongwoo David Seo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | | | | | - Elizabeth M. Burton
- Strategic Translational Research Initiative Development, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Farah A. Alayli
- Parker Institute for Cancer Immunotherapy, San Francisco, California.
| | | | - Shikha Gautam
- Parker Institute for Cancer Immunotherapy, San Francisco, California.
| | - Ashish Damania
- Platform for Innovative Microbiome and Translational Research, Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Julie Densmore
- Parker Institute for Cancer Immunotherapy, San Francisco, California.
| | - Justin Fairchild
- Parker Institute for Cancer Immunotherapy, San Francisco, California.
- Portage Biotech, Westport, Connecticut.
| | | | - Matthew C. Wong
- Platform for Innovative Microbiome and Translational Research, Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | | | | | - John Aunins
- Seres Therapeutics, Cambridge, Massachusetts.
| | | | - Emily Walsh
- Seres Therapeutics, Cambridge, Massachusetts.
| | - Michael T. Tetzlaff
- Department of Pathology, University of California San Francisco, San Francisco, California.
| | - Omid Hamid
- Cutaneous Oncology, The Angeles Clinic and Research Institute, A Cedars-Sinai Affiliate, Los Angeles, California.
| | - Patrick A. Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Genevieve M. Boland
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
| | - Ryan J. Sullivan
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | | | - Nadim J. Ajami
- Platform for Innovative Microbiome and Translational Research, Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Theresa LaVallee
- Parker Institute for Cancer Immunotherapy, San Francisco, California.
- Coherus BioSciences, Redwood City, California.
| | | | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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16
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Robertson BM, Fane ME, Weeraratna AT, Rebecca VW. Determinants of resistance and response to melanoma therapy. NATURE CANCER 2024; 5:964-982. [PMID: 39020103 DOI: 10.1038/s43018-024-00794-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/05/2024] [Indexed: 07/19/2024]
Abstract
Metastatic melanoma is among the most enigmatic advanced cancers to clinically manage despite immense progress in the way of available therapeutic options and historic decreases in the melanoma mortality rate. Most patients with metastatic melanoma treated with modern targeted therapies (for example, BRAFV600E/K inhibitors) and/or immune checkpoint blockade (for example, anti-programmed death 1 therapy) will progress, owing to profound tumor cell plasticity fueled by genetic and nongenetic mechanisms and dichotomous host microenvironmental influences. Here we discuss the determinants of tumor heterogeneity, mechanisms of therapy resistance and effective therapy regimens that hold curative promise.
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Affiliation(s)
- Bailey M Robertson
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mitchell E Fane
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Vito W Rebecca
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
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17
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Glehr G, Riquelme P, Kronenberg K, Lohmayer R, López-Madrona VJ, Kapinsky M, Schlitt HJ, Geissler EK, Spang R, Haferkamp S, Hutchinson JA. Restricting datasets to classifiable samples augments discovery of immune disease biomarkers. Nat Commun 2024; 15:5417. [PMID: 38926389 PMCID: PMC11208602 DOI: 10.1038/s41467-024-49094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Immunological diseases are typically heterogeneous in clinical presentation, severity and response to therapy. Biomarkers of immune diseases often reflect this variability, especially compared to their regulated behaviour in health. This leads to a common difficulty that frustrates biomarker discovery and interpretation - namely, unequal dispersion of immune disease biomarker expression between patient classes necessarily limits a biomarker's informative range. To solve this problem, we introduce dataset restriction, a procedure that splits datasets into classifiable and unclassifiable samples. Applied to synthetic flow cytometry data, restriction identifies biomarkers that are otherwise disregarded. In advanced melanoma, restriction finds biomarkers of immune-related adverse event risk after immunotherapy and enables us to build multivariate models that accurately predict immunotherapy-related hepatitis. Hence, dataset restriction augments discovery of immune disease biomarkers, increases predictive certainty for classifiable samples and improves multivariate models incorporating biomarkers with a limited informative range. This principle can be directly extended to any classification task.
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Affiliation(s)
- Gunther Glehr
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Paloma Riquelme
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | | | - Robert Lohmayer
- Algorithmic Bioinformatics Research Group, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | | | - Hans J Schlitt
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Edward K Geissler
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - Sebastian Haferkamp
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - James A Hutchinson
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany.
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18
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Haddad A, Holder AM. Microbiome and Immunotherapy for Melanoma: Are We Ready for Clinical Application? Hematol Oncol Clin North Am 2024:S0889-8588(24)00059-5. [PMID: 38908958 DOI: 10.1016/j.hoc.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
The microbiome plays a substantial role in the efficacy of immune checkpoint blockade (ICB) in patients with metastatic melanoma. While the exact gut microbiome composition and the pathways involved in this interaction are not clearly delineated, novel studies and ongoing clinical trials are likely to reveal findings applicable to the clinical setting for the prediction and optimization of response to ICB. Nevertheless, lifestyle modifications, including high fiber diet, avoidance of unnecessary antibiotic prescriptions, and careful use of probiotics may be helpful to optimize the "health" of the gut microbiome and potentially enhance response to ICB in patients with melanoma.
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Affiliation(s)
- Antony Haddad
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX 77030, USA. https://twitter.com/Haddad_Antony
| | - Ashley M Holder
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX 77030, USA.
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19
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Ning L, Hong J. Gut microbiome ecological topology as next-generation biomarkers for cancer immunotherapy. Cell 2024; 187:3231-3232. [PMID: 38906099 DOI: 10.1016/j.cell.2024.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 06/23/2024]
Abstract
Numerous studies have evaluated the gut microbiome as a biomarker for predicting cancer immunotherapy, but the heterogeneity among different studies has hindered its applications. In this issue of Cell, Derosa et al. report a biomarker based on the ecological topology of the gut microbiota that can predict immunotherapy efficacy effectively.
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Affiliation(s)
- Lijun Ning
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China
| | - Jie Hong
- State Key Laboratory of Systems Medicine for Cancer, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai 200001, China.
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20
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Derosa L, Iebba V, Silva CAC, Piccinno G, Wu G, Lordello L, Routy B, Zhao N, Thelemaque C, Birebent R, Marmorino F, Fidelle M, Messaoudene M, Thomas AM, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Sibilot DM, Goldwasser F, Scherpereel A, Pegliasco H, Ghiringhelli F, Bouchard N, Sow C, Darik I, Zoppi S, Ly P, Reni A, Daillère R, Deutsch E, Lee KA, Bolte LA, Björk JR, Weersma RK, Barlesi F, Padilha L, Finzel A, Isaksen ML, Escudier B, Albiges L, Planchard D, André F, Cremolini C, Martinez S, Besse B, Zhao L, Segata N, Wojcik J, Kroemer G, Zitvogel L. Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome. Cell 2024; 187:3373-3389.e16. [PMID: 38906102 DOI: 10.1016/j.cell.2024.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/16/2024] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The gut microbiota influences the clinical responses of cancer patients to immunecheckpoint inhibitors (ICIs). However, there is no consensus definition of detrimental dysbiosis. Based on metagenomics (MG) sequencing of 245 non-small cell lung cancer (NSCLC) patient feces, we constructed species-level co-abundance networks that were clustered into species-interacting groups (SIGs) correlating with overall survival. Thirty-seven and forty-five MG species (MGSs) were associated with resistance (SIG1) and response (SIG2) to ICIs, respectively. When combined with the quantification of Akkermansia species, this procedure allowed a person-based calculation of a topological score (TOPOSCORE) that was validated in an additional 254 NSCLC patients and in 216 genitourinary cancer patients. Finally, this TOPOSCORE was translated into a 21-bacterial probe set-based qPCR scoring that was validated in a prospective cohort of NSCLC patients as well as in colorectal and melanoma patients. This approach could represent a dynamic diagnosis tool for intestinal dysbiosis to guide personalized microbiota-centered interventions.
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Affiliation(s)
- Lisa Derosa
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France.
| | - Valerio Iebba
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | - Guojun Wu
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Leonardo Lordello
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Bertrand Routy
- Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Department of Medicine, Montréal, QC, Canada; Centre de Recherche du CHUM (CRCHUM), Montréal, QC, Canada
| | - Naisi Zhao
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Cassandra Thelemaque
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Roxanne Birebent
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Federica Marmorino
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marine Fidelle
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | | | - Gerard Zalcman
- Université Paris Cité, Thoracic Oncology Department-CIC1425/CLIP2 Paris-Nord, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Sylvie Friard
- Pneumology Department, Foch Hospital, Suresnes, France
| | - Julien Mazieres
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | | | - Denis Moro- Sibilot
- Department of Thoracic Oncology, Centre Hospitalier Universitaire, Grenoble, France
| | - François Goldwasser
- INSERM U1016-CNRS UMR8104, Paris Cité University, Paris, France; Department of Medical Oncology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Immunomodulatory Therapies Multidisciplinary Study Group (CERTIM), Paris, France
| | - Arnaud Scherpereel
- Department of Pulmonary and Thoracic Oncology, University of Lille, University Hospital (CHU), Lille, France
| | | | - François Ghiringhelli
- Cancer Biology Transfer Platform, Centre Georges-François Leclerc, Dijon, France; Centre de Recherche INSERM LNC-UMR1231, Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | | | - Cissé Sow
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Ines Darik
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Silvia Zoppi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Pierre Ly
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Anna Reni
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Section of Oncology, Department of Medicine, University of Verona School of Medicine and Verona University Hospital Trust, Verona, Italy
| | | | - Eric Deutsch
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Radiation Oncology, Gustave Roussy, Villejuif, France; INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Lucas Padilha
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | - Ana Finzel
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | | | - Bernard Escudier
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Laurence Albiges
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - David Planchard
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Fabrice André
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Chiara Cremolini
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Stéphanie Martinez
- Service des Maladies Respiratoires, Centre Hospitalier d'Aix-en-Provence, Aix-en-Provence, France
| | - Benjamin Besse
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Liping Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA; State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Guido Kroemer
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Centre de Recherche des Cordeliers, Equipe labellisée-Ligue contre le cancer, Université de Paris Cité, Sorbonne Université, Institut Universitaire de France, Inserm U1138, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS) 1428, Villejuif, France.
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21
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Trepka KR, Kidder WA, Kyaw TS, Olson CA, Upadhyay V, Noecker C, Stanfield D, Steiding P, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ. Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597471. [PMID: 38895199 PMCID: PMC11185696 DOI: 10.1101/2024.06.04.597471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Herein, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal study of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. 16S rRNA gene and metagenomic sequencing revealed significant shifts in gut microbial community structure during treatment with oral fluoropyrimidines, which was validated in an independent cohort. Gene abundance was also markedly changed by oral fluoropyrimidines, including an enrichment for the preTA operon, which is sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). Higher levels of preTA led to increased 5-FU depletion by the gut microbiota grown ex vivo. Germ-free and antibiotic-treated mice had increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA+ E. coli, or CRC patient stool with high preTA levels. preTA abundance was negatively associated with patient toxicities. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach is generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.
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Affiliation(s)
- Kai R. Trepka
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Wesley A. Kidder
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Than S. Kyaw
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Christine A. Olson
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Vaibhav Upadhyay
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Dalila Stanfield
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Paige Steiding
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Darren Dumlao
- Department of Gastroenterology, University of California San Francisco; San Francisco, USA
| | - Jessie A. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Matthew D. Stachler
- Department of Pathology, University of California San Francisco; San Francisco, USA
| | - Erin L. Van Blarigan
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco; San Francisco, USA
- Department of Urology, University of California San Francisco; San Francisco, USA
| | - Alan P. Venook
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Chloe E. Atreya
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
- Chan Zuckerberg Biohub-San Francisco; San Francisco, USA
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22
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Chan PY, Corrie PG. Curing Stage IV Melanoma: Where Have We Been and Where Are We? Am Soc Clin Oncol Educ Book 2024; 44:e438654. [PMID: 38669609 DOI: 10.1200/edbk_438654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Little more than 10 years ago, metastatic melanoma was considered to have one of the poorest cancer outcomes, associated with a median overall survival of 6-8 months. Cytotoxic chemotherapy offered modest response rates of 20%-30%, but no clear survival benefit. Patients were routinely enrolled in clinical trials as their first-line therapy in the search for effective novel therapeutics. Remarkable developments in molecular biology, cancer genomics, immunology, and drug discovery have dominated the early part of the 21st century, and nowhere have the benefits been better realized than in the transformation of outcomes for patients with metastatic melanoma: since 2011, 14 new agents have been approved that significantly increase survival, with long-term remissions and, possibly now, potential for cure. Even so, there is still much work to be done, given that most treated patients still die of their disease. Although most survival gains have so far been realized for cutaneous melanoma, improving treatment options for those 10% of patients with rarer, noncutaneous melanomas is a high priority. Key novel therapeutic approaches aimed at improving outcomes with potential for curing patients with melanoma are considered.
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Affiliation(s)
- Pui Ying Chan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Pippa G Corrie
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
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23
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Nguyen NTA, Jiang Y, McQuade JL. Eating away cancer: the potential of diet and the microbiome for shaping immunotherapy outcome. Front Immunol 2024; 15:1409414. [PMID: 38873602 PMCID: PMC11169628 DOI: 10.3389/fimmu.2024.1409414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
The gut microbiome (GMB) plays a substantial role in human health and disease. From affecting gut barrier integrity to promoting immune cell differentiation, the GMB is capable of shaping host immunity and thus oncogenesis and anti-cancer therapeutic response, particularly with immunotherapy. Dietary patterns and components are key determinants of GMB composition, supporting the investigation of the diet-microbiome-immunity axis as a potential avenue to enhance immunotherapy response in cancer patients. As such, this review will discuss the role of the GMB and diet on anti-cancer immunity. We demonstrate that diet affects anti-cancer immunity through both GMB-independent and GMB-mediated mechanisms, and that different diet patterns mold the GMB's functional and taxonomic composition in distinctive ways. Dietary modulation therefore shows promise as an intervention for improving cancer outcome; however, further and more extensive research in human cancer populations is needed.
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Affiliation(s)
| | | | - Jennifer L. McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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24
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Li Z, Xiong W, Liang Z, Wang J, Zeng Z, Kołat D, Li X, Zhou D, Xu X, Zhao L. Critical role of the gut microbiota in immune responses and cancer immunotherapy. J Hematol Oncol 2024; 17:33. [PMID: 38745196 PMCID: PMC11094969 DOI: 10.1186/s13045-024-01541-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiota plays a critical role in the progression of human diseases, especially cancer. In recent decades, there has been accumulating evidence of the connections between the gut microbiota and cancer immunotherapy. Therefore, understanding the functional role of the gut microbiota in regulating immune responses to cancer immunotherapy is crucial for developing precision medicine. In this review, we extract insights from state-of-the-art research to decipher the complicated crosstalk among the gut microbiota, the systemic immune system, and immunotherapy in the context of cancer. Additionally, as the gut microbiota can account for immune-related adverse events, we discuss potential interventions to minimize these adverse effects and discuss the clinical application of five microbiota-targeted strategies that precisely increase the efficacy of cancer immunotherapy. Finally, as the gut microbiota holds promising potential as a target for precision cancer immunotherapeutics, we summarize current challenges and provide a general outlook on future directions in this field.
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Affiliation(s)
- Zehua Li
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, England
| | - Weixi Xiong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Institute of Brain Science and Brain-Inspired Technology of West China Hospital, Sichuan University, Chengdu, China
| | - Zhu Liang
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, England
- Target Discovery Institute, Center for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, England
| | - Jinyu Wang
- Departments of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Ziyi Zeng
- Department of Neonatology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz, Poland
| | - Xi Li
- Department of Urology, Churchill Hospital, Oxford University Hospitals NHS Foundation, Oxford, UK
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Institute of Brain Science and Brain-Inspired Technology of West China Hospital, Sichuan University, Chengdu, China
| | - Xuewen Xu
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Linyong Zhao
- Department of General Surgery and Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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25
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Kim CW, Kim HJ, Lee HK. Microbiome dynamics in immune checkpoint blockade. Trends Endocrinol Metab 2024:S1043-2760(24)00096-1. [PMID: 38705760 DOI: 10.1016/j.tem.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024]
Abstract
Immune checkpoint blockade (ICB) is one of the leading immunotherapies, although a variable extent of resistance has been observed among patients and across cancer types. Among the efforts underway to overcome this challenge, the microbiome has emerged as a factor affecting the responsiveness and efficacy of ICB. Active research, facilitated by advances in sequencing techniques, is assessing the predominant influence of the intestinal microbiome, as well as the effects of the presence of an intratumoral microbiome. In this review, we describe recent findings from clinical trials, observational studies of human patients, and animal studies on the impact of the microbiome on the efficacy of ICB, highlighting the role of the intestinal and tumor microbiomes and the contribution of methodological advances in their study.
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Affiliation(s)
- Chae Won Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; Life Science Institute, KAIST, Daejeon 34141, Republic of Korea
| | - Hyun-Jin Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; Life Science Institute, KAIST, Daejeon 34141, Republic of Korea
| | - Heung Kyu Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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26
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Ma Y, Wang T, Zhang X, Wang P, Long F. The role of circular RNAs in regulating resistance to cancer immunotherapy: mechanisms and implications. Cell Death Dis 2024; 15:312. [PMID: 38697964 PMCID: PMC11066075 DOI: 10.1038/s41419-024-06698-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/05/2024]
Abstract
Cancer immunotherapy has rapidly transformed cancer treatment, yet resistance remains a significant hurdle, limiting its efficacy in many patients. Circular RNAs (circRNAs), a novel class of non-coding RNAs, have emerged as pivotal regulators of gene expression and cellular processes. Increasing evidence indicates their involvement in modulating resistance to cancer immunotherapy. Notably, certain circRNAs function as miRNA sponges or interact with proteins, influencing the expression of immune-related genes, including crucial immune checkpoint molecules. This, in turn, shapes the tumor microenvironment and significantly impacts the response to immunotherapy. In this comprehensive review, we explore the evolving role of circRNAs in orchestrating resistance to cancer immunotherapy, with a specific focus on their mechanisms in influencing immune checkpoint gene expression. Additionally, we underscore the potential of circRNAs as promising therapeutic targets to augment the effectiveness of cancer immunotherapy. Understanding the role of circRNAs in cancer immunotherapy resistance could contribute to the development of new therapeutic strategies to overcome resistance and improve patient outcomes.
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Affiliation(s)
- Yu Ma
- Department of Clinical Research, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Ting Wang
- Department of Clinical Research, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Xudong Zhang
- Department of Clinical Research, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Pinghan Wang
- Laboratory Medicine Center, Sichuan Provincial Maternity and Child Health Care Hospital, Affiliated Women's and Children's Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610032, China
| | - Fangyi Long
- Laboratory Medicine Center, Sichuan Provincial Maternity and Child Health Care Hospital, Affiliated Women's and Children's Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, 610032, China.
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27
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Blake SJ, Wolf Y, Boursi B, Lynn DJ. Role of the microbiota in response to and recovery from cancer therapy. Nat Rev Immunol 2024; 24:308-325. [PMID: 37932511 DOI: 10.1038/s41577-023-00951-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/08/2023]
Abstract
Our understanding of how the microbiota affects the balance between response to and failure of cancer treatment by modulating the tumour microenvironment and systemic immune system has advanced rapidly in recent years. Microbiota-targeting interventions in patients with cancer are an area of intensive investigation. Promisingly, phase I-II clinical trials have shown that interventions such as faecal microbiota transplantation can overcome resistance to immune checkpoint blockade in patients with melanoma, improve therapeutic outcomes in treatment-naive patients and reduce therapy-induced immunotoxicities. Here, we synthesize the evidence showing that the microbiota is an important determinant of both cancer treatment efficacy and treatment-induced acute and long-term toxicity, and we discuss the complex and inter-related mechanisms involved. We also assess the potential of microbiota-targeting interventions, including bacterial engineering and phage therapy, to optimize the response to and recovery from cancer therapy.
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Affiliation(s)
- Stephen J Blake
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Yochai Wolf
- Ella Lemelbaum Institute for Immuno-oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Israel
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ben Boursi
- School of Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Oncology, Sheba Medical Center, Tel Hashomer, Israel
- Center of Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, PA, USA
| | - David J Lynn
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
- College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia.
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28
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Zakharevich NV, Morozov MD, Kanaeva VA, Filippov MS, Zyubko TI, Ivanov AB, Ulyantsev VI, Klimina KM, Olekhnovich EI. Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy. Life Sci Alliance 2024; 7:e202302480. [PMID: 38448159 PMCID: PMC10917649 DOI: 10.26508/lsa.202302480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
Immunotherapy has proven to be a boon for patients battling metastatic melanoma, significantly improving their clinical condition and overall quality of life. A compelling link between the composition of the gut microbiome and the efficacy of immunotherapy has been established in both animal models and human patients. However, the precise biological mechanisms by which gut microbes influence treatment outcomes remain poorly understood. Using a robust dataset of 680 fecal metagenomes from melanoma patients, a detailed catalog of metagenome-assembled genomes (MAGs) was constructed to explore the compositional and functional properties of the gut microbiome. Our study uncovered significant findings that deepen the understanding of the intricate relationship between gut microbes and the efficacy of melanoma immunotherapy. In particular, we discovered the specific metagenomic profile of patients with favorable treatment outcomes, characterized by a prevalence of MAGs with increased overall metabolic potential and proficiency in polysaccharide utilization, along with those responsible for cobalamin and amino acid production. Furthermore, our investigation of the biosynthetic pathways of short-chain fatty acids, known for their immunomodulatory role, revealed a differential abundance of these pathways among the specific MAGs. Among others, the cobalamin-dependent Wood-Ljungdahl pathway of acetate synthesis was directly associated with responsiveness to melanoma immunotherapy.
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Affiliation(s)
- Natalia V Zakharevich
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
| | - Maxim D Morozov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
| | - Vera A Kanaeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
- Moscow Institute of Physics and Technology, Moscow, Russian
| | - Mikhail S Filippov
- https://ror.org/04btxg914 Bioinformatics Institute, Saint Petersburg, Russian
| | - Tatyana I Zyubko
- https://ror.org/04btxg914 Bioinformatics Institute, Saint Petersburg, Russian
| | - Artem B Ivanov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
- ITMO University, Saint Petersburg, Russian
| | | | - Ksenia M Klimina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
| | - Evgenii I Olekhnovich
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
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29
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Sang Y, Zheng K, Zhao Y, Liu Y, Zhu S, Xie X, Shang L, Liu J, Li L. Efficacy and regulatory strategies of gut microbiota in immunotherapy: a narrative review. Transl Cancer Res 2024; 13:2043-2063. [PMID: 38737692 PMCID: PMC11082673 DOI: 10.21037/tcr-24-316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/29/2024] [Indexed: 05/14/2024]
Abstract
Background and Objective With advances in gut microbiome research, it has been recognized that the gut microbiome has an important and far-reaching impact on many human diseases, including cancer. Therefore, more and more researchers are focusing on the treatment of gut flora in tumors. In this article, we present a review of the mechanisms of gut microbes in tumor immunotherapy and related studies to provide reference for further research and insights into the clinical application of gut microbes. Methods Between April 25, 2023, and November 25, 2023, we searched for articles published only in English between 1984 and 2023 using the databases PubMed, American Medical Association and Elsevier ScienceDirect using the keywords "gut microbiology" and "tumor" or "immunotherapy". Key Content and Findings The gastrointestinal tract contains the largest number of microorganisms in the human body. Microorganisms are involved in regulating many physiological activities of the body. Studies have shown that gut microbes and their derivatives are involved in the occurrence and development of a variety of inflammations and tumors, and changes in their abundance and proportion affect the degree of cancer progression and sensitivity to immunotherapy. Gut microbiota-based drug research is ongoing, and some anti-tumor studies have entered the clinical trial stage. Conclusions The abundance and proportion of intestinal microorganisms influence the susceptibility of tumors to tumor immunotherapy. This article reviewed the effects and mechanisms of gut microbes on tumor immunotherapy to further explore the medical value of gut microbes in tumor immunotherapy.
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Affiliation(s)
- Yaodong Sang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Kexin Zheng
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Yulong Zhao
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yuan Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Siqiang Zhu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiaozhou Xie
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Jin Liu
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
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30
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Karaman I, Pathak A, Bayik D, Watson DC. Harnessing Bacterial Extracellular Vesicle Immune Effects for Cancer Therapy. Pathog Immun 2024; 9:56-90. [PMID: 38690563 PMCID: PMC11060327 DOI: 10.20411/pai.v9i1.657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
There are a growing number of studies linking the composition of the human microbiome to disease states and treatment responses, especially in the context of cancer. This has raised significant interest in developing microbes and microbial products as cancer immunotherapeutics that mimic or recapitulate the beneficial effects of host-microbe interactions. Bacterial extracellular vesicles (bEVs) are nano-sized, membrane-bound particles secreted by essentially all bacteria species and contain a diverse bioactive cargo of the producing cell. They have a fundamental role in facilitating interactions among cells of the same species, different microbial species, and even with multicellular host organisms in the context of colonization (microbiome) and infection. The interaction of bEVs with the immune system has been studied extensively in the context of infection and suggests that bEV effects depend largely on the producing species. They thus provide functional diversity, while also being nonreplicative, having inherent cell-targeting qualities, and potentially overcoming natural barriers. These characteristics make them highly appealing for development as cancer immunotherapeutics. Both natively secreted and engineered bEVs are now being investigated for their application as immunotherapeutics, vaccines, drug delivery vehicles, and combinations of the above, with promising early results. This suggests that both the intrinsic immunomodulatory properties of bEVs and their ability to be modified could be harnessed for the development of next-generation microbe-inspired therapies. Nonetheless, there remain major outstanding questions regarding how the observed preclinical effectiveness will translate from murine models to primates, and humans in particular. Moreover, research into the pharmacology, toxicology, and mass manufacturing of this potential novel therapeutic platform is still at early stages. In this review, we highlight the breadth of bEV interactions with host cells, focusing on immunologic effects as the main mechanism of action of bEVs currently in preclinical development. We review the literature on ongoing efforts to develop natively secreted and engineered bEVs from a variety of bacterial species for cancer therapy and finally discuss efforts to overcome outstanding challenges that remain for clinical translation.
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Affiliation(s)
- Irem Karaman
- Bahcesehir University School of Medicine, Istanbul, Turkey
| | - Asmita Pathak
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Florida
| | - Defne Bayik
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Florida
| | - Dionysios C. Watson
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Florida
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31
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Usyk M, Hayes RB, Knight R, Gonzalez A, Li H, Osman I, Weber JS, Ahn J. Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589761. [PMID: 38659744 PMCID: PMC11042335 DOI: 10.1101/2024.04.16.589761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The gut microbiome (GMB) has been associated with outcomes of immune checkpoint blockade therapy in melanoma, but there is limited consensus on the specific taxa involved, particularly across different geographic regions. We analyzed pre-treatment stool samples from 674 melanoma patients participating in a phase-III trial of adjuvant nivolumab plus ipilimumab versus nivolumab, across three continents and five regions. Longitudinal analysis revealed that GMB was largely unchanged following treatment, offering promise for lasting GMB-based interventions. In region-specific and cross-region meta-analyses, we identified pre-treatment taxonomic markers associated with recurrence, including Eubacterium, Ruminococcus, Firmicutes, and Clostridium. Recurrence prediction by these markers was best achieved across regions by matching participants on GMB compositional similarity between the intra-regional discovery and external validation sets. AUCs for prediction ranged from 0.83-0.94 (depending on the initial discovery region) for patients closely matched on GMB composition (e.g., JSD ≤0.11). This evidence indicates that taxonomic markers for prediction of recurrence are generalizable across regions, for individuals of similar GMB composition.
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Affiliation(s)
- Mykhaylo Usyk
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Richard B. Hayes
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Rob Knight
- Departments of Pediatrics, Computer Science & Engineering, and Bioengineering; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Antonio Gonzalez
- Departments of Pediatrics, Computer Science & Engineering, and Bioengineering; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Huilin Li
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Iman Osman
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
- The Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Jeffrey S. Weber
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Jiyoung Ahn
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
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32
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Zhu X, Huang X, Hu M, Sun R, Li J, Wang H, Pan X, Ma Y, Ning L, Tong T, Zhou Y, Ding J, Zhao Y, Xuan B, Fang JY, Hong J, Hon Wong JW, Zhang Y, Chen H. A specific enterotype derived from gut microbiome of older individuals enables favorable responses to immune checkpoint blockade therapy. Cell Host Microbe 2024; 32:489-505.e5. [PMID: 38513657 DOI: 10.1016/j.chom.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Immunotherapy has revolutionized cancer treatment, but inconsistent responses persist. Our study delves into the intriguing phenomenon of enhanced immunotherapy sensitivity in older individuals with cancers. Through a meta-analysis encompassing 25 small-to-mid-sized trials of immune checkpoint blockade (ICB), we demonstrate that older individuals exhibit heightened responsiveness to ICB therapy. To understand the underlying mechanism, we reanalyze single-cell RNA sequencing (scRNA-seq) data from multiple studies and unveil distinct upregulation of exhausted and cytotoxic T cell markers within the tumor microenvironment (TME) of older patients. Recognizing the potential role of gut microbiota in modulating the efficacy of immunotherapy, we identify an aging-enriched enterotype linked to improved immunotherapy outcomes in older patients. Fecal microbiota transplantation experiments in mice confirm the therapeutic potential of the aging-enriched enterotype, enhancing treatment sensitivity and reshaping the TME. Our discoveries confront the prevailing paradox and provide encouraging paths for tailoring cancer immunotherapy strategies according to an individual's gut microbiome profile.
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Affiliation(s)
- Xiaoqiang Zhu
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Centre for Oncology and Immunology, Hong Kong Science Park. Hong Kong, Hong Kong SAR, China; Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowen Huang
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Muni Hu
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rongrong Sun
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Jiantao Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Hai Wang
- Department of Endoscopy, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Xuefeng Pan
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Yanru Ma
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lijun Ning
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tianying Tong
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yilu Zhou
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jinmei Ding
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhao
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baoqin Xuan
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jason Wing Hon Wong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Centre for Oncology and Immunology, Hong Kong Science Park. Hong Kong, Hong Kong SAR, China.
| | - Youwei Zhang
- Department of Medical Oncology, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou, China.
| | - Haoyan Chen
- State Key Laboratory of Systems Medicine for Cancer, Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Zhao X, Liu S, Li S, Jiang W, Wang J, Xiao J, Chen T, Ma J, Khan MZ, Wang W, Li M, Li S, Cao Z. Unlocking the power of postbiotics: A revolutionary approach to nutrition for humans and animals. Cell Metab 2024; 36:725-744. [PMID: 38569470 DOI: 10.1016/j.cmet.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/25/2024] [Accepted: 03/10/2024] [Indexed: 04/05/2024]
Abstract
Postbiotics, which comprise inanimate microorganisms or their constituents, have recently gained significant attention for their potential health benefits. Extensive research on postbiotics has uncovered many beneficial effects on hosts, including antioxidant activity, immunomodulatory effects, gut microbiota modulation, and enhancement of epithelial barrier function. Although these features resemble those of probiotics, the stability and safety of postbiotics make them an appealing alternative. In this review, we provide a comprehensive summary of the latest research on postbiotics, emphasizing their positive impacts on both human and animal health. As our understanding of the influence of postbiotics on living organisms continues to grow, their application in clinical and nutritional settings, as well as animal husbandry, is expected to expand. Moreover, by substituting postbiotics for antibiotics, we can promote health and productivity while minimizing adverse effects. This alternative approach holds immense potential for improving health outcomes and revolutionizing the food and animal products industries.
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Affiliation(s)
- Xinjie Zhao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sumin Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wen Jiang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jingjun Wang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianyu Chen
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jiaying Ma
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Faculty of Veterinary and Animal Sciences, Department of Animal Breeding and Genetics, The University of Agriculture, Dera Ismail Khan 29220, Pakistan
| | - Wei Wang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Mengmeng Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Asnicar F, Thomas AM, Passerini A, Waldron L, Segata N. Machine learning for microbiologists. Nat Rev Microbiol 2024; 22:191-205. [PMID: 37968359 DOI: 10.1038/s41579-023-00984-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/17/2023]
Abstract
Machine learning is increasingly important in microbiology where it is used for tasks such as predicting antibiotic resistance and associating human microbiome features with complex host diseases. The applications in microbiology are quickly expanding and the machine learning tools frequently used in basic and clinical research range from classification and regression to clustering and dimensionality reduction. In this Review, we examine the main machine learning concepts, tasks and applications that are relevant for experimental and clinical microbiologists. We provide the minimal toolbox for a microbiologist to be able to understand, interpret and use machine learning in their experimental and translational activities.
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Affiliation(s)
- Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Andrew Maltez Thomas
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Andrea Passerini
- Department of Information Engineering and Computer Science, University of Trento, Trento, Italy
| | - Levi Waldron
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- Department of Epidemiology and Biostatistics, City University of New York, New York, NY, USA.
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy.
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35
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Chovet F, Passot AS, Mangon Q, Rouzaire P, Dougé A. [The circulating PD-L1: An emerging predictive biomarker for immune checkpoint inhibitors response]. Bull Cancer 2024; 111:416-427. [PMID: 38438284 DOI: 10.1016/j.bulcan.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 03/06/2024]
Abstract
Immune checkpoint inhibitors (ICI) have recently become the standard of care for many metastatic solid tumors, with considerable improvements in patient prognosis. However, a non-negligible proportion of patients does not respond to this type of treatment, making it essential to identify predictive factors of this response in order to better adapt the therapy. Among the biomarkers that have been most extensively studied in recent years, tumor PD-L1 levels come out on top, with controversial results for predicting response to ICI. The determination of circulating PD-L1 (or soluble PD-L1) in peripheral blood seems to be an interesting emerging biomarker. Indeed, several studies have investigated its prognostic value, and/or its potential predictive value of response to immunotherapy, and it would appear that there is a correlation between the level of soluble PD-L1 and the level of tumor aggressiveness and therefore prognosis. Furthermore, the results suggest that higher PD-L1 levels are associated with a poorer response to immunotherapy, although this remains to be confirmed in large-scale studies.
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Affiliation(s)
- Fanny Chovet
- Service d'oncologie médicale, CHU Gabriel-Montpied, 63000 Clermont-Ferrand, France
| | - Anne-Sophie Passot
- Service d'oncologie médicale, CHU Gabriel-Montpied, 63000 Clermont-Ferrand, France
| | - Quentin Mangon
- Service d'oncologie médicale, CHU Gabriel-Montpied, 63000 Clermont-Ferrand, France
| | - Paul Rouzaire
- Service d'histocompatibilité et d'immunogénétique, CHU Gabriel-Montpied, 63000 Clermont-Ferrand, France
| | - Aurore Dougé
- Service d'oncologie médicale, CHU Gabriel-Montpied, 63000 Clermont-Ferrand, France.
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36
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Liu B, Liu Z, Jiang T, Gu X, Yin X, Cai Z, Zou X, Dai L, Zhang B. Univariable and multivariable Mendelian randomization study identified the key role of gut microbiota in immunotherapeutic toxicity. Eur J Med Res 2024; 29:161. [PMID: 38475836 DOI: 10.1186/s40001-024-01741-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND In cancer patients receiving immune checkpoint inhibitors (ICIs), there is emerging evidence suggesting a correlation between gut microbiota and immune-related adverse events (irAEs). However, the exact roles of gut microbiota and the causal associations are yet to be clarified. METHODS To investigate this, we first conducted a univariable bi-directional two-sample Mendelian randomization (MR) analysis. Instrumental variables (IVs) for gut microbiota were retrieved from the MiBioGen consortium (18,340 participants). GWAS summary data for irAEs were gathered from an ICIs-treated cohort with 1,751 cancer patients. Various MR analysis methods, including inverse variance weighted (IVW), MR PRESSO, maximum likelihood (ML), weighted median, weighted mode, and cML-MA-BIC, were used. Furthermore, multivariable MR (MVMR) analysis was performed to account for possible influencing instrumental variables. RESULTS Our analysis identified fourteen gut bacterial taxa that were causally associated with irAEs. Notably, Lachnospiraceae was strongly associated with an increased risk of both high-grade and all-grade irAEs, even after accounting for the effect of BMI in the MVMR analysis. Akkermansia, Verrucomicrobiaceae, and Anaerostipes were found to exert protective roles in high-grade irAEs. However, Ruminiclostridium6, Coprococcus3, Collinsella, and Eubacterium (fissicatena group) were associated with a higher risk of developing high-grade irAEs. RuminococcaceaeUCG004, and DefluviitaleaceaeUCG011 were protective against all-grade irAEs, whereas Porphyromonadaceae, Roseburia, Eubacterium (brachy group), and Peptococcus were associated with an increased risk of all-grade irAEs. CONCLUSIONS Our analysis highlights a strong causal association between Lachnospiraceae and irAEs, along with some other gut microbial taxa. These findings provide potential modifiable targets for managing irAEs and warrant further investigation.
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Affiliation(s)
- Baike Liu
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zheran Liu
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Tianxiang Jiang
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiangshuai Gu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiaonan Yin
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zhaolun Cai
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiaoqiao Zou
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Lei Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, Sichuan, People's Republic of China.
| | - Bo Zhang
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
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37
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Longitudinal analysis shows how microbiome changes might influence responses to immune checkpoint blockade. Nat Med 2024; 30:644-645. [PMID: 38388842 DOI: 10.1038/s41591-024-02830-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
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38
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Gunjur A, Shao Y, Rozday T, Klein O, Mu A, Haak BW, Markman B, Kee D, Carlino MS, Underhill C, Frentzas S, Michael M, Gao B, Palmer J, Cebon J, Behren A, Adams DJ, Lawley TD. A gut microbial signature for combination immune checkpoint blockade across cancer types. Nat Med 2024; 30:797-809. [PMID: 38429524 PMCID: PMC10957475 DOI: 10.1038/s41591-024-02823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/12/2024] [Indexed: 03/03/2024]
Abstract
Immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte protein 4 (CTLA-4) can induce remarkable, yet unpredictable, responses across a variety of cancers. Studies suggest that there is a relationship between a cancer patient's gut microbiota composition and clinical response to ICB; however, defining microbiome-based biomarkers that generalize across cohorts has been challenging. This may relate to previous efforts quantifying microbiota to species (or higher taxonomic rank) abundances, whereas microbial functions are often strain specific. Here, we performed deep shotgun metagenomic sequencing of baseline fecal samples from a unique, richly annotated phase 2 trial cohort of patients with diverse rare cancers treated with combination ICB (n = 106 discovery cohort). We demonstrate that strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival relative to models built using species-rank quantifications or comprehensive pretreatment clinical factors. Through a meta-analysis of gut metagenomes from a further six comparable studies (n = 364 validation cohort), we found cross-cancer (and cross-country) validity of strain-response signatures, but only when the training and test cohorts used concordant ICB regimens (anti-PD-1 monotherapy or combination anti-PD-1 plus anti-CTLA-4). This suggests that future development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen rather than according to cancer type.
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Affiliation(s)
- Ashray Gunjur
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK.
| | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Timothy Rozday
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bastiaan W Haak
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, Netherlands
| | - Ben Markman
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Alfred Health, Melbourne, Victoria, Australia
- School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Damien Kee
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Rare Cancer Laboratory, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Matteo S Carlino
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
- Melanoma Institute of Australia, University of Sydney, Sydney, New South Wales, Australia
| | - Craig Underhill
- Border Medical Oncology and Haematology Research Unit, Albury-Wodonga Regional Cancer Centre, Albury-Wodonga, New South Wales, Australia
- Rural Medical School, University of New South Wales, Albury, New South Wales, Australia
| | - Sophia Frentzas
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
| | - Michael Michael
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Bo Gao
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
| | - Jodie Palmer
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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Wang H, Ülgen M, Trajkovski M. Importance of temperature on immuno-metabolic regulation and cancer progression. FEBS J 2024; 291:832-845. [PMID: 36152006 DOI: 10.1111/febs.16632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
Cancer immunotherapies emerge as promising strategies for restricting tumour growth. The tumour microenvironment (TME) has a major impact on the anti-tumour immune response and on the efficacy of the immunotherapies. Recent studies have linked changes in the ambient temperature with particular immuno-metabolic reprogramming and anti-cancer immune response in laboratory animals. Here, we describe the energetic balance of the organism during change in temperature, and link this to the immune alterations that could be of relevance for cancer, as well as for other human diseases. We highlight the contribution of the gut microbiota in modifying this interaction. We describe the overall metabolic response and underlying mechanisms of tumourigenesis in mouse models at varying ambient temperatures and shed light on their potential importance in developing therapeutics against cancer.
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Affiliation(s)
- Haiping Wang
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire (CMU), University of Geneva, Geneva, Switzerland
- Faculty of Medicine, Diabetes Center, University of Geneva, Geneva, Switzerland
| | - Melis Ülgen
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire (CMU), University of Geneva, Geneva, Switzerland
- Faculty of Medicine, Diabetes Center, University of Geneva, Geneva, Switzerland
| | - Mirko Trajkovski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire (CMU), University of Geneva, Geneva, Switzerland
- Faculty of Medicine, Diabetes Center, University of Geneva, Geneva, Switzerland
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40
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Björk JR, Bolte LA, Maltez Thomas A, Lee KA, Rossi N, Wind TT, Smit LM, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Spector TD, Bataille V, Segata N, Hospers GAP, Weersma RK. Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. Nat Med 2024; 30:785-796. [PMID: 38365950 PMCID: PMC10957474 DOI: 10.1038/s41591-024-02803-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/03/2024] [Indexed: 02/18/2024]
Abstract
Multiple clinical trials targeting the gut microbiome are being conducted to optimize treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these interventions, understanding gut microbiome changes during ICB is urgently needed. Here through longitudinal microbiome profiling of 175 patients treated with ICB for advanced melanoma, we show that several microbial species-level genome bins (SGBs) and pathways exhibit distinct patterns from baseline in patients achieving progression-free survival (PFS) of 12 months or longer (PFS ≥12) versus patients with PFS shorter than 12 months (PFS <12). Out of 99 SGBs that could discriminate between these two groups, 20 were differentially abundant only at baseline, while 42 were differentially abundant only after treatment initiation. We identify five and four SGBs that had consistently higher abundances in patients with PFS ≥12 and <12 months, respectively. Constructing a log ratio of these SGBs, we find an association with overall survival. Finally, we find different microbial dynamics in different clinical contexts including the type of ICB regimen, development of immune-related adverse events and concomitant medication use. Insights into the longitudinal dynamics of the gut microbiome in association with host factors and treatment regimens will be critical for guiding rational microbiome-targeted therapies aimed at enhancing ICB efficacy.
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Affiliation(s)
- Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
| | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Andrew Maltez Thomas
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Niccolo Rossi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Thijs T Wind
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Lotte M Smit
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Federica Armanini
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Francesco Asnicar
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Aitor Blanco-Miguez
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Neus Calbet-Llopart
- Department of Dermatology, Melanoma Group, Hospital Clínic Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Lisa Derosa
- Gustave Roussy Cancer Center, U1015 INSERM and Oncobiome Network, University Paris Saclay, Villejuif-Grand-Paris, France
| | - Nathalie Dhomen
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Kelly Brooks
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Mark Harries
- Department of Medical Oncology, Guys Cancer Centre, Guy's and St Thomas' NHS Trust, London, UK
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona and IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Paolo Manghi
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Richard Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Luigi Nezi
- European Institute of Oncology (Istituto Europeo di Oncologia), Milan, Italy
| | - Federica Pinto
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Miriam Potrony
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona and IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Susana Puig
- Department of Dermatology, Melanoma Group, Hospital Clínic Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | | | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Herts NHS Trust, Northwood, UK
| | - Sabrina Tamburini
- European Institute of Oncology (Istituto Europeo di Oncologia), Milan, Italy
| | - Sara Valpione
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Levi Waldron
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Laurence Zitvogel
- Gustave Roussy Cancer Center, U1015 INSERM and Oncobiome Network, University Paris Saclay, Villejuif-Grand-Paris, France
| | - Moreno Zolfo
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Elisabeth G E de Vries
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Paul Nathan
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona and IDIBAPS, University of Barcelona, Barcelona, Spain
- Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Herts NHS Trust, Northwood, UK
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Véronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, Mount Vernon Cancer Centre, Northwood, UK
- Department of Dermatology, Hemel Hempstead Hospital, West Hertfordshire NHS Trust, Hemel Hempstead, UK
| | - Nicola Segata
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
- European Institute of Oncology (Istituto Europeo di Oncologia), Milan, Italy
| | - Geke A P Hospers
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
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41
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Alves Costa Silva C, Piccinno G, Suissa D, Bourgin M, Schreibelt G, Durand S, Birebent R, Fidelle M, Sow C, Aprahamian F, Manghi P, Punčochář M, Asnicar F, Pinto F, Armanini F, Terrisse S, Routy B, Drubay D, Eggermont AMM, Kroemer G, Segata N, Zitvogel L, Derosa L, Bol KF, de Vries IJM. Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial. Nat Commun 2024; 15:1633. [PMID: 38395948 PMCID: PMC10891084 DOI: 10.1038/s41467-024-45357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Tumor immunosurveillance plays a major role in melanoma, prompting the development of immunotherapy strategies. The gut microbiota composition, influencing peripheral and tumoral immune tonus, earned its credentials among predictors of survival in melanoma. The MIND-DC phase III trial (NCT02993315) randomized (2:1 ratio) 148 patients with stage IIIB/C melanoma to adjuvant treatment with autologous natural dendritic cell (nDC) or placebo (PL). Overall, 144 patients collected serum and stool samples before and after 2 bimonthly injections to perform metabolomics (MB) and metagenomics (MG) as prespecified exploratory analysis. Clinical outcomes are reported separately. Here we show that different microbes were associated with prognosis, with the health-related Faecalibacterium prausnitzii standing out as the main beneficial taxon for no recurrence at 2 years (p = 0.008 at baseline, nDC arm). Therapy coincided with major MB perturbations (acylcarnitines, carboxylic and fatty acids). Despite randomization, nDC arm exhibited MG and MB bias at baseline: relative under-representation of F. prausnitzii, and perturbations of primary biliary acids (BA). F. prausnitzii anticorrelated with BA, medium- and long-chain acylcarnitines. Combined, these MG and MB biomarkers markedly determined prognosis. Altogether, the host-microbial interaction may play a role in localized melanoma. We value systematic MG and MB profiling in randomized trials to avoid baseline differences attributed to host-microbe interactions.
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Grants
- The MIND-DC trial was funded by ZonMw, Ministry of Health, Welfare and Sport (VWS), Stichting ATK, Miltenyi Biotec (in-kind). This work was supported by SEERAVE Foundation, European Union Horizon 2020:Project Number: 825410 and Project Acronym: ONCOBIOME, Institut National du Cancer (INCa), ANR Ileobiome - 19-CE15-0029-01, ANR RHU5 “ANR-21-RHUS-0017” IMMUNOLIFE&#x201D;, MAdCAM INCA_ 16698, Ligue contre le cancer, LABEX OncoImmunology, la direction generale de l&#x2019;offre de soins (DGOS), Universite Paris-Sud, SIRIC SOCRATE (INCa/DGOS/INSERM 6043), and PACRI network. G.K. is supported by the Ligue contre le Cancer (équipe labellis&#x00E9;e); Agence National de la Recherche (ANR) – Projets blancs; AMMICa US23/CNRS UMS3655; Association pour la recherche sur le cancer (ARC); Canc&#x00E9;rop&#x00F4;le Ile-de-France; Fondation pour la Recherche M&#x00E9;dicale (FRM); a donation by Elior; Equipex Onco-Pheno-Screen; European Joint Programme on Rare Diseases (EJPRD); European Research Council Advanced Investigator Award (ERC-2021-ADG, ICD-Cancer, Grant No. 101052444), European Union Horizon 2020 Projects Oncobiome, Prevalung (grant No. 101095604) and Crimson; Fondation Carrefour; Institut National du Cancer (INCa); Institut Universitaire de France; LabEx Immuno-Oncology (ANR-18-IDEX-0001); a Cancer Research ASPIRE Award from the Mark Foundation; the RHU Immunolife; Seerave Foundation; SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE); and SIRIC Cancer Research and Personalized Medicine (CARPEM). This study contributes to the IdEx Universit&#x00E9; de Paris ANR-18-IDEX-0001. This work is supported by the Prism project funded by the Agence Nationale de la Recherche under grant number ANR-18-IBHU-0002. CACS was funded by MSD Avenir. MF is funded by SEERAVE Foundation and MERCK Foundation. LD and BR were supported by Philantropia at Gustave Roussy Foundation.
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Affiliation(s)
- Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Gianmarco Piccinno
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Déborah Suissa
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Mélanie Bourgin
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Gerty Schreibelt
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Roxanne Birebent
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Marine Fidelle
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Cissé Sow
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Fanny Aprahamian
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
| | - Paolo Manghi
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michal Punčochář
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Asnicar
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Safae Terrisse
- Oncology Department, Assistance Publique Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, Paris, France
| | - Bertrand Routy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, QC, Canada
| | - Damien Drubay
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Office of Biostatistics and Epidemiology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Inserm, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif, France
| | - Alexander M M Eggermont
- Princess Máxima Center and University Medical Center Utrecht, 3584 CS Utrecht, The Netherlands
- Comprehensive Cancer Center Munich, Technical University Munich & Ludwig Maximiliaan University, Munich, Germany
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM U1138, Équipe Labellisée - Ligue Nationale contre le Cancer, Université Paris Cité, Sorbonne Université, Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France.
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France.
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France.
- Center of Clinical Investigations BIOTHERIS, INSERM CIC1428, Villejuif, France.
| | - Lisa Derosa
- Gustave Roussy Cancer Campus (GRCC), ClinicObiome, Villejuif Cedex, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicêtre, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Équipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
| | - Kalijn F Bol
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherlands
| | - I Jolanda M de Vries
- Medical BioSciences, Radboud Institute for Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
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Austin GI, Kav AB, Park H, Biermann J, Uhlemann AC, Korem T. Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579716. [PMID: 38405914 PMCID: PMC10888995 DOI: 10.1101/2024.02.09.579716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Every step in common microbiome profiling protocols has variable efficiency for each microbe. For example, different DNA extraction kits may have different efficiency for Gram-positive and -negative bacteria. These variable efficiencies, combined with technical variation, create strong processing biases, which impede the identification of signals that are reproducible across studies and the development of generalizable and biologically interpretable prediction models. "Batch-correction" methods have been used to alleviate these issues computationally with some success. However, many make strong parametric assumptions which do not necessarily apply to microbiome data or processing biases, or require the use of an outcome variable, which risks overfitting. Lastly and importantly, existing transformations used to correct microbiome data are largely non-interpretable, and could, for example, introduce values to features that were initially mostly zeros. Altogether, processing bias currently compromises our ability to glean robust and generalizable biological insights from microbiome data. Here, we present DEBIAS-M (Domain adaptation with phenotype Estimation and Batch Integration Across Studies of the Microbiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using benchmarks of HIV and colorectal cancer classification from gut microbiome data, and cervical neoplasia prediction from cervical microbiome data, we demonstrate that DEBIAS-M outperforms batch-correction methods commonly used in the field. Notably, we show that the inferred bias-correction factors are stable, interpretable, and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M allows for better modeling of microbiome data and identification of interpretable signals that are reproducible across studies.
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Affiliation(s)
- George I. Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aya Brown Kav
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Jana Biermann
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
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43
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Lu YQ, Qiao H, Tan XR, Liu N. Broadening oncological boundaries: the intratumoral microbiota. Trends Microbiol 2024:S0966-842X(24)00007-6. [PMID: 38310023 DOI: 10.1016/j.tim.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 02/05/2024]
Abstract
The microbiota of solid tumors was identified >100 years ago; however, heterogeneous composition and diversity have been revealed only recently. Growing evidence has suggested that several functional mechanisms of the intratumoral microbiota affect tumorigenesis and progression, suggesting that the intratumoral microbiota is a promising biomarker for multiple cancers. The low biomass of the intratumoral microbiota poses a major challenge to related research, thus necessitating the use of a multiple-modality integrated framework to resolve this dilemma. Advanced techniques such as single-cell sequencing provide significant clues, and the gradual optimization of functional experiments and culture-based methods enables deeper investigation of the underlying mechanisms involved. In this review, we outline the current state of research on the intratumoral microbiota and describe the challenges and comprehensive strategies for future research.
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Affiliation(s)
- Ying-Qi Lu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Han Qiao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Xi-Rong Tan
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Na Liu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China.
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44
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Jiang H, Zhang Q. Gut microbiota influences the efficiency of immune checkpoint inhibitors by modulating the immune system (Review). Oncol Lett 2024; 27:87. [PMID: 38249807 PMCID: PMC10797324 DOI: 10.3892/ol.2024.14221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) are commonly utilized in tumor treatment. However, they still have limitations, including insufficient effectiveness and unavoidable adverse events. It has been demonstrated that gut microbiota can influence the effectiveness of ICIs, although the precise mechanism remains unclear. Gut microbiota plays a crucial role in the formation and development of the immune system. Gut microbiota and their associated metabolites play a regulatory role in immune balance. Tumor occurrence and development are linked to their ability to evade recognition and destruction by the immune system. The purpose of ICIs treatment is to reinitiate the immune system's elimination of tumor cells. Thus, the immune system acts as a communication bridge between gut microbiota and ICIs. Varied composition and characteristics of gut microbiota result in diverse outcomes in ICIs treatment. Certain gut microbiota-related metabolites also influence the therapeutic efficacy of ICIs to some extent. The administration of antibiotics before or during ICIs treatment can diminish treatment effectiveness. The utilization of probiotics and fecal transplantation can partially alter the outcome of ICIs treatment. The present review synthesized previous studies to examine the association between gut microbiota and ICIs, elucidated the role of gut microbiota and its associated factors in ICIs treatment, and offered direction for future research.
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Affiliation(s)
- Haihong Jiang
- Department of Oncology, Huaihe Hospital of Henan University, Kaifeng, Henan 475001, P.R. China
| | - Qinlu Zhang
- Department of Endocrinology, Huaihe Hospital of Henan University, Kaifeng, Henan 475001, P.R. China
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45
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Yang Y, An Y, Dong Y, Chu Q, Wei J, Wang B, Cao H. Fecal microbiota transplantation: no longer cinderella in tumour immunotherapy. EBioMedicine 2024; 100:104967. [PMID: 38241975 PMCID: PMC10831174 DOI: 10.1016/j.ebiom.2024.104967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/08/2023] [Accepted: 01/02/2024] [Indexed: 01/21/2024] Open
Abstract
The incidence of cancer has shown a great increase during the past decades and poses tough challenges to cancer treatment. Anti-tumour immunotherapy, represented by immune checkpoint inhibitors (ICIs), possesses favorable remission in unrestricted spectrum of cancer types. However, its efficacy seems to be heterogeneous among accumulating studies. Emerging evidences suggest that gut microbiota can modulate anti-tumour immuno-response and predict clinical prognosis. Therefore, remodeling microbiota characteristics with fecal microbiota transplantation (FMT) may be capable of reinforcing host ICIs performance by regulating immune-tumour cell interactions and altering microbial metabolites, thereby imperceptibly shifting the tumour microenvironment. However, the long-term safety of FMT is under concern, which calls for more rigorous screening. In this review, we examine current experimental and clinical evidences supporting the FMT efficacy in boosting anti-tumour immuno-response and lessening tumour-related complications. Moreover, we discuss the challenges in FMT and propose feasible resolutions, which may offer crucial guidance for future clinical operations.
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Affiliation(s)
- Yunwei Yang
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin, China
| | - Yaping An
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin, China
| | - Yue Dong
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin, China
| | - Qiao Chu
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin, China
| | - Jingge Wei
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin, China.
| | - Hailong Cao
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin, China.
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46
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Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G. mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. Nat Methods 2024; 21:236-246. [PMID: 38177508 DOI: 10.1038/s41592-023-02125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.
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Affiliation(s)
- Lei Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan Tourancheau
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Ksiezarek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tonny Koo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Gitman
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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47
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Verdegaal AA, Goodman AL. Integrating the gut microbiome and pharmacology. Sci Transl Med 2024; 16:eadg8357. [PMID: 38295186 DOI: 10.1126/scitranslmed.adg8357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024]
Abstract
The gut microbiome harbors trillions of organisms that contribute to human health and disease. These bacteria can also affect the properties of medical drugs used to treat these diseases, and drugs, in turn, can reshape the microbiome. Research addressing interdependent microbiome-host-drug interactions thus has broad impact. In this Review, we discuss these interactions from the perspective of drug bioavailability, absorption, metabolism, excretion, toxicity, and drug-mediated microbiome modulation. We survey approaches that aim to uncover the mechanisms underlying these effects and opportunities to translate this knowledge into new strategies to improve the development, administration, and monitoring of medical drugs.
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Affiliation(s)
- Andrew A Verdegaal
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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48
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Ganguly D. Multi-omics studies in interpreting the evolving standard model for immune functions. Brief Funct Genomics 2024; 23:75-81. [PMID: 36905355 DOI: 10.1093/bfgp/elad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 03/12/2023] Open
Abstract
A standard model that is able to generalize data on myriad involvement of the immune system in organismal physio-pathology and to provide a unified evolutionary teleology for immune functions in multicellular organisms remains elusive. A number of such 'general theories of immunity' have been proposed based on contemporaneously available data, starting with the usual description of self-nonself discrimination, followed by the 'danger model' and the more recent 'discontinuity theory.' More recent data deluge on involvement of immune mechanisms in a wide variety of clinical contexts, a number of which fail to get readily accommodated into the available teleologic standard models, makes deriving a standard model of immunity more challenging. But technological advances enabling multi-omics investigations into an ongoing immune response, covering genome, epigenome, coding and regulatory transcriptome, proteome, metabolome and tissue-resident microbiome, bring newer opportunities for developing a more integrative insight into immunocellular mechanisms within different clinical contexts. The new ability to map the heterogeneity of composition, trajectory and endpoints of immune responses, in both health and disease, also necessitates incorporation into the potential standard model of immune functions, which again can only be achieved through multi-omics probing of immune responses and integrated analyses of the multi-dimensional data.
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Affiliation(s)
- Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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49
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Cheng S, Han Z, Dai D, Li F, Zhang X, Lu M, Lu Z, Wang X, Zhou J, Li J, Guo X, Song P, Qiu C, Shen W, Zhang Q, Zhu N, Wang X, Tan Y, Kou Y, Yin X, Shen L, Peng Z. Multi-omics of the gut microbial ecosystem in patients with microsatellite-instability-high gastrointestinal cancer resistant to immunotherapy. Cell Rep Med 2024; 5:101355. [PMID: 38194971 PMCID: PMC10829783 DOI: 10.1016/j.xcrm.2023.101355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/17/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Despite the encouraging efficacy of anti-PD-1/PD-L1 immunotherapy in microsatellite-instability-high/deficient mismatch repair (MSI-H/dMMR) advanced gastrointestinal cancer, many patients exhibit primary or acquired resistance. Using multi-omics approaches, we interrogate gut microbiome, blood metabolome, and cytokines/chemokines of patients with MSI-H/dMMR gastrointestinal cancer (N = 77) at baseline and during the treatment. We identify a number of microbes (e.g., Porphyromonadaceae) and metabolites (e.g., arginine) highly associated with primary resistance to immunotherapy. An independent validation cohort (N = 39) and mouse model are used to further confirm our findings. A predictive machine learning model for primary resistance is also built and achieves an accuracy of 0.79 on the external validation set. Furthermore, several microbes are pinpointed that gradually changed during the process of acquired resistance. In summary, our study demonstrates the essential role of gut microbiome in drug resistance, and this can be utilized as a preventative diagnosis tool and therapeutic target in the future.
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Affiliation(s)
- Siyuan Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Department of Medical Oncology and Radiation Sickness, Peking University Third Hospital, Beijing 100191, China
| | - Zihan Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Department of Colorectal Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Die Dai
- Xbiome, Shenzhen 518055, China
| | - Fang Li
- Xbiome, Shenzhen 518055, China
| | - Xiaotian Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ming Lu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhihao Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xicheng Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jun Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaohuan Guo
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Panwei Song
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing 100084, China
| | | | | | | | | | - Xi Wang
- Xbiome, Shenzhen 518055, China
| | - Yan Tan
- Xbiome, Shenzhen 518055, China
| | - Yan Kou
- Xbiome, Shenzhen 518055, China
| | | | - Lin Shen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China.
| | - Zhi Peng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China.
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50
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Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. CELL GENOMICS 2024; 4:100444. [PMID: 38190106 PMCID: PMC10794784 DOI: 10.1016/j.xgen.2023.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/12/2023] [Accepted: 10/24/2023] [Indexed: 01/09/2024]
Abstract
Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.
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Affiliation(s)
- Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA
| | - Catherine J Wu
- Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02138, USA; The Ludwig Center at Harvard, Boston, MA 02115, USA.
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