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Robinson I, Hochmair MJ, Schmidinger M, Absenger G, Pichler M, Nguyen VA, Richtig E, Rainer BM, Ay L, Jansen C, Pacífico C, Knabl A, Sladek B, Gasche N, Valipour A. Assessing the Performance of a Novel Stool-Based Microbiome Test That Predicts Response to First Line Immune Checkpoint Inhibitors in Multiple Cancer Types. Cancers (Basel) 2023; 15:3268. [PMID: 37444378 DOI: 10.3390/cancers15133268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
The intestinal microbiome is by now an undebatable key player in the clinical outcome of ICI therapies. However, no microbiome profiling method to aid therapy decision is yet validated. We conducted a multi-centric study in patients with stage III/IV melanoma, NSCLC, or RCC receiving ICI treatment. The stool microbiome profile of 63 patients was analyzed with BiomeOne®, a microbiome-based algorithm that anticipates whether a patient will achieve clinical benefit with ICIs prior to therapy initiation. Classification of patient samples as Rs and NRs was achieved with a sensitivity of 81% and a specificity of 50% in this validation cohort. An ICI-favorable response was characterized by an intestinal microbiome rich in bacteria such as Oscillospira sp., Clostridia UCG-014, Lachnospiraceae UCG-010 sp., Prevotella copri, and a decrease in Sutterella sp., Lactobacillales, and Streptococcus sp. Patients who developed immune-related adverse events (irAEs) had an overall increased microbial diversity and richness, and a stool microbiome depleted in Agathobacter. When compared with the programmed death-ligand 1 (PD-L1) expression test in the subcohort of NSCLC patients (n = 38), BiomeOne® exhibited a numerically higher sensitivity (78.6%) in identifying responders when compared with the PD-L1 test (67.9%). This study provides an evaluation of BiomeOne®, the first microbiome-based test for prediction of ICI response, to achieve market authorization. Validation with further indications and expansion to other microbiome-based interventions will be essential to bring microbiome-based diagnostics into standard clinical practice.
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Affiliation(s)
- Irina Robinson
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
| | - Maximilian Johannes Hochmair
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
| | - Manuela Schmidinger
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Gudrun Absenger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036 Graz, Austria
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036 Graz, Austria
| | - Van Anh Nguyen
- Department of Dermatology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Erika Richtig
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria
| | | | - Leyla Ay
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
| | | | | | | | | | | | - Arschang Valipour
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
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Brezina S, Borkovec M, Baierl A, Bastian F, Futschik A, Gasche N, Gruenberger T, Hallas M, Jannsen C, Leeb G, Lutz R, Sladek B, Gsur A. Using fecal immmunochemical cartridges for gut microbiome analysis within a colorectal cancer screening program. Gut Microbes 2023; 15:2176119. [PMID: 36794815 PMCID: PMC9980522 DOI: 10.1080/19490976.2023.2176119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
The colorectal cancer (CRC) screening program B-PREDICT is an invited two-stage screening project using a fecal immunochemical test (FIT) for initial screening followed by a colonoscopy for those with a positive FIT. Since the gut microbiome likely plays a role in the etiology of CRC, microbiome-based biomarkers in combination with FIT could be a promising tool for optimizing CRC screening. Therefore, we evaluated the usability of FIT cartridges for microbiome analysis and compared it to Stool Collection and Preservation Tubes. Corresponding FIT cartridges as well as Stool Collection and Preservation Tubes were collected from participants of the B-PREDICT screening program to perform 16S rRNA gene sequencing. We calculated intraclass correlation coefficients (ICCs) based on center log ratio transformed abundances and used ALDEx2 to test for significantly differential abundant taxa between the two sample types. Additionally, FIT and Stool Collection and Preservation Tube triplicate samples were obtained from volunteers to estimate variance components of microbial abundances. FIT and Preservation Tube samples produce highly similar microbiome profiles which cluster according to subject. Significant differences between the two sample types can be found for abundances of some bacterial taxa (e.g. 33 genera) but are minor compared to the differences between the subjects. Analysis of triplicate samples revealed slightly worse repeatability of results for FIT than for Preservation Tube samples. Our findings indicate that FIT cartridges are appropriate for gut microbiome analysis nested within CRC screening programs.
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Affiliation(s)
- Stefanie Brezina
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Martin Borkovec
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, Vienna, Austria
| | | | - Andreas Futschik
- Department of Applied Statistics, Johannes Kepler University Linz, Linz, Austria
| | | | | | - Michael Hallas
- Institute of Pathology and Bacteriology, Clinic Favoriten, Vienna, Austria
| | | | - Gernot Leeb
- Department of Internal Medicine, Hospital Oberpullendorf, Oberpullendorf, Austria
| | - Rebecca Lutz
- Department of Surgery, Clinic Favoriten, Vienna, Austria
| | | | - Andrea Gsur
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria,CONTACT Andrea Gsur Center for Cancer Research, Medical University of Vienna, Vienna, Austria
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Baumgartner M, Zirnbauer R, Schlager S, Mertens D, Gasche N, Sladek B, Herbold C, Bochkareva O, Emelianenko V, Vogelsang H, Lang M, Klotz A, Moik B, Makristathis A, Berry D, Dabsch S, Khare V, Gasche C. Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes 2022; 14:2143218. [PMID: 36415023 PMCID: PMC9704410 DOI: 10.1080/19490976.2022.2143218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic E. coli (aEPEC) with IBD disease activity. The presence of diarrheagenic E. coli was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins espV and espG2 distinguish aEPEC cultured from UC and Crohn's disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune-microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.
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Affiliation(s)
- Maximilian Baumgartner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Rebecca Zirnbauer
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Sabine Schlager
- National Reference Laboratory for Escherichia coli, Austrian Agency for Health and Food Safety, Graz, Austria
| | - Daniel Mertens
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | | | | | - Craig Herbold
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Olga Bochkareva
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Vera Emelianenko
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Harald Vogelsang
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Michaela Lang
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria,Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Anton Klotz
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Birgit Moik
- National Reference Laboratory for Escherichia coli, Austrian Agency for Health and Food Safety, Graz, Austria
| | - Athanasios Makristathis
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria,Division of Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria,Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Stefanie Dabsch
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Vineeta Khare
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Christoph Gasche
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria,CONTACT Christoph Gasche Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, Vienna, A-1090Austria
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Robinson I, Schmidinger M, Hochmair M, Ay L, Absenger G, Pichler M, Nguyen V, Richtig E, Rainer B, Jansen C, Sladek B, Knabl A, Gasche N, Valipour A. 117P BiomeOne: Multi-centric validation of a novel microbiome-based biomarker to predict response to cancer immunotherapy. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Hochmair M, Absenger G, Ay L, Robinson I, Jansen C, Sladek B, Knabl A, Gasche N, Valipou A. EP16.01-015 Introducing "BiomeOne” a Microbiome-based bBiomarker to Predict Immune Checkpoint Inhibitor Response in NSCLC 1patients. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.1015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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