1
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Elkrief A, Waters NR, Smith N, Dai A, Slingerland J, Aleynick N, Febles B, Gogia P, Socci ND, Lumish M, Giardina PA, Chaft JE, Eng J, Motzer RJ, Mendelsohn RB, Markey KA, Zhuang M, Li Y, Yang Z, Hollmann TJ, Rudin CM, van den Brink MR, Shia J, DeWolf S, Schoenfeld AJ, Hellmann MD, Babady NE, Faleck DM, Peled JU. Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation. Cancer Immunol Res 2024; 12:308-321. [PMID: 38108398 PMCID: PMC10932930 DOI: 10.1158/2326-6066.cir-23-0498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/08/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Colitis induced by treatment with immune-checkpoint inhibitors (ICI), termed irColitis, is a substantial cause of morbidity complicating cancer treatment. We hypothesized that abnormal fecal microbiome features would be present at the time of irColitis onset and that restoring the microbiome with fecal transplant from a healthy donor would mitigate disease severity. Herein, we present fecal microbiota profiles from 18 patients with irColitis from a single center, 5 of whom were treated with healthy-donor fecal microbial transplantation (FMT). Although fecal samples collected at onset of irColitis had comparable α-diversity to that of comparator groups with gastrointestinal symptoms, irColitis was characterized by fecal microbial dysbiosis. Abundances of Proteobacteria were associated with irColitis in multivariable analyses. Five patients with irColitis refractory to steroids and biologic anti-inflammatory agents received healthy-donor FMT, with initial clinical improvement in irColitis symptoms observed in four of five patients. Two subsequently exhibited recurrence of irColitis symptoms following courses of antibiotics. Both received a second "salvage" FMT that was, again, followed by clinical improvement of irColitis. In summary, we observed distinct microbial community changes that were present at the time of irColitis onset. FMT was followed by clinical improvements in several cases of steroid- and biologic-agent-refractory irColitis. Strategies to restore or prevent microbiome dysbiosis in the context of immunotherapy toxicities should be further explored in prospective clinical trials.
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Affiliation(s)
- Arielle Elkrief
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas R. Waters
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Natalie Smith
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angel Dai
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John Slingerland
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nathan Aleynick
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Binita Febles
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pooja Gogia
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas D. Socci
- Bioinformatics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melissa Lumish
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul A. Giardina
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamie E. Chaft
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Juliana Eng
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Robert J. Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Robin B. Mendelsohn
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Kate A. Markey
- Fred Hutchinson Cancer Center, Seattle, Washington; Division of Medical Oncology, University of Washington, Seattle, Washington
| | - Mingqiang Zhuang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanyun Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zhifan Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Travis J. Hollmann
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bristol Myers Squibb, Princeton, NJ, USA
| | - Charles M. Rudin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Marcel R.M. van den Brink
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Susan DeWolf
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Adam J. Schoenfeld
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Matthew D. Hellmann
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - N. Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine and the Infectious Disease Service, Department of Medicine Memorial Sloan Kettering Cancer Center, New York, NY
| | - David M. Faleck
- Gastroenterology, Hepatology & Nutrition Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Jonathan U. Peled
- Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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2
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Lindner S, Miltiadous O, Ramos RJF, Paredes J, Kousa AI, Dai A, Fei T, Lauder E, Frame J, Waters NR, Sadeghi K, Armijo GK, Ghale R, Victor K, Gipson B, Monette S, Russo MV, Nguyen CL, Slingerland J, Taur Y, Markey KA, Andrlova H, Giralt S, Perales MA, Reddy P, Peled JU, Smith M, Cross JR, Burgos da Silva M, Campbell C, van den Brink MRM. Altered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease. Nat Microbiol 2024; 9:614-630. [PMID: 38429422 DOI: 10.1038/s41564-024-01617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024]
Abstract
Microbial transformation of bile acids affects intestinal immune homoeostasis but its impact on inflammatory pathologies remains largely unknown. Using a mouse model of graft-versus-host disease (GVHD), we found that T cell-driven inflammation decreased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and reduced the levels of unconjugated and microbe-derived bile acids. Several microbe-derived bile acids attenuated farnesoid X receptor (FXR) activation, suggesting that loss of these metabolites during inflammation may increase FXR activity and exacerbate the course of disease. Indeed, mortality increased with pharmacological activation of FXR and decreased with its genetic ablation in donor T cells during mouse GVHD. Furthermore, patients with GVHD after allogeneic hematopoietic cell transplantation showed similar loss of BSH and the associated reduction in unconjugated and microbe-derived bile acids. In addition, the FXR antagonist ursodeoxycholic acid reduced the proliferation of human T cells and was associated with a lower risk of GVHD-related mortality in patients. We propose that dysbiosis and loss of microbe-derived bile acids during inflammation may be an important mechanism to amplify T cell-mediated diseases.
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Affiliation(s)
- Sarah Lindner
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oriana Miltiadous
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ruben J F Ramos
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Paredes
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anastasia I Kousa
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anqi Dai
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emma Lauder
- Transplantation and Cell Therapy Program, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - John Frame
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas R Waters
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keimya Sadeghi
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gabriel K Armijo
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romina Ghale
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristen Victor
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brianna Gipson
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastien Monette
- Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marco Vincenzo Russo
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Chi L Nguyen
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Taur
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kate A Markey
- Division of Medical Oncology, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hana Andrlova
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergio Giralt
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Pavan Reddy
- Transplantation and Cell Therapy Program, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Jonathan U Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Melody Smith
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina Burgos da Silva
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Clarissa Campbell
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Marcel R M van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, USA.
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA, USA.
- Comprehensive Cancer Center, City of Hope, Los Angeles, CA, USA.
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3
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Fei T, Funnell T, Waters NR, Raj SS, Sadeghi K, Dai A, Miltiadous O, Shouval R, Lv M, Peled JU, Ponce DM, Perales MA, Gönen M, van den Brink MRM. Enhanced Feature Selection for Microbiome Data using FLORAL: Scalable Log-ratio Lasso Regression. bioRxiv 2023:2023.05.02.538599. [PMID: 37205350 PMCID: PMC10187229 DOI: 10.1101/2023.05.02.538599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Identifying predictive biomarkers of patient outcomes from high-throughput microbiome data is of high interest, while existing computational methods do not satisfactorily account for complex survival endpoints, longitudinal samples, and taxa-specific sequencing biases. We present FLORAL (https://vdblab.github.io/FLORAL/), an open-source computational tool to perform scalable log-ratio lasso regression and microbial feature selection for continuous, binary, time-to-event, and competing risk outcomes, with compatibility of longitudinal microbiome data as time-dependent covariates. The proposed method adapts the augmented Lagrangian algorithm for a zero-sum constraint optimization problem while enabling a two-stage screening process for extended false-positive control. In extensive simulation and real-data analyses, FLORAL achieved consistently better false-positive control compared to other lasso-based approaches, and better sensitivity over popular differential abundance testing methods for datasets with smaller sample size. In a survival analysis in allogeneic hematopoietic-cell transplant, we further demonstrated considerable improvement by FLORAL in microbial feature selection by utilizing longitudinal microbiome data over only using baseline microbiome data.
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Affiliation(s)
- Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center
| | - Tyler Funnell
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Nicholas R. Waters
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Sandeep S. Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Keimya Sadeghi
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Anqi Dai
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | | | - Roni Shouval
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center
- Department of Medicine, Weill Cornell Medical College
| | - Meng Lv
- Institute of Hematology, Peking University People’s Hospital
| | - Jonathan U. Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center
- Department of Medicine, Weill Cornell Medical College
| | - Doris M. Ponce
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center
- Department of Medicine, Weill Cornell Medical College
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center
- Department of Medicine, Weill Cornell Medical College
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center
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4
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DeWolf S, Elhanati Y, Nichols K, Waters NR, Nguyen CL, Slingerland JB, Rodriguez N, Lyudovyk O, Giardina PA, Kousa AI, Andrlová H, Ceglia N, Fei T, Kappagantula R, Li Y, Aleynick N, Baez P, Murali R, Hayashi A, Lee N, Gipson B, Rangesa M, Katsamakis Z, Dai A, Blouin AG, Arcila M, Masilionis I, Chaligne R, Ponce DM, Landau HJ, Politikos I, Tamari R, Hanash AM, Jenq RR, Giralt SA, Markey KA, Zhang Y, Perales MA, Socci ND, Greenbaum BD, Iacobuzio-Donahue CA, Hollmann TJ, van den Brink MR, Peled JU. Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse. Sci Transl Med 2023; 15:eabq0476. [PMID: 37494469 PMCID: PMC10758167 DOI: 10.1126/scitranslmed.abq0476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/06/2023] [Indexed: 07/28/2023]
Abstract
T cells are the central drivers of many inflammatory diseases, but the repertoire of tissue-resident T cells at sites of pathology in human organs remains poorly understood. We examined the site-specificity of T cell receptor (TCR) repertoires across tissues (5 to 18 tissues per patient) in prospectively collected autopsies of patients with and without graft-versus-host disease (GVHD), a potentially lethal tissue-targeting complication of allogeneic hematopoietic cell transplantation, and in mouse models of GVHD. Anatomic similarity between tissues was a key determinant of TCR repertoire composition within patients, independent of disease or transplant status. The T cells recovered from peripheral blood and spleens in patients and mice captured a limited portion of the TCR repertoire detected in tissues. Whereas few T cell clones were shared across patients, motif-based clustering revealed shared repertoire signatures across patients in a tissue-specific fashion. T cells at disease sites had a tissue-resident phenotype and were of donor origin based on single-cell chimerism analysis. These data demonstrate the complex composition of T cell populations that persist in human tissues at the end stage of an inflammatory disorder after lymphocyte-directed therapy. These findings also underscore the importance of studying T cell in tissues rather than blood for tissue-based pathologies and suggest the tissue-specific nature of both the endogenous and posttransplant T cell landscape.
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Affiliation(s)
- Susan DeWolf
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuval Elhanati
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine Nichols
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas R. Waters
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chi L. Nguyen
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John B. Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natasia Rodriguez
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olga Lyudovyk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul A. Giardina
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anastasia I. Kousa
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hana Andrlová
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nick Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rajya Kappagantula
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center; New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyun Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nathan Aleynick
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Priscilla Baez
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Akimasa Hayashi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Kyorin University, Mitaka City, Tokyo, Japan
| | - Nicole Lee
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brianna Gipson
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Madhumitha Rangesa
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zoe Katsamakis
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anqi Dai
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amanda G. Blouin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ignas Masilionis
- Program for Computational and System Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Program for Computational and System Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Doris M. Ponce
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Heather J. Landau
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Ioannis Politikos
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Roni Tamari
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Alan M. Hanash
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert R. Jenq
- Departments of Genomic Medicine and Stem Cell Transplantation Cellular Therapy, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergio A. Giralt
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Kate A. Markey
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Medical Oncology, University of Washington; Seattle, WA, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Nicholas D. Socci
- Bioinformatics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Travis J. Hollmann
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Bristol Myers Squibb, Lawrenceville, NJ 08540
| | - Marcel R.M. van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Jonathan U. Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
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5
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Shouval R, Waters NR, Gomes ALC, Zuanelli Brambilla C, Fei T, Devlin SM, Nguyen CL, Markey KA, Dai A, Slingerland JB, Clurman AG, Fontana E, Amoretti LA, Wright RJ, Hohl TM, Taur Y, Sung AD, Weber D, Hashimoto D, Teshima T, Chao NJ, Holler E, Scordo M, Giralt SA, Perales MA, Peled JU, van den Brink MRM. Conditioning Regimens are Associated with Distinct Patterns of Microbiota Injury in Allogeneic Hematopoietic Cell Transplantation. Clin Cancer Res 2023; 29:165-173. [PMID: 36322005 PMCID: PMC9812902 DOI: 10.1158/1078-0432.ccr-22-1254] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/13/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022]
Abstract
PURPOSE The gut microbiota is subject to multiple insults in allogeneic hematopoietic cell transplantation (allo-HCT) recipients. We hypothesized that preparative conditioning regimens contribute to microbiota perturbation in allo-HCT. EXPERIMENTAL DESIGN This was a retrospective study that evaluated the relationship between conditioning regimens exposure in 1,188 allo-HCT recipients and the gut microbiome. Stool samples collected from 20 days before transplantation up to 30 days after were profiled using 16S rRNA sequencing. Microbiota injury was quantified by changes in α-diversity. RESULTS We identified distinct patterns of microbiota injury that varied by conditioning regimen. Diversity loss was graded into three levels of conditioning-associated microbiota injury (CMBI) in a multivariable model that included antibiotic exposures. High-intensity regimens, such as total body irradiation (TBI)-thiotepa-cyclophosphamide, were associated with the greatest injury (CMBI III). In contrast, the nonmyeloablative regimen fludarabine-cyclophosphamide with low-dose TBI (Flu/Cy/TBI200) had a low-grade injury (CMBI I). The risk of acute GVHD correlated with CMBI degree. Pretransplant microbial compositions were best preserved with Flu/Cy/TBI200, whereas other regimens were associated with loss of commensal bacteria and expansion of Enterococcus. CONCLUSIONS Our findings support an interaction between conditioning at the regimen level and the extent of microbiota injury.
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Affiliation(s)
- Roni Shouval
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nicholas R. Waters
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio L. C. Gomes
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Corrado Zuanelli Brambilla
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Hematology Unit, Department of Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean M. Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chi L. Nguyen
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kate A. Markey
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anqi Dai
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John B Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Annelie G Clurman
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Fontana
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luigi A Amoretti
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roberta J Wright
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias M Hohl
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Taur
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony D. Sung
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Daniela Weber
- Department of Internal Medicine, University Medical Center, University of Regensburg, Regensburg, Germany
| | - Daigo Hashimoto
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Nelson J. Chao
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ernst Holler
- Department of Internal Medicine, University Medical Center, University of Regensburg, Regensburg, Germany
| | - Michael Scordo
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sergio A. Giralt
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jonathan U. Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marcel R. M. van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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6
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Miltiadous O, Waters NR, Andrlová H, Dai A, Nguyen CL, Burgos da Silva M, Lindner S, Slingerland J, Giardina P, Clurman A, Armijo GK, Gomes ALC, Lakkaraja M, Maslak P, Scordo M, Shouval R, Staffas A, O'Reilly R, Taur Y, Prockop S, Boelens JJ, Giralt S, Perales MA, Devlin SM, Peled JU, Markey KA, van den Brink MRM. Early intestinal microbial features are associated with CD4 T-cell recovery after allogeneic hematopoietic transplant. Blood 2022; 139:2758-2769. [PMID: 35061893 PMCID: PMC9074404 DOI: 10.1182/blood.2021014255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022] Open
Abstract
Low intestinal microbial diversity is associated with poor outcomes after allogeneic hematopoietic cell transplantation (HCT). Using 16S rRNA sequencing of 2067 stool samples and flow cytometry data from 2370 peripheral blood samples drawn from 894 patients who underwent allogeneic HCT, we have linked features of the early post-HCT microbiome with subsequent immune cell recovery. We examined lymphocyte recovery and microbiota features in recipients of both unmodified and CD34-selected allografts. We observed that fecal microbial diversity was an independent predictor of CD4 T-cell count 3 months after HCT in recipients of a CD34-selected allograft, who are dependent on de novo lymphopoiesis for their immune recovery. In multivariate models using clinical factors and microbiota features, we consistently observed that increased fecal relative abundance of genus Staphylococcus during the early posttransplant period was associated with worse CD4 T-cell recovery. Our observations suggest that the intestinal bacteria, or the factors they produce, can affect early lymphopoiesis and the homeostasis of allograft-derived T cells after transplantation.
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Affiliation(s)
- Oriana Miltiadous
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas R Waters
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Hana Andrlová
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Anqi Dai
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Chi L Nguyen
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Marina Burgos da Silva
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Sarah Lindner
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - John Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Paul Giardina
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Annelie Clurman
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Gabriel K Armijo
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Antonio L C Gomes
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
| | - Madhavi Lakkaraja
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - Peter Maslak
- Immunology Laboratory Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Michael Scordo
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Roni Shouval
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Staffas
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Sweden
- Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Richard O'Reilly
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Taur
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Susan Prockop
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jaap Jan Boelens
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio Giralt
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Miguel-Angel Perales
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sean M Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jonathan U Peled
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kate A Markey
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA; and
- Division of Medical Oncology, University of Washington, Seattle, WA
| | - Marcel R M van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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7
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Waters NR, Abram F, Brennan F, Holmes A, Pritchard L. Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool. Access Microbiol 2020; 2:acmi000143. [PMID: 33195978 PMCID: PMC7656184 DOI: 10.1099/acmi.0.000143] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/20/2020] [Indexed: 12/31/2022] Open
Abstract
The Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont – a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.
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Affiliation(s)
- Nicholas R Waters
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.,Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Florence Abram
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Fiona Brennan
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.,Soil and Environmental Microbiology, Environmental Research Centre, Teagasc, Johnstown Castle, Wexford, Ireland
| | - Ashleigh Holmes
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Leighton Pritchard
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland.,Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, Scotland
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8
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Waters NR, Abram F, Brennan F, Holmes A, Pritchard L. riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions. Nucleic Acids Res 2019; 46:e68. [PMID: 29608703 PMCID: PMC6009695 DOI: 10.1093/nar/gky212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/12/2018] [Indexed: 11/12/2022] Open
Abstract
The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome’s rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome.
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Affiliation(s)
- Nicholas R Waters
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland.,Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Florence Abram
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland
| | - Fiona Brennan
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland.,Soil and Environmental Microbiology, Environmental Research Centre, Teagasc, Johnstown Castle, Wexford, Y35 TC97, Ireland
| | - Ashleigh Holmes
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Leighton Pritchard
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
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9
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Nolan S, Waters NR, Brennan F, Auer A, Fenton O, Richards K, Bolton DJ, Pritchard L, O'Flaherty V, Abram F. Toward Assessing Farm-Based Anaerobic Digestate Public Health Risks: Comparative Investigation With Slurry, Effect of Pasteurization Treatments, and Use of Miniature Bioreactors as Proxies for Pathogen Spiking Trials. Front Sustain Food Syst 2018. [DOI: 10.3389/fsufs.2018.00041] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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10
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Waters NR, Samuels DJ, Behera RK, Livny J, Rhee KY, Sadykov MR, Brinsmade SR. A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus. Mol Microbiol 2016; 101:495-514. [PMID: 27116338 DOI: 10.1111/mmi.13404] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2016] [Indexed: 12/14/2022]
Abstract
The global regulator CodY controls the expression of dozens of metabolism and virulence genes in the opportunistic pathogen Staphylococcus aureus in response to the availability of isoleucine, leucine and valine (ILV), and GTP. Using RNA-Seq transcriptional profiling and partial activity variants, we reveal that S. aureus CodY activity grades metabolic and virulence gene expression as a function of ILV availability, mediating metabolic reorganization and controlling virulence factor production in vitro. Strains lacking CodY regulatory activity produce a PIA-dependent biofilm, but development is restricted under conditions that confer partial CodY activity. CodY regulates the expression of thermonuclease (nuc) via the Sae two-component system, revealing cascading virulence regulation and factor production as CodY activity is reduced. Proteins that mediate the host-pathogen interaction and subvert the immune response are shut off at intermediate levels of CodY activity, while genes coding for enzymes and proteins that extract nutrients from tissue, that kill host cells, and that synthesize amino acids are among the last genes to be derepressed. We conclude that S. aureus uses CodY to limit host damage to only the most severe starvation conditions, providing insight into one potential mechanism by which S. aureus transitions from a commensal bacterium to an invasive pathogen.
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Affiliation(s)
| | - David J Samuels
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Ranjan K Behera
- Department of Biology, Georgetown University, Washington, DC, USA
| | | | - Kyu Y Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, USA
| | - Marat R Sadykov
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
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