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Ma B, Gavzy SJ, France M, Song Y, Lwin HW, Kensiski A, Saxena V, Piao W, Lakhan R, Iyyathurai J, Li L, Paluskievicz C, Wu L, WillsonShirkey M, Mongodin EF, Mas VR, Bromberg JS. Rapid intestinal and systemic metabolic reprogramming in an immunosuppressed environment. BMC Microbiol 2023; 23:394. [PMID: 38066426 PMCID: PMC10709923 DOI: 10.1186/s12866-023-03141-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Intrinsic metabolism shapes the immune environment associated with immune suppression and tolerance in settings such as organ transplantation and cancer. However, little is known about the metabolic activities in an immunosuppressive environment. In this study, we employed metagenomic, metabolomic, and immunological approaches to profile the early effects of the immunosuppressant drug tacrolimus, antibiotics, or both in gut lumen and circulation using a murine model. Tacrolimus induced rapid and profound alterations in metabolic activities within two days of treatment, prior to alterations in gut microbiota composition and structure. The metabolic profile and gut microbiome after seven days of treatment was distinct from that after two days of treatment, indicating continuous drug effects on both gut microbial ecosystem and host metabolism. The most affected taxonomic groups are Clostriales and Verrucomicrobiae (i.e., Akkermansia muciniphila), and the most affected metabolic pathways included a group of interconnected amino acids, bile acid conjugation, glucose homeostasis, and energy production. Highly correlated metabolic changes were observed between lumen and serum metabolism, supporting their significant interactions. Despite a small sample size, this study explored the largely uncharacterized microbial and metabolic events in an immunosuppressed environment and demonstrated that early changes in metabolic activities can have significant implications that may serve as antecedent biomarkers of immune activation or quiescence. To understand the intricate relationships among gut microbiome, metabolic activities, and immune cells in an immune suppressed environment is a prerequisite for developing strategies to monitor and optimize alloimmune responses that determine transplant outcomes.
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Affiliation(s)
- Bing Ma
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Samuel J Gavzy
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michael France
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yang Song
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hnin Wai Lwin
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Allison Kensiski
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vikas Saxena
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Wenji Piao
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ram Lakhan
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jegan Iyyathurai
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lushen Li
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina Paluskievicz
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Long Wu
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Marina WillsonShirkey
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Emmanuel F Mongodin
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Division of Lung Diseases, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Valeria R Mas
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA
| | - Jonathan S Bromberg
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA.
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Picard D, Felsberg J, Langini M, Stachura P, Qin N, Macas J, Reiss Y, Bartl J, Selt F, Sigaud R, Meyer FD, Stefanski A, Stühler K, Roque L, Roque R, Pandyra AA, Brozou T, Knobbe-Thomsen C, Plate KH, Roesch A, Milde T, Reifenberger G, Leprivier G, Faria CC, Remke M. Integrative multi-omics reveals two biologically distinct groups of pilocytic astrocytoma. Acta Neuropathol 2023; 146:551-564. [PMID: 37656187 PMCID: PMC10500011 DOI: 10.1007/s00401-023-02626-5] [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: 05/11/2023] [Revised: 08/04/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
Pilocytic astrocytoma (PA), the most common pediatric brain tumor, is driven by aberrant mitogen-activated protein kinase signaling most commonly caused by BRAF gene fusions or activating mutations. While 5-year overall survival rates exceed 95%, tumor recurrence or progression constitutes a major clinical challenge in incompletely resected tumors. Here, we used similarity network fusion (SNF) analysis in an integrative multi-omics approach employing RNA transcriptomic and mass spectrometry-based proteomic profiling to molecularly characterize PA tissue samples from 62 patients. Thereby, we uncovered that PAs segregated into two molecularly distinct groups, namely, Group 1 and Group 2, which were validated in three non-overlapping cohorts. Patients with Group 1 tumors were significantly younger and showed worse progression-free survival compared to patients with group 2 tumors. Ingenuity pathways analysis (IPA) and gene set enrichment analysis (GSEA) revealed that Group 1 tumors were enriched for immune response pathways, such as interferon signaling, while Group 2 tumors showed enrichment for action potential and neurotransmitter signaling pathways. Analysis of immune cell-related gene signatures showed an enrichment of infiltrating T Cells in Group 1 versus Group 2 tumors. Taken together, integrative multi-omics of PA identified biologically distinct and prognostically relevant tumor groups that may improve risk stratification of this single pathway driven tumor type.
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Affiliation(s)
- Daniel Picard
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Jörg Felsberg
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Maike Langini
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Molecular Proteomics Laboratory, Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Molecular Medicine I, Heinrich Heine University Medical Faculty, Düsseldorf, Germany
| | - Paweł Stachura
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Institute for Molecular Medicine II, Heinrich Heine University Medical Faculty, Düsseldorf, Germany
| | - Nan Qin
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Jadranka Macas
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Frankfurt, Germany
- Frankfurt Cancer Institute, Frankfurt, Germany
| | - Yvonne Reiss
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Frankfurt, Germany
- Frankfurt Cancer Institute, Frankfurt, Germany
| | - Jasmin Bartl
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Romain Sigaud
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Frauke-D Meyer
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Molecular Medicine I, Heinrich Heine University Medical Faculty, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Molecular Medicine I, Heinrich Heine University Medical Faculty, Düsseldorf, Germany
| | - Lucia Roque
- Portuguese Cancer Institute, Unidade de Investigação em Patobiologia Molecular (UIPM), IPOLFG, Lisbon, Portugal
| | - Rafael Roque
- Laboratory of Neuropathology, Neurology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Aleksandra A Pandyra
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Christiane Knobbe-Thomsen
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Karl H Plate
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Frankfurt, Germany
- Frankfurt Cancer Institute, Frankfurt, Germany
| | - Alexander Roesch
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Guido Reifenberger
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Gabriel Leprivier
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Claudia C Faria
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, da Universidade de Lisboa, Lisbon, Portugal
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany.
- Institute of Neuropathology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
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