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Spohr P, Scharf S, Rommerskirchen A, Henrich B, Jäger P, Klau GW, Haas R, Dilthey A, Pfeffer K. Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing. Sci Rep 2024; 14:4068. [PMID: 38374282 PMCID: PMC10876974 DOI: 10.1038/s41598-024-53506-1] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.
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Affiliation(s)
- Philipp Spohr
- Chair Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Düsseldorf, Germany
| | - Sebastian Scharf
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Anna Rommerskirchen
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Paul Jäger
- Department of Hematology, Immunology, and Clinical Immunology, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Gunnar W Klau
- Chair Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Center for Digital Medicine, Düsseldorf, Germany.
| | - Rainer Haas
- Department of Hematology, Immunology, and Clinical Immunology, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
- Center for Digital Medicine, Düsseldorf, Germany.
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
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Nachtkamp K, Kobbe G, Gattermann N, Germing U. Myelodysplastic Syndromes: New Methods of Diagnosis, Prognostication, and Treatment. DEUTSCHES ARZTEBLATT INTERNATIONAL 2023; 120:203-210. [PMID: 36718105 PMCID: PMC10264648 DOI: 10.3238/arztebl.m2023.0005] [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] [Revised: 08/25/2022] [Accepted: 01/11/2023] [Indexed: 02/01/2023]
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) are malignant diseases arising from hematopoietic stem cells. Their overall incidence is 4 cases per 100 000 persons per year, and they are usually diagnosed when evaluating cytopenia. The median survival time is three years. Myelodysplastic syndromes take a variable course; one-quarter of patients go on to develop acute leukemia. METHODS This review is based on publications retrieved by a selective search of the literature from 2013 to 2022, including relevant guidelines, in the PubMed database. The time period was chosen to reflect developments since the publication of the latest EHA guidelines in 2013. RESULTS The gold standard of diagnosis is cytomorphology of the blood and bone marrow, supplemented by banding cytogenetics, histomorphology, and somatic mutation analyses. The new classification proposed by the WHO incorporates the molecular and cytogenetic findings. The Molecular International Prognostic Scoring System (IPSS-M), which takes somatic mutations into account, is now available as an aid to prognostication. Quality of life evaluation with standardized instruments is helpful in many ways. Low-risk patients are treated supportively with erythrocyte transfusions and iron chelation therapy. Erythropoietin-a can be given to patients whose erythropoietin level is less than 200ng/mL, lenalidomide to those with a 5q deletion, and luspatercept to those with an SF3B1 mutation. High-risk patients should be evaluated as early as possible for allogeneic hematopoietic stem cell transplantation with curative intent. 5-azacytidine improves outcomes in patients for whom stem cell transplantation is not suitable. CONCLUSION Once a precise diagnosis has been established, new prognostic instruments such as the IPSS-M enable risk-adapted treatment based on the biological aspects of the patient's disease as well as his or her age and comorbidities.
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Affiliation(s)
- Kathrin Nachtkamp
- Department of Hematology, Oncology and Clinical Immunology, University Hospital of Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Guido Kobbe
- Department of Hematology, Oncology and Clinical Immunology, University Hospital of Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, University Hospital of Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, University Hospital of Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
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Wang T, Wang Z, Qi W, Jiang G, Wang G. The role, targets and mechanisms of traditional Chinese medicine in regulating the balance of T helper type 17/regulatory Tcells in rheumatoid arthritis. Int J Rheum Dis 2023; 26:613-624. [PMID: 36680325 DOI: 10.1111/1756-185x.14560] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/14/2022] [Accepted: 12/24/2022] [Indexed: 01/22/2023]
Abstract
Rheumatoid arthritis (RA) is a persistent systemic autoimmune disease, having all the hallmarks of joint swelling, joint tenderness, and progressive joint destruction, with synovitis and pannus formation as the basic pathological changes. T-lymphocyte infiltration is the key to its pathogenesis. During the growth of RA, the share of regulatory T (Treg) cells decreases, while the percentage of T helper type 17 (Th17) cells increases, giving rise to an imbalance of Th17/Treg cells. Modern medicine has made great advances in the treatment of RA and the selection of available drugs, but there are also the disadvantages of gastrointestinal reaction, high price, and low patient compliance. Therapy of RA remains a problem. Traditional Chinese medicine (TCM) has RA therapy developments, both in experimental research and clinical research, and its advantages of lasting effects and less detrimental reactions and fewer adverse effects are accepted by most patients. Numerous clinical and experimental studies have been performed in TCM on regulating Th17/Treg balance. However, the detailed mechanism of TCM intervention in Th17/Treg equilibrium in preventing and treating RA has not been discovered. In this article, the theory of regulating Th17/Treg cell equilibrium in RA is described from the perspectives of single Chinese medicine, active components of Chinese medicine, Chinese medicine compounds, and other therapies of TCM. It was found that TCM can regulate Th17/Treg cell balance and inhibit immunoreaction by intervening in cytokines, transcription factors, and signal pathways. It enables us to comprehensively and deeply understand the mechanism of TCM intervening in Th17/Treg balance in RA; provides direction for clinical therapy of RA; and offers new thoughts for understanding the pathogenesis of RA.
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Affiliation(s)
- Tao Wang
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Zhandong Wang
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Wenxia Qi
- Gansu University of Chinese Medicine, Lanzhou, China
| | | | - Gang Wang
- Affiliated Hospital of Gansu University of Chinese Medicine, Lanzhou, China
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Cheng WY, Satija A, Cheung HC, Hill K, Wert T, Laliberté F, Lefebvre P. Persistence to hypomethylating agents and clinical and economic outcomes among patients with myelodysplastic syndromes. ACTA ACUST UNITED AC 2021; 26:261-270. [PMID: 33631084 DOI: 10.1080/16078454.2021.1889161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVES To evaluate hypomethylating agent (HMA) persistence in patients with myelodysplastic syndromes (MDS), and examine its association with healthcare resource utilization (HRU) and progression to acute myeloid leukemia (AML). METHODS A total of 2,400 adults diagnosed with MDS initiating HMAs were included from IBM MarketScan databases during 1/1/2011-3/31/2018. The index date was HMA initiation following MDS diagnosis. Patients were classified according to their persistence status by the end of a fixed 'landmark period' of 4 months post-index. RESULTS Median persistence to HMAs was 5.6 months (95% CI: 5.2, 6.1); HMA non-persistence increased with time. Non-persistent patients had a significantly higher non-HMA-related HRU burden than persistent patients [adjusted incidence rate ratios, outpatient visits: 1.12 (95% CI: 1.10, 1.14); inpatient visits: 1.48 (95% CI: 1.30, 1.69); emergency department visits 1.30 (95% CI: 1.12, 1.50); all p-values < 0.001]. All-cause and HMA-related outpatient visits were lower among non-persistent patients, likely because of fewer HMA administration-related visits. The incidence rate of AML was numerically, although not significantly, higher in non-persistent patients, when starting follow-up at the end of the landmark period. When follow-up began at the index date, non-persistent patients had a significantly higher rate of AML [adjusted hazard ratio, 1.88 (95% CI: 1.53, 2.32); p-value < 0.001]. CONCLUSIONS HMA non-persistence, which increased over time, was associated with significantly higher non-HMA-related HRU, and numerically higher AML progression in MDS patients initiating HMAs. Future studies should evaluate predictors of HMA non-persistence in this patient population.
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Affiliation(s)
| | | | | | - Kala Hill
- Taiho Oncology, Inc., Princeton, NJ, USA
| | - Tim Wert
- Taiho Oncology, Inc., Princeton, NJ, USA
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Schroeder T, Wegener N, Lauseker M, Rautenberg C, Nachtkamp K, Schuler E, Kondakci M, Haas R, Germing U, Kobbe G. Comparison between Upfront Transplantation and different Pretransplant Cytoreductive Treatment Approaches in Patients with High-Risk Myelodysplastic Syndrome and Secondary Acute Myelogenous Leukemia. Biol Blood Marrow Transplant 2019; 25:1550-1559. [DOI: 10.1016/j.bbmt.2019.03.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/11/2019] [Indexed: 12/14/2022]
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Germing U, Schroeder T, Kaivers J, Kündgen A, Kobbe G, Gattermann N. Novel therapies in low- and high-risk myelodysplastic syndrome. Expert Rev Hematol 2019; 12:893-908. [PMID: 31353975 DOI: 10.1080/17474086.2019.1647778] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: Myelodysplastic syndromes (MDS) comprise a heterogeneous group of myeloid neoplasms with diverse clinical courses. The revised version of the international prognostic scoring system (IPSS-R) provides risk stratification into 5 different groups. Areas covered: For lower-risk patients, red blood cell transfusions and iron chelation are the backbone of supportive care. In addition, erythropoiesis-stimulating agents (ESA) are used to ameliorate anemia. Lenalidomide is approved for the treatment of lower-risk patients with del(5q) who are transfusion-dependent. Patients with higher-risk disease should be offered allogeneic stem cell transplantation whenever possible. If they are unfit for transplantation or an appropriate donor cannot be found, hypomethylating agents may be used. Expert opinion: New therapeutic options for lower-risk patients include thrombopoietin analogues, the TGF-beta family ligand trapping drug Luspatercept, and the telomerase inhibitor Imetelstat. Combinations of hypomethylating agents (HMA) with other compounds, and inhibitors of bcl2, such as venetoclax are being developed for higher-risk patients. Finally, hypomethylating agents in combination with donor lymphocytes may lead to long-term remission following molecular or hematological relapse after allogeneic SCT.
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Affiliation(s)
- Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf , Düsseldorf , Germany
| | - Thomas Schroeder
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf , Düsseldorf , Germany
| | - Jennifer Kaivers
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf , Düsseldorf , Germany
| | - Andrea Kündgen
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf , Düsseldorf , Germany
| | - Guido Kobbe
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf , Düsseldorf , Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf , Düsseldorf , Germany
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Kobbe G, Schroeder T, Rautenberg C, Kaivers J, Gattermann N, Haas R, Germing U. Molecular genetics in allogeneic blood stem cell transplantation for myelodysplastic syndromes. Expert Rev Hematol 2019; 12:821-831. [DOI: 10.1080/17474086.2019.1645004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Guido Kobbe
- Departments of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Thomas Schroeder
- Departments of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Christina Rautenberg
- Departments of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Jennifer Kaivers
- Departments of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Norbert Gattermann
- Departments of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Rainer Haas
- Departments of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ulrich Germing
- Departments of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
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