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Bansal R, Park H, Taborda CC, Gordillo C, Mapara MY, Assal A, Uhlemann AC, Reshef R. Antibiotic Exposure, Not Alloreactivity, Is the Major Driver of Microbiome Changes in Hematopoietic Cell Transplantation. Transplant Cell Ther 2022; 28:135-144. [PMID: 34958974 PMCID: PMC8923982 DOI: 10.1016/j.jtct.2021.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 12/31/2022]
Abstract
Both autologous hematopoietic cell transplantation (auto-HCT) and allogeneic hematopoietic cell transplantation (allo-HCT) are associated with significant alterations in the intestinal microbiome. The relative contributions of antibiotic use and alloreactivity to microbiome dynamics have not yet been elucidated, however. There is a lack of data on the kinetics of microbiome changes beyond 30 days post-transplantation and how they might differ between different transplantation modalities. A direct comparison of the differential effects of auto-HCT and allo-HCT on the microbiome may shed light on these dynamics. This study was conducted to compare intestinal microbial diversity between auto-HCT recipients and allo-HCT recipients from pre-transplantation to 100 days post-transplantation, and to examine the effect of antibiotics, transplant type (auto versus allo), and conditioning regimens on the dynamics of microbiome recovery. We conducted a longitudinal analysis of changes in the intestinal microbiome in 35 patients undergoing HCT (17 auto-HCT, 18 allo-HCT) at 4 time points: pre-conditioning and 14, 28, and 100 days post-transplantation. Granular data on antibiotic exposure from day -30 pre-transplantation to day +100 post-transplantation were collected. Pre-transplantation, allo-HCT recipients had lower α-diversity in the intestinal microbiome compared with auto-HCT recipients, which correlated with greater pre-transplantation antibiotic use in allo-HCT recipients. The microbiome diversity declined at days +14 and +28 post-transplantation in both cohorts but generally returned to baseline by day +100. Conditioning regimen intensity did not significantly affect post-transplantation α-diversity. Through differential abundance analysis, we show that commensal bacterial taxa involved with maintenance of gut epithelial integrity and production of short-chain fatty acids were depleted after both auto-HCT and allo-HCT. In our dataset, antibiotic exposure was the major driver of post-transplantation microbiome changes rather than alloreactivity, conditioning intensity, or immunosuppression. Our findings also suggest that interventions to limit microbiome injury, such as limiting the use of broad-spectrum antibiotics, should target the pre-transplantation period and not only the peri-transplantation period.
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Affiliation(s)
- Rajat Bansal
- Blood and Marrow Transplantation and Cell Therapy Program,
Columbia University Irving Medical Center,Division of Hematologic Malignancies and Cellular
Therapeutics, University of Kansas Medical Center
| | - Heekuk Park
- Division of Infectious Diseases, Columbia University Irving
Medical Center
| | - Cristian C Taborda
- Columbia Center for Translational Immunology, Columbia
University Irving Medical Center
| | - Christian Gordillo
- Blood and Marrow Transplantation and Cell Therapy Program,
Columbia University Irving Medical Center,Columbia Center for Translational Immunology, Columbia
University Irving Medical Center
| | - Markus Y Mapara
- Blood and Marrow Transplantation and Cell Therapy Program,
Columbia University Irving Medical Center,Columbia Center for Translational Immunology, Columbia
University Irving Medical Center
| | - Amer Assal
- Blood and Marrow Transplantation and Cell Therapy Program,
Columbia University Irving Medical Center
| | | | - Ran Reshef
- Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, New York; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York.
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Paralkar VR, Taborda CC, Huang P, Yao Y, Kossenkov AV, Prasad R, Luan J, Davies JOJ, Hughes JR, Hardison RC, Blobel GA, Weiss MJ. Unlinking an lncRNA from Its Associated cis Element. Mol Cell 2016; 62:104-10. [PMID: 27041223 DOI: 10.1016/j.molcel.2016.02.029] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/01/2016] [Accepted: 02/24/2016] [Indexed: 01/24/2023]
Abstract
Long non-coding (lnc) RNAs can regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (lncRNA downstream of Cdkn1b), a 434-nt polyadenylated lncRNA originating 4 kb 3' to the Cdkn1b gene. Deletion of the 25-kb Lockd locus reduced Cdkn1b transcription by approximately 70% in an erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by >90% with no effect on Cdkn1b transcription. The Lockd promoter contains a DNase-hypersensitive site, binds numerous transcription factors, and physically associates with the Cdkn1b promoter in chromosomal conformation capture studies. Therefore, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element, whereas the lncRNA itself is dispensable, which may be the case for other lncRNAs.
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Affiliation(s)
- Vikram R Paralkar
- Division of Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Cristian C Taborda
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew V Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Rishi Prasad
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jing Luan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James O J Davies
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Jim R Hughes
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16801, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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