1
|
Attard TM, Septer S, Lawson CE, Attard MI, Lee STM, Umar S. Microbiome insights into pediatric familial adenomatous polyposis. Orphanet J Rare Dis 2022; 17:416. [PMID: 36376984 PMCID: PMC9664625 DOI: 10.1186/s13023-022-02569-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/30/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Individuals with familial adenomatous polyposis (FAP) harbor numerous polyps with inevitable early progression to colon cancer. Complex microbiotic-tumor microenvironment perturbations suggest a dysbiotic relationship between polyp and microbiome. In this study, we performed comprehensive analyses of stool and tissue microbiome of pediatric FAP subjects and compared with unaffected cohabiting relatives through 16S V4 region amplicon sequencing and machine learning platforms. RESULTS Within our FAP and control patient population, Firmicutes and Bacteroidetes were the predominant phyla in the tissue and stool samples, while Proteobacteria dominated the polyp/non-polyp mucosa. A decline in Faecalibacterium in polyps contrasted with a decline in Bacteroides in the FAP stool. The alpha- and beta-diversity indices differed significantly within the polyp/non-polyp groups, with a concurrent shift towards lower diversity in polyps. In a limited 3-year longitudinal study, the relative abundance of Proteobacteria and Fusobacteria was higher in polyps compared to non-polyp and stool specimens over time. Through machine learning, we discovered that Archaeon_enrichment_culture_clone_A13, Micrococcus_luteus, and Eubacterium_hallii in stool and PL-11B10, S1-80, and Blastocatellaceae in tissues were significantly different between patients with and without polyps. CONCLUSIONS Detection of certain bacterial concentrations within stool or biopsied polyps could serve as adjuncts to current screening modalities to help identify higher-risk patients.
Collapse
Affiliation(s)
- Thomas M. Attard
- grid.239559.10000 0004 0415 5050Department of Gastroenterology, Children’s Mercy Hospital, 1MO2.37, 2401 Gilham Road, Kansas City, MO 64108 USA
| | - Seth Septer
- grid.413957.d0000 0001 0690 7621Department of Pediatric Gastroenterology, Children’s Hospital Colorado, Aurora, CO USA
| | - Caitlin E. Lawson
- grid.239559.10000 0004 0415 5050Division of Genetics, Children’s Mercy Hospital, Kansas City, MO USA
| | - Mark I. Attard
- grid.413208.c0000 0004 0624 2334Neonatal Unit, Aberdeen Maternity Hospital, Aberdeen, AB25 2ZL UK
| | - Sonny T. M. Lee
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Shahid Umar
- grid.412016.00000 0001 2177 6375Department of Surgery, University of Kansas Medical Center, 3901 Rainbow Blvd, 4028 Wahl Hall East, Kansas City, KS 66160 USA
| |
Collapse
|
2
|
Attard MI, Dawes TJW, de Marvao A, Biffi C, Shi W, Wharton J, Rhodes CJ, Ghataorhe P, Gibbs JSR, Howard LSGE, Rueckert D, Wilkins MR, O'Regan DP. Metabolic pathways associated with right ventricular adaptation to pulmonary hypertension: 3D analysis of cardiac magnetic resonance imaging. Eur Heart J Cardiovasc Imaging 2020; 20:668-676. [PMID: 30535300 PMCID: PMC6529902 DOI: 10.1093/ehjci/jey175] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/27/2018] [Indexed: 12/14/2022] Open
Abstract
Aims We sought to identify metabolic pathways associated with right ventricular (RV) adaptation to pulmonary hypertension (PH). We evaluated candidate metabolites, previously associated with survival in pulmonary arterial hypertension, and used automated image segmentation and parametric mapping to model their relationship to adverse patterns of remodelling and wall stress. Methods and results In 312 PH subjects (47.1% female, mean age 60.8 ± 15.9 years), of which 182 (50.5% female, mean age 58.6 ± 16.8 years) had metabolomics, we modelled the relationship between the RV phenotype, haemodynamic state, and metabolite levels. Atlas-based segmentation and co-registration of cardiac magnetic resonance imaging was used to create a quantitative 3D model of RV geometry and function—including maps of regional wall stress. Increasing mean pulmonary artery pressure was associated with hypertrophy of the basal free wall (β = 0.29) and reduced relative wall thickness (β = −0.38), indicative of eccentric remodelling. Wall stress was an independent predictor of all-cause mortality (hazard ratio = 1.27, P = 0.04). Six metabolites were significantly associated with elevated wall stress (β = 0.28–0.34) including increased levels of tRNA-specific modified nucleosides and fatty acid acylcarnitines, and decreased levels (β = −0.40) of sulfated androgen. Conclusion Using computational image phenotyping, we identify metabolic profiles, reporting on energy metabolism and cellular stress-response, which are associated with adaptive RV mechanisms to PH.
Collapse
Affiliation(s)
- Mark I Attard
- MRC London Institute of Medical Sciences, Du Cane Road, London, UK.,Division of Experimental Medicine, Department of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Timothy J W Dawes
- MRC London Institute of Medical Sciences, Du Cane Road, London, UK.,Division of Experimental Medicine, Department of Medicine, Imperial College London, Du Cane Road, London, UK.,Royal Brompton Cardiovascular Research Centre, National Heart & Lung Institute, Imperial College London, Dovehouse Street, London, UK
| | | | - Carlo Biffi
- MRC London Institute of Medical Sciences, Du Cane Road, London, UK.,Department of Computing, Imperial College London, South Kensington Campus, Queen's Gate, London, UK
| | - Wenzhe Shi
- MRC London Institute of Medical Sciences, Du Cane Road, London, UK.,Department of Computing, Imperial College London, South Kensington Campus, Queen's Gate, London, UK
| | - John Wharton
- Division of Experimental Medicine, Department of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Christopher J Rhodes
- Division of Experimental Medicine, Department of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Pavandeep Ghataorhe
- Division of Experimental Medicine, Department of Medicine, Imperial College London, Du Cane Road, London, UK
| | - J Simon R Gibbs
- Royal Brompton Cardiovascular Research Centre, National Heart & Lung Institute, Imperial College London, Dovehouse Street, London, UK
| | | | - Daniel Rueckert
- Department of Computing, Imperial College London, South Kensington Campus, Queen's Gate, London, UK
| | - Martin R Wilkins
- Division of Experimental Medicine, Department of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Du Cane Road, London, UK
| |
Collapse
|
3
|
Biffi C, de Marvao A, Attard MI, Dawes TJW, Whiffin N, Bai W, Shi W, Francis C, Meyer H, Buchan R, Cook SA, Rueckert D, O’Regan DP. Three-dimensional cardiovascular imaging-genetics: a mass univariate framework. Bioinformatics 2018; 34:97-103. [PMID: 28968671 PMCID: PMC5870605 DOI: 10.1093/bioinformatics/btx552] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/10/2017] [Accepted: 09/01/2017] [Indexed: 01/19/2023] Open
Abstract
Motivation Left ventricular (LV) hypertrophy is a strong predictor of cardiovascular outcomes, but its genetic regulation remains largely unexplained. Conventional phenotyping relies on manual calculation of LV mass and wall thickness, but advanced cardiac image analysis presents an opportunity for high-throughput mapping of genotype-phenotype associations in three dimensions (3D). Results High-resolution cardiac magnetic resonance images were automatically segmented in 1124 healthy volunteers to create a 3D shape model of the heart. Mass univariate regression was used to plot a 3D effect-size map for the association between wall thickness and a set of predictors at each vertex in the mesh. The vertices where a significant effect exists were determined by applying threshold-free cluster enhancement to boost areas of signal with spatial contiguity. Experiments on simulated phenotypic signals and SNP replication show that this approach offers a substantial gain in statistical power for cardiac genotype-phenotype associations while providing good control of the false discovery rate. This framework models the effects of genetic variation throughout the heart and can be automatically applied to large population cohorts. Availability and implementation The proposed approach has been coded in an R package freely available at https://doi.org/10.5281/zenodo.834610 together with the clinical data used in this work. Contact declan.oregan@imperial.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Carlo Biffi
- Department of Computing, Imperial College London, South Kensington Campus, London, UK
- Cardiovascular Magnetic Resonance Imaging and Genetics, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Antonio de Marvao
- Cardiovascular Magnetic Resonance Imaging and Genetics, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Mark I Attard
- Cardiovascular Magnetic Resonance Imaging and Genetics, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Timothy J W Dawes
- Cardiovascular Magnetic Resonance Imaging and Genetics, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
- Quantitative Physiology and Genetics, National Heart and Lung Institute, Imperial College London, London, UK
| | - Nicola Whiffin
- Cardiovascular Magnetic Resonance Imaging and Genetics, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
- Quantitative Physiology and Genetics, National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Wenjia Bai
- Department of Computing, Imperial College London, South Kensington Campus, London, UK
| | - Wenzhe Shi
- Department of Computing, Imperial College London, South Kensington Campus, London, UK
| | - Catherine Francis
- Quantitative Physiology and Genetics, National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Hannah Meyer
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Rachel Buchan
- Quantitative Physiology and Genetics, National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Stuart A Cook
- Cardiovascular Magnetic Resonance Imaging and Genetics, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
- Quantitative Physiology and Genetics, National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
- Department of Cardiology, National Heart Centre Singapore, Singapore
- Programme in Cardiovascular and Metabolic Disorders, Duke National University Singapore, Singapore
| | - Daniel Rueckert
- Department of Computing, Imperial College London, South Kensington Campus, London, UK
| | - Declan P O’Regan
- Cardiovascular Magnetic Resonance Imaging and Genetics, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
| |
Collapse
|