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Couto-Rodriguez M, Danko DC, Jirau Serrano XO, Paisie T, Papciak JC, Szollosi E, Mason CE, Otto C, O’Hara NB, Nagy-Szakal D. 322. Clinical-Grade Metagenomics in Urinary Tract Infections: Improving Performance of Next-Generation Sequencing Assays Using Internal Controls and Machine Learning. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Shotgun sequencing-based metagenomics is a useful approach to profiling microbiomes in environmental and patient samples. In a clinical setting, metagenomic techniques have the advantage of identifying organisms, which cannot be readily cultured or confirmed by other techniques. We have developed a clinical-grade, streamlined metagenomics-based pipeline that includes regulatory compliant method considerations, such as an internal control followed by a machine-based learning (ML) process to identify pathogens in urine samples.
Methods
We built an optimized novel end-to-end NGS assay pipeline that harnesses pathogen-specific genome data to detect bacterial species. We processed de-identified clinical urine specimens, collected from patients symptomatic for urinary tract infection (UTI). This workflow includes an IPC, QIACube-MDx extraction, library preparation and Illumina NextSeq 550 sequencing and a novel interpretable ML based analytic approach, Biotia-DX. Clinical culture results and qPCR were used as a baseline for the assay to train the ML model and to establish accuracy relative to the clinical standard of care.
Results
We clinically validated over 40 key uropathogens and conducted clinical studies of specificity, intra/inter reproducibility, accuracy in urine specimens (n=300), and limit of detection in E. coli, K. pneumoniae, P. mirabilis, S. aureus, E. faecalis and Candida. Additionally, the implementation of an internal control coupled with our Biotia-DX software provides an accurate (F1 score 94.3%) and highly sensitive clinical grade diagnostic tool.
Conclusion
Urine has historically presented a challenge for diagnostics via culturing, with a high rate of culture-negative results (∼30% on average). We improved the clinical utility of an NGS urine assay by leveraging an IPC and ML software. This decreased the rate of false positive species called in a sample relative to other NGS techniques and allows for greater sensitivity and taxonomic specificity. This assay may be especially useful for low colony-count or negative-culture samples to diagnose and guide patient treatment.
Disclosures
Mara Couto-Rodriguez, MS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company David C. Danko, PhD, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Xavier O. Jirau Serrano, MS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Taylor Paisie, MS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company John C. Papciak, BS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Eszter Szollosi, BS, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company Christopher E. Mason, PhD, Biotia Inc.: Advisor/Consultant|Biotia Inc.: Board Member|Biotia Inc.: Ownership Interest Caitlin Otto, PhD, D(ABMM), Biotia Inc.: Advisor/Consultant Niamh B. O'Hara, PhD, Biotia Inc.: Board Member|Biotia Inc.: Ownership Interest Dorottya Nagy-Szakal, MD PhD, Biotia Inc.: Employee of Biotia Inc. a for-profit biotechnology company|Biotia Inc.: Stocks/Bonds.
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Connor BA, Rogova M, Garcia J, Patel D, Couto-Rodriguez M, Nagy-Szakal D, Rendel M. Comparative Effectiveness of Single vs Repeated Rapid SARS-CoV-2 Antigen Testing Among Asymptomatic Individuals in a Workplace Setting. JAMA Netw Open 2022; 5:e223073. [PMID: 35302635 PMCID: PMC8933730 DOI: 10.1001/jamanetworkopen.2022.3073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This comparative effectiveness research study assesses the accuracy of single vs repeated antigen testing for diagnosis of COVID-19 among asymptomatic individuals in a workplace setting.
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Affiliation(s)
- Bradley A. Connor
- Weill Cornell Medicine, New York, New York
- The New York Center for Travel and Tropical Medicine, New York
| | - Marina Rogova
- The New York Center for Travel and Tropical Medicine, New York
| | | | | | | | - Dorottya Nagy-Szakal
- Biotia, Inc, New York, New York
- Department Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, New York, New York
| | - Michael Rendel
- Mount Sinai School of Medicine, New York, New York
- Goldman Sachs Group Inc, New York, New York
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Kellermayer R, Wu Q, Nagy-Szakal D, Queliza K, Ihekweazu FD, Bocchini CE, Magee AR, Oezguen N, Spinler JK, Hollister EB, Shulman RJ, Versalovic J, Luna RA, Savidge TC. Fecal Microbiota Transplantation Commonly Failed in Children With Co-Morbidities. J Pediatr Gastroenterol Nutr 2022; 74:227-235. [PMID: 34724447 PMCID: PMC8799498 DOI: 10.1097/mpg.0000000000003336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Fecal microbiota transplantation (FMT) is arguably the most effective treatment for recurrent Clostridioides difficile infection (rCDI). Clinical reports on pediatric FMT have not systematically evaluated microbiome restoration in patients with co-morbidities. Here, we determined whether FMT recipient age and underlying co-morbidity influenced clinical outcomes and microbiome restoration when treated from shared fecal donor sources. METHODS Eighteen rCDI patients participating in a single-center, open-label prospective cohort study received fecal preparation from a self-designated (single case) or two universal donors. Twelve age-matched healthy children and four pediatric ulcerative colitis (UC) cases from an independent serial FMT trial, but with a shared fecal donor were examined as controls for microbiome restoration using 16S rRNA gene sequencing of longitudinal fecal specimens. RESULTS FMT was significantly more effective in rCDI recipients without underlying chronic co-morbidities where fecal microbiome composition in post-transplant responders was restored to levels of healthy children. Microbiome reconstitution was not associated with symptomatic resolution in some rCDI patients who had co-morbidities. Significant elevation in Bacteroidaceae, Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae was consistently observed in pediatric rCDI responders, while Enterobacteriaceae decreased, correlating with augmented complex carbohydrate degradation capacity. CONCLUSION Recipient background disease was a significant risk factor influencing FMT outcomes. Special attention should be taken when considering FMT for pediatric rCDI patients with underlying co-morbidities.
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Affiliation(s)
- Richard Kellermayer
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
- USDA/ARS Children’s Nutrition Research Center, Houston, Texas, USA
| | - Qinglong Wu
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Dorottya Nagy-Szakal
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Karen Queliza
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Faith D. Ihekweazu
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Claire E. Bocchini
- Pediatric Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Abria R. Magee
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Numan Oezguen
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Emily B. Hollister
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Robert J. Shulman
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Tor C. Savidge
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
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Wells HL, Barrows J, Couto-Rodriguez M, Jirau Serrano XO, Debieu M, Wessel K, Jonsson CB, Connor BA, Mason C, Nagy-Szakal D, O’Hara NB. 355. A Novel Likelihood-Based Model to Estimate SARS-CoV-2 Viral Titer from Next-Generation Sequencing Data. Open Forum Infect Dis 2021. [PMCID: PMC8690726 DOI: 10.1093/ofid/ofab466.556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/25/2022] Open
Abstract
Background The quantitative level of pathogens present in a host is a major driver of infectious disease (ID) state and outcome. However, the majority of ID diagnostics are qualitative. Next-generation sequencing (NGS) is an emerging ID diagnostics and research tool to provide insights, including tracking transmission, evolution, and identifying novel strains. Methods We built a novel likelihood-based computational method to leverage pathogen-specific genome-wide NGS data to detect SARS-CoV-2, profile genetic variants, and furthermore quantify levels of these pathogens. We used de-identified clinical specimens tested for SARS-CoV-2 using RT-PCR, SARS-CoV-2 NGS Assay (hybrid capture, Twist Bioscience), or ARTIC (amplicon-based) platform, and COVID-DX software. A training (n=87) and validation (n=22) set was selected to establish the strength of our quantification model. We fit non-uniform probabilistic error profiles to a deterministic sigmoidal equation that more realistically represents observed data and used likelihood maximized over several different read depths to improve accuracy over a wide range of values of viral load. Given the proportion of the genome covered at varying depths for a single sample as input data, our model estimated the Ct of that sample as the value that produces the maximum likelihood of generating the observed genome coverage data. Results The model fit on 87 SARS-CoV-2 NGS Assay training samples produced a good fit to the 22 validation samples, with a coefficient of correlation (r2) of ~0.8. The accuracy of the model was high (mean absolute % error of ~10%, meaning our model is able to predict the Ct value of each sample within a margin of ±10% on average). Because of the nature of the commonly used ARTIC protocol, we found that all quantitative signals in this data were lost during PCR amplification and the model is not applicable for quantification of samples captured this way. The ability to model quantification is a major advantage of the SARS-CoV-2 NGS assay protocol. The likelihood-based model to estimate SARS-CoV-2 viral titer ![]()
Left Observed genome coverage (y-axis) plotted against Ct value (x-axis). The best-fitting logistic curve is demonstrated with a red line with shaded areas above and below representing the fitted error profile. RIGHT: Model-estimated Ct values (y-axis) compared to laboratory Ct values (x-axis) with grey bars representing estimated confidence intervals. The 1:1 diagonal is shown as a dotted line. Conclusion To our knowledge, this is the first model to incorporate sequence data mapped across the genome of a pathogen to quantify the level of that pathogen in a clinical specimen. This has implications in ID diagnostics, research, and metagenomics. Disclosures Heather L. Wells, MPH, Biotia, Inc. (Consultant) Joseph Barrows, MS, Biotia (Employee) Mara Couto-Rodriguez, MS, Biotia (Employee) Xavier O. Jirau Serrano, B.S., Biotia (Employee) Marilyne Debieu, PhD, Biotia (Employee) Karen Wessel, PhD, Labor Zotz/Klimas (Employee) Christopher Mason, PhD, Biotia (Board Member, Advisor or Review Panel member, Shareholder) Dorottya Nagy-Szakal, MD PhD, Biotia Inc (Employee, Shareholder) Niamh B. O’Hara, PhD, Biotia (Board Member, Employee, Shareholder)
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Affiliation(s)
| | | | | | | | | | - Karen Wessel
- Labor Zotz/Klimas, Duesseldorf, Nordrhein-Westfalen, Germany
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Harry BL, Qiu Y, Lu L, Couto-Rodriguez M, Nagy-Szakal D, O’Hara NB, Lu SL. 149. Extraction-free RT-PCR to Detect SARS-CoV-2 Variants of Concern. Open Forum Infect Dis 2021. [PMCID: PMC8644938 DOI: 10.1093/ofid/ofab466.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/25/2022] Open
Abstract
Background SARS-CoV-2 variants of concern (VOC) have challenged real-time reverse transcriptase polymerase chain reaction (RT-PCR) methods for the diagnosis of COVID-19. Methods The CDC 2019-Novel Coronavirus real-time RT-PCR panel was modified to create a single-plex extraction-free proxy RT-PCR assay, VOCFast™. This assay uses the nucleocapsid N1 as well as novel primer/probe pairs to target VOC mutations in the Orf1a and spike (S) genes. For analytical validation of VOCFast, synthetic controls for the Wuhan, alpha/B.1.1.7, beta/B.1.351, and gamma/P.1 strains were tested at various concentrations. Clinical validation was performed using patient anterior nares swab and saliva specimens collected in the Denver, CO area between Nov 2020 and Feb 2021 or in March 2021. Orthogonal next-generation sequencing (NGS) was also performed. ![]()
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Results Similar N1 quantification cycle (Cq) values corresponding to viral load were observed for all strains, suggesting that VOC mutations do not affect performance of the N1 primer/probe. Orf1a-mut and S1-mut primer/probes generated a stable high Cq value for the Wuhan strain. Conversely, Orf1a-mut Cq values were inversely correlated with viral load for all VOC. The S1-mut Cq was inversely correlated with viral load of the alpha strain, but did not reliably amplify beta/gamma VOC. The limit of detection was 8 copies/uL. The first set of COVID-19 patient specimens revealed no amplification using Orf1a-mut whereas 53% of specimens collected in Mar 2021 demonstrated amplification by Orf-1a. Orthogonal testing by the SARS-CoV-2 NGS Assay and COVID-DX software demonstrated that 12/12 alpha strains, 2/2 beta/gamma strains, and 33/33 Wuhan strains were correctly identified by VOCFast. ![]()
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Detection of VOC in clinical specimens and validation by NGS ![]()
Conclusion The combination of the N1, Orf1a-mut, and S1-mut primers/probes in VOCFast can distinguish the Wuhan, alpha, and beta/gamma strains and it consistent with NGS results. Testing of clinical samples revealed that VOC emerged in Denver, CO in March 2021. Future work to discriminate beta, gamma, and emerging VOC is ongoing. In summary, VOCFast is an extraction-free RT-PCR assay for nasal swab and saliva specimens that can identify VOC with a turnaround time suitable for clinical testing. ![]()
Disclosures Brian L. Harry, MD PhD, Summit Biolabs Inc. (Grant/Research Support, Shareholder) Mara Couto-Rodriguez, MS, Biotia (Employee) Dorottya Nagy-Szakal, MD PhD, Biotia Inc (Employee, Shareholder) Niamh B. O’Hara, PhD, Biotia (Board Member, Employee, Shareholder) Shi-Long Lu, MD PhD, Summit Biolabs Inc. (Grant/Research Support, Shareholder)
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Affiliation(s)
| | - Yue Qiu
- University of Colorado, Aurora, CO
| | - Ling Lu
- University of Colorado, Aurora, CO
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Antaki D, Couto-Rodriguez M, Liu T, Butcher K, Toro E, Höglund B, Jirau Serrano XO, Barrows J, Connor BA, Mason C, O’Hara NB, Nagy-Szakal D. 368. Performance Characteristics of Sequencing Assays for Identification of the SARS-CoV-2 Viral Genome. Open Forum Infect Dis 2021. [PMCID: PMC8690673 DOI: 10.1093/ofid/ofab466.569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background As the SARS-CoV-2 (SCV-2) virus evolves, diagnostics and vaccines against novel strains rely on viral genome sequencing. Researchers have gravitated towards the cost-effective and highly sensitive amplicon-based (e.g. ARTIC) and hybrid capture sequencing (e.g. SARS-CoV-2 NGS Assay) to selectively target the SCV-2 genome. We provide an in silico model to compare these 2 technologies and present data on the high scalability of the Research Use Only (RUO) workflow of the SARS-CoV-2 NGS Assay. Methods In silico work included alignments of 383,656 high-quality genome sequences belonging to variant of concern (VOC) or variant of interest (VOI) isolates (GISAID). We profiled mismatches and sequencing dropouts using the ARTIC V3 primers, SARS-CoV-2 NGS Assay probes (Twist Bioscience) and 11 synthesized viral sequences containing mutations and compared the performance of these assays using clinical samples. Further, the miniaturized hybrid capture workflow was optimized and evaluated to support high-throughput (384-plex). The sequencing data was processed by COVID-DX software. Results We detected 101,432 viruses (27%) with > = 1 mismatch in the last 6 base pairs of the 3’ end of ARTIC primers; of these, 413 had > = 2 mismatches in one primer. In contrast, only 38 viruses (0.01%) had enough mutations ( > = 10) in a hybrid capture probe to have a similar effect on coverage. We observed that mutations in ARTIC primers led to complete dropout of the amplicon for 4/11 isolates and diminished coverage in additional 4. Twist probes showed uniform coverage throughout with little to no dropouts. Both assays detected a wide range of variants (~99.9% coverage at 5X depth) in clinical samples (CT value < 30) collected in NY (Spring 2020-Spring 2021). The distribution of the number of reads and on target rates were more uniform among specimens within amplicon-based sequencing. However, uneven genome coverage and primer dropouts, some in the spike protein, were observed on VOC/VOI and other isolates highlighting limitations of an amplicon-based approach. Conclusion The RUO workflow of the SARS-CoV-2 NGS Assay is a comprehensive and scalable sequencing tool for variant profiling, yields more consistent coverage and smaller dropout rate compared to ARTIC (0.05% vs. 7.7%). Disclosures Danny Antaki, PhD, Twist Bioscience (Employee, Shareholder) Mara Couto-Rodriguez, MS, Biotia (Employee) Kristin Butcher, MS, Twist Bioscience (Employee, Shareholder) Esteban Toro, PhD, Twist Bioscience (Employee) Bryan Höglund, BS, Twist Bioscience (Employee, Shareholder) Xavier O. Jirau Serrano, B.S., Biotia (Employee) Joseph Barrows, MS, Biotia (Employee) Christopher Mason, PhD, Biotia (Board Member, Advisor or Review Panel member, Shareholder) Niamh B. O’Hara, PhD, Biotia (Board Member, Employee, Shareholder) Dorottya Nagy-Szakal, MD PhD, Biotia Inc (Employee, Shareholder)
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Affiliation(s)
- Danny Antaki
- Twist Bioscience, South San Francisco, California
| | | | - Tong Liu
- Twist Bioscience, South San Francisco, California
| | | | - Esteban Toro
- Twist Bioscience, South San Francisco, California
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Connor BA, Couto-Rodriguez M, Barrows JE, Gardner M, Rogova M, O'Hara NB, Nagy-Szakal D. Monoclonal Antibody Therapy in a Vaccine Breakthrough SARS-CoV-2 Hospitalized Delta (B.1.617.2) Variant Case. Int J Infect Dis 2021; 110:232-234. [PMID: 34271202 PMCID: PMC8276551 DOI: 10.1016/j.ijid.2021.07.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 06/25/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022] Open
Abstract
We present two Delta (B.1.617.2) vaccine breakthrough individuals, a father and son living in separate households. The older, 63-year-old patient's symptoms were severe enough to require hospitalization. Despite having a high titer of anti-spike IgG in his serum, his symptoms resolved within 24 hours following monoclonal antibody (bamlanivimab/etesevimab) therapy.
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Affiliation(s)
- Bradley A Connor
- Weill Cornell Medicine, New York, NY, USA; The New York Center for Travel and Tropical Medicine, New York, NY, USA; GeoSentinel, New York, NY, USA.
| | | | | | - Morgan Gardner
- The New York Center for Travel and Tropical Medicine, New York, NY, USA; GeoSentinel, New York, NY, USA
| | - Marina Rogova
- The New York Center for Travel and Tropical Medicine, New York, NY, USA; GeoSentinel, New York, NY, USA
| | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA; SUNY Downstate Health Sciences University, The Department Cell Biology/College of Medicine, New York, NY, USA
| | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA; SUNY Downstate Health Sciences University, The Department Cell Biology/College of Medicine, New York, NY, USA
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Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun 2021; 12:1660. [PMID: 33712587 PMCID: PMC7954844 DOI: 10.1038/s41467-021-21361-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, Columbia, NY, USA
| | - Evan T Sholle
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Craig D Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ciaran Hassan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | | | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | | | | | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | - Jeffrey A Rosenfeld
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
- Department of Pathology, Robert Wood Johnson Medical School, New York, NJ, USA
| | - Ying Chen
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
| | - Peter A D Steel
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amos J Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Thomas R Campion
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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9
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Nagy-Szakal D, Couto-Rodriguez M, Barrows J, Wells HL, Debieu M, Hager C, Butcher K, Chen S, Boorstein R, Mason C, O’Hara NB. 423. SARS-CoV-2 NGS Assay Powered by Biotia COVID-DX Software. Open Forum Infect Dis 2020. [PMCID: PMC7777289 DOI: 10.1093/ofid/ofaa439.617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background COVID-19 had spread quickly, causing an international public health emergency with an alarming global shortage of COVID-19 diagnostic tests. We developed and clinically validated a next-generation sequencing (NGS)-based target enrichment assay with the COVID-DX Software tailored for the detection, characterization, and surveillance of the SARS-CoV-2 viral genome. Methods The SARS-CoV-2 NGS assay consists of components including library preparation, target enrichment, sequencing, and a COVID-DX Software analysis tool. The NGS library preparation starts with extracted RNA from nasopharyngeal (NP) swabs followed by cDNA synthesis and conversion to Illumina TruSeq-compatible libraries using the Twist Library Preparation Kit via Enzymatic Fragmentation and Unique Dual Indices (UDI). The library is then enriched for SARS-CoV-2 sequences using a panel of dsDNA biotin-labeled probes, specifically designed to target the SARS-CoV-2 genome, then sequenced on an Illumina NextSeq 550 platform. The COVID-DX Software analyzes sequence results and provides a clinically oriented report, including the presence/absence of SARS-CoV-2 for diagnostic use. An additional research use only report describes the assay performance, estimated viral titer, coverage across the viral genome, genetic variants, and phylogenetic analysis. Results The SARS-CoV-2 NGS Assay was validated on 30 positive and 30 negative clinical samples. To measure the sensitivity and specificity of the assay, the positive and negative percent agreement (PPA, NPA) was defined in comparison to an orthogonal EUA RT-PCR assay (PPA [95% CI]: 96.77% [90.56%-100%] and NPA [95% CI]: 100% [100%-100%]). Data reported using our assay defined the limit of detection to be 40 copies/ml using heat-inactivated SARS-CoV-2 viral genome in clinical matrices. In-silico analysis provided >99.9% coverage across the SARS-CoV-2 viral genome and no cross-reactivity with evolutionarily similar respiratory pathogens. Conclusion The SARS-CoV-2 NGS Assay powered by the COVID-DX Software can be used to detect the SARS-CoV-2 virus and provide additional insight into viral titer and genetic variants to track transmission, stratify risk, predict outcome and therapeutic response, and control the spread of infectious disease. Disclosures Dorottya Nagy-Szakal, MD PhD, Biotia (Employee) Mara Couto-Rodriguez, MS, Biotia (Employee) Joseph Barrows, MS, Biotia, Inc. (Employee, Shareholder) Heather L. Wells, MPH, Biotia (Consultant) Marilyne Debieu, PhD, Biotia (Employee) Courteny Hager, BS, Biotia (Employee) Kristin Butcher, MS, Twist Bioscience (Employee) Siyuan Chen, PhD, Twist Bioscience (Employee) Christopher Mason, PhD, Biotia (Board Member, Employee, Shareholder) Niamh B. O’Hara, PhD, Biotia (Board Member, Employee, Shareholder)Twist (Other Financial or Material Support, I am CEO of Biotia and Biotia has business partnership with Twist)
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Affiliation(s)
| | | | | | | | | | | | | | - Siyuan Chen
- Twist Bioscience, South San Francisco, California
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10
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Spinner JA, Bocchini CE, Luna RA, Thapa S, Balderas MA, Denfield SW, Dreyer WJ, Nagy-Szakal D, Ihekweazu FD, Versalovic J, Savidge T, Kellermayer R. Fecal microbiota transplantation in a toddler after heart transplant was a safe and effective treatment for recurrent Clostridiodes difficile infection: A case report. Pediatr Transplant 2020; 24:e13598. [PMID: 31617299 PMCID: PMC6982574 DOI: 10.1111/petr.13598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/19/2019] [Accepted: 09/01/2019] [Indexed: 12/17/2022]
Abstract
Pediatric recipients of SOT have a significantly increased risk of Clostridiodes (formerly Clostridium) difficile infection (CDI), which is associated with adverse outcomes after SOT. Alterations to the intestinal microbiota community structure increase the risk of CDI. FMT is a safe and effective treatment for recurrent CDI in immunocompetent children and adults. While there are increasing data that FMT in immunosuppressed patients is safe and effective without increased risk of infection, data regarding safety and efficacy of FMT in children after SOT are limited. To our knowledge, we report the youngest immunocompromised patient to undergo FMT and the third overall case of FMT in a child after HTx. Our patient presented with five episodes of rCDI in 6 months, and 16S rRNA genetic analysis revealed significant loss of overall microbiota community structure and diversity prior to FMT compared with a donor and a healthy, age-matched control. After FMT, marked and prolonged (at least 16 months) shifts in the recipient microbiota community structure and diversity were evident, approaching that of donor and healthy, age-matched control. FMT was well tolerated, restored microbial diversity without any graft or transplant complications, and prevented further rCDI episodes after more than 4 years of follow-up.
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Affiliation(s)
- Joseph A Spinner
- Section of Pediatric Cardiology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - Claire E Bocchini
- Section of Pediatric Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - Ruth A Luna
- Texas Children’s Microbiome Center and Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Santosh Thapa
- Texas Children’s Microbiome Center and Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Miriam A Balderas
- Texas Children’s Microbiome Center and Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Susan W Denfield
- Section of Pediatric Cardiology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - William J Dreyer
- Section of Pediatric Cardiology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - Dorottya Nagy-Szakal
- Section of Pediatric Gastroenterology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX,USDA/ARS Children’s Nutrition Research Center, Houston, TX, USA
| | - Faith D Ihekweazu
- Section of Pediatric Gastroenterology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - James Versalovic
- Texas Children’s Microbiome Center and Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Tor Savidge
- Texas Children’s Microbiome Center and Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX,USDA/ARS Children’s Nutrition Research Center, Houston, TX, USA
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11
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Ihekweazu FD, Fofanova TY, Queliza K, Nagy-Szakal D, Stewart CJ, Engevik MA, Hulten KG, Tatevian N, Graham DY, Versalovic J, Petrosino JF, Kellermayer R. Bacteroides ovatus ATCC 8483 monotherapy is superior to traditional fecal transplant and multi-strain bacteriotherapy in a murine colitis model. Gut Microbes 2019; 10:504-520. [PMID: 30663928 PMCID: PMC6748610 DOI: 10.1080/19490976.2018.1560753] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [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] [Indexed: 02/06/2023] Open
Abstract
Background and aims: Bacteriotherapy aimed at addressing dysbiosis may be therapeutic for Inflammatory Bowel Diseases (IBDs). We sought to determine if defined Bacteroides-based bacteriotherapy could be an effective and consistent alternative to fecal microbiota transplantation (FMT) in a murine model of IBD. Methods: We induced experimental colitis in 8- 12-week-old C57BL/6 mice using 2-3% dextran sodium sulfate. Mice were simultaneously treated by oral gavage with a triple-Bacteroides cocktail, individual Bacteroides strains, FMT using stool from healthy donor mice, or their own stool as a control. Survival, weight loss and markers of inflammation (histology, serum amyloid A, cytokine production) were correlated to 16S rRNA gene profiling of fecal and mucosal microbiomes. Results: Triple-Bacteroides combination therapy was more protective against weight loss and mortality than traditional FMT therapy. B. ovatus ATCC8483 was more effective than any individual strain, or a combination of strains, in preventing weight loss, decreasing histological damage, dampening inflammatory response, and stimulating epithelial recovery. Irrespective of the treatment group, overall Bacteroides abundance associated with treatment success and decreased cytokine production while the presence of Akkermansia correlated with treatment failure. However, the therapeutic benefit associated with high Bacteroides abundance was negated in the presence of Streptococcus. Conclusions: Bacteroides ovatus monotherapy was more consistent and effective than traditional FMT at ameliorating colitis and stimulating epithelial recovery in a murine model of IBD. Given the tolerability of Bacteroides ovatus ATCC 8483 in an active, on-going human study, this therapy may be repurposed for the management of IBD in a clinically expedient timeline.
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Affiliation(s)
- Faith D. Ihekweazu
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA,CONTACT Faith D. Ihekweazu Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, 1102 Bates Ave, FT860.28, Houston, TX 77030, USA
| | | | - Karen Queliza
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA
| | - Dorottya Nagy-Szakal
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Christopher J. Stewart
- Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Melinda A. Engevik
- Pediatric Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Kristina G. Hulten
- Pediatric Infectious Disease, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA
| | - Nina Tatevian
- Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David Y. Graham
- Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | - James Versalovic
- Pediatric Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | | | - Richard Kellermayer
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA
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12
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Anderson ME, Nagy-Szakal D, Jain K, Patrone CC, Frattini MG, Lipkin WI, Geskin LJ. Highly Sensitive Virome Capture Sequencing Technique VirCapSeq-VERT Identifies Partial Noncoding Sequences but no Active Viral Infection in Cutaneous T-Cell Lymphoma. J Invest Dermatol 2018; 138:1671-1673. [PMID: 29427587 DOI: 10.1016/j.jid.2018.01.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 11/18/2022]
Affiliation(s)
- Mary E Anderson
- Department of Dermatology, Columbia University Medical Center, New York, New York, USA
| | - Dorottya Nagy-Szakal
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Christina C Patrone
- Department of Dermatology, Columbia University Medical Center, New York, New York, USA
| | - Mark G Frattini
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Larisa J Geskin
- Department of Dermatology, Columbia University Medical Center, New York, New York, USA.
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13
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Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M, Lipkin WI. Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome 2017; 5:44. [PMID: 28441964 PMCID: PMC5405467 DOI: 10.1186/s40168-017-0261-y] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/04/2017] [Indexed: 05/27/2023]
Abstract
BACKGROUND Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained persistent fatigue, commonly accompanied by cognitive dysfunction, sleeping disturbances, orthostatic intolerance, fever, lymphadenopathy, and irritable bowel syndrome (IBS). The extent to which the gastrointestinal microbiome and peripheral inflammation are associated with ME/CFS remains unclear. We pursued rigorous clinical characterization, fecal bacterial metagenomics, and plasma immune molecule analyses in 50 ME/CFS patients and 50 healthy controls frequency-matched for age, sex, race/ethnicity, geographic site, and season of sampling. RESULTS Topological analysis revealed associations between IBS co-morbidity, body mass index, fecal bacterial composition, and bacterial metabolic pathways but not plasma immune molecules. IBS co-morbidity was the strongest driving factor in the separation of topological networks based on bacterial profiles and metabolic pathways. Predictive selection models based on bacterial profiles supported findings from topological analyses indicating that ME/CFS subgroups, defined by IBS status, could be distinguished from control subjects with high predictive accuracy. Bacterial taxa predictive of ME/CFS patients with IBS were distinct from taxa associated with ME/CFS patients without IBS. Increased abundance of unclassified Alistipes and decreased Faecalibacterium emerged as the top biomarkers of ME/CFS with IBS; while increased unclassified Bacteroides abundance and decreased Bacteroides vulgatus were the top biomarkers of ME/CFS without IBS. Despite findings of differences in bacterial taxa and metabolic pathways defining ME/CFS subgroups, decreased metabolic pathways associated with unsaturated fatty acid biosynthesis and increased atrazine degradation pathways were independent of IBS co-morbidity. Increased vitamin B6 biosynthesis/salvage and pyrimidine ribonucleoside degradation were the top metabolic pathways in ME/CFS without IBS as well as in the total ME/CFS cohort. In ME/CFS subgroups, symptom severity measures including pain, fatigue, and reduced motivation were correlated with the abundance of distinct bacterial taxa and metabolic pathways. CONCLUSIONS Independent of IBS, ME/CFS is associated with dysbiosis and distinct bacterial metabolic disturbances that may influence disease severity. However, our findings indicate that dysbiotic features that are uniquely ME/CFS-associated may be masked by disturbances arising from the high prevalence of IBS co-morbidity in ME/CFS. These insights may enable more accurate diagnosis and lead to insights that inform the development of specific therapeutic strategies in ME/CFS subgroups.
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Affiliation(s)
- Dorottya Nagy-Szakal
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | - Brent L. Williams
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | - Nischay Mishra
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | - Bohyun Lee
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | | | - Nancy G. Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314 USA
- Miami VA Medical Center, Miami, FL 33125 USA
| | | | | | | | - Daniel L. Peterson
- Sierra Internal Medicine at Incline Village, Incline Village, NV 89451 USA
| | | | - Komal Jain
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | - Meredith L. Eddy
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | - Mady Hornig
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, 722 W 168th Street 17th Floor, New York,, NY 10032 USA
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14
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Shah R, Cope JL, Nagy-Szakal D, Dowd S, Versalovic J, Hollister EB, Kellermayer R. Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis. Gut Microbes 2016; 7:384-96. [PMID: 27217061 PMCID: PMC5046168 DOI: 10.1080/19490976.2016.1190073] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic intestinal inflammatory disorders characterized by a complex disruption of the physiologic interaction between the host immune system and intestinal microbes precipitated by environmental factors. Numerous observations indicate the altered composition and function of the intestinal microbiome of patients with ulcerative colitis (UC), a subtype of IBD. The accuracy of these results may be limited by confounding factors, such as concurrent medication use. To address these limitations, we examined the colonic mucosal microbiome of pediatric patients with UC prior to initiating treatment. Based on bacterial 16S rRNA gene sequencing, we identified a significant decrease in the phylum Verrucomicrobia in patients with UC. At the genus level, we observed a significant decrease in the short chain fatty acid producer Roseburia. Despite these compositional changes, we did not identify inferred gene content differences between the UC and control groups. To determine if microbial taxa may be associated with clinical outcomes, we retrospectively assessed the clinical course of the UC patients. Despite similar metrics of OTU richness and diversity, multiple OTU differences were observed between patients who responded to therapy and those who did not. Our observations regarding the mucosal microbiome and the associations with differential clinical outcomes support the contributions of gut microbes to disease onset and modulation.
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Affiliation(s)
- Rajesh Shah
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Julia L. Cope
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Dorottya Nagy-Szakal
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,USDA/ARS Children's Nutrition Research Center, Texas Children's Hospital, Houston, TX, USA
| | - Scot Dowd
- Molecular Research (MR DNA), Shallowater, TX, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Emily B. Hollister
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Richard Kellermayer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,USDA/ARS Children's Nutrition Research Center, Texas Children's Hospital, Houston, TX, USA
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15
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Nagy-Szakal D, Mir SAV, Harris RA, Dowd SE, Yamada T, Lacorazza HD, Tatevian N, Smith CW, de Zoeten EF, Klein J, Kellermayer R. Loss of n-6 fatty acid induced pediatric obesity protects against acute murine colitis. FASEB J 2015; 29:3151-9. [PMID: 25903104 DOI: 10.1096/fj.14-267690] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 12/01/2014] [Accepted: 03/31/2015] [Indexed: 12/22/2022]
Abstract
Dietary influences may affect microbiome composition and host immune responses, thereby modulating propensity toward inflammatory bowel diseases (IBDs): Crohn disease (CD) and ulcerative colitis (UC). Dietary n-6 fatty acids have been associated with UC in prospective studies. However, the critical developmental period when (n-6) consumption may induce UC is not known. We examined the effects of transiently increased n-6 consumption during pediatric development on subsequent dextran-sulfate-sodium (DSS)-induced acute murine colitis. The animals transiently became obese then rapidly lost this phenotype. Interestingly, mice were protected against DSS colitis 40 days after n-6 consumption. The transient high n-6-induced protection against colitis was fat type- and dietary reversal-dependent and could be transferred to germ-free mice by fecal microbiota transplantation. We also detected decreased numbers of chemokine receptor (Cxcr)5(+) CD4(+) T cells in the mesenteric lymph nodes (MLNs) of transiently n-6-fed mice. Further experiments revealed that anti-chemokine ligand (Cxcl)13 (the ligand of Cxcr5) antibody treatment decreased DSS colitis severity, implicating the importance of the Cxcr5-Cxcl13 pathway in mammalian colitis. Consecutively, we found elevated CXCL13 concentrations (CD: 1.8-fold, P = 0.0077; UC: 1.9-fold, P = 0.056) in the serum of untreated pediatric IBD patients. The human serologic observations supported the translational relevance of our findings.
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Affiliation(s)
- Dorottya Nagy-Szakal
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - Sabina A V Mir
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - R Alan Harris
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - Scot E Dowd
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - Takeshi Yamada
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - H Daniel Lacorazza
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - Nina Tatevian
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - C Wayne Smith
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - Edwin F de Zoeten
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - John Klein
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
| | - Richard Kellermayer
- *Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children Hospital, Houston, Texas, USA; U.S. Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Molecular Research LP, Shallowater, Texas, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA; Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, USA; Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA; and **School of Dentistry, The University of Texas Health Science Center, Houston, Texas, USA
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Kellermayer R, Nagy-Szakal D, Harris RA, Luna RA, Pitashny M, Schady D, Mir SA, Lopez ME, Gilger MA, Belmont J, Hollister EB, Versalovic J. Serial fecal microbiota transplantation alters mucosal gene expression in pediatric ulcerative colitis. Am J Gastroenterol 2015; 110:604-6. [PMID: 25853207 PMCID: PMC4883582 DOI: 10.1038/ajg.2015.19] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Richard Kellermayer
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA,USDA/ARS Children's Nutrition Research Center, Houston, Texas, USA
| | - Dorottya Nagy-Szakal
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA,USDA/ARS Children's Nutrition Research Center, Houston, Texas, USA
| | - R. Alan Harris
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ruth Ann Luna
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Milena Pitashny
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Deborah Schady
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Sabina A.V. Mir
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA,USDA/ARS Children's Nutrition Research Center, Houston, Texas, USA
| | - Monica E. Lopez
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Mark A. Gilger
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA
| | - John Belmont
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Emily B. Hollister
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - James Versalovic
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
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Harris RA, Nagy-Szakal D, Mir SAV, Frank E, Szigeti R, Kaplan JL, Bronsky J, Opekun A, Ferry GD, Winter H, Kellermayer R. DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis. Epigenetics 2014; 9:1131-7. [PMID: 24937444 PMCID: PMC4164498 DOI: 10.4161/epi.29446] [Citation(s) in RCA: 50] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are emerging globally, indicating that environmental factors may be important in their pathogenesis. Colonic mucosal epigenetic changes, such as DNA methylation, can occur in response to the environment and have been implicated in IBD pathology. However, mucosal DNA methylation has not been examined in treatment-naïve patients. We studied DNA methylation in untreated, left sided colonic biopsy specimens using the Infinium HumanMethylation450 BeadChip array. We analyzed 22 control (C) patients, 15 untreated Crohn’s disease (CD) patients, and 9 untreated ulcerative colitis (UC) patients from two cohorts. Samples obtained at the time of clinical remission from two of the treatment-naïve UC patients were also included into the analysis. UC-specific gene expression was interrogated in a subset of adjacent samples (5 C and 5 UC) using the Affymetrix GeneChip PrimeView Human Gene Expression Arrays. Only treatment-naïve UC separated from control. One-hundred-and-twenty genes with significant expression change in UC (> 2-fold, P < 0.05) were associated with differentially methylated regions (DMRs). Epigenetically associated gene expression changes (including gene expression changes in the IFITM1, ITGB2, S100A9, SLPI, SAA1, and STAT3 genes) were linked to colonic mucosal immune and defense responses. These findings underscore the relationship between epigenetic changes and inflammation in pediatric treatment-naïve UC and may have potential etiologic, diagnostic, and therapeutic relevance for IBD.
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Affiliation(s)
- R Alan Harris
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston, TX USA
| | - Dorottya Nagy-Szakal
- Department of Pediatrics; Baylor College of Medicine; USDA/ARS Children's Nutrition Research Center; Texas Children's Hospital; Houston, TX USA
| | - Sabina A V Mir
- Department of Pediatrics; Baylor College of Medicine; USDA/ARS Children's Nutrition Research Center; Texas Children's Hospital; Houston, TX USA
| | - Eibe Frank
- Department of Computer Science; University of Waikato; Hamilton, New Zealand
| | - Reka Szigeti
- Department of Pathology; Baylor College of Medicine; Houston, TX USA
| | - Jess L Kaplan
- Department of Pediatrics; MassGeneral Hospital for Children; Boston, MA USA
| | - Jiri Bronsky
- Department of Pediatrics; Charles University and University Hospital Motol; Prague, Czech Republic
| | - Antone Opekun
- Department of Gastroenterology; Baylor College of Medicine; Houston, TX USA
| | - George D Ferry
- Department of Pediatrics; Baylor College of Medicine; USDA/ARS Children's Nutrition Research Center; Texas Children's Hospital; Houston, TX USA
| | - Harland Winter
- Department of Pediatrics; MassGeneral Hospital for Children; Boston, MA USA
| | - Richard Kellermayer
- Department of Pediatrics; Baylor College of Medicine; USDA/ARS Children's Nutrition Research Center; Texas Children's Hospital; Houston, TX USA
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18
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Affiliation(s)
- Sabina A V Mir
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA.
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19
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Mir SA, Nagy-Szakal D, Dowd SE, Szigeti RG, Smith CW, Kellermayer R. Prenatal methyl-donor supplementation augments colitis in young adult mice. PLoS One 2013; 8:e73162. [PMID: 23977377 PMCID: PMC3747105 DOI: 10.1371/journal.pone.0073162] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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: 03/20/2013] [Accepted: 07/17/2013] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD) have become highly prevalent in developed countries. Environmentally triggered exaggerated immune responses against the intestinal microbiome are thought to mediate the disorders. The potential dietary origins of the disease group have been implicated. However, the effects of environmental influences on prenatal developmental programming in respect to orchestrating postnatal microbiome composition and predilection towards mammalian colitis have not been examined. We tested how transient prenatal exposure to methyl donor micronutrient (MD) supplemented diets may impact predilection towards IBD in a murine dextran sulfate sodium (DSS) colitis model. Prenatal MD supplementation was sufficient to modulate colonic mucosal Ppara expression (3.2 fold increase; p=0.022) and worsen DSS colitis in young adulthood. The prenatal dietary exposure shifted the postnatal colonic mucosal and cecal content microbiomes. Transfer of the gut microbiome from prenatally MD supplemented young adult animals into germ free mice resulted in increased colitis susceptibility in the recipients compared to controls. Therefore, the prenatal dietary intervention induced the postnatal nurturing of a colitogenic microbiome. Our results show that prenatal nutritional programming can modulate the mammalian host to harbor a colitogenic microbiome. These findings may be relevant for the nutritional developmental origins of IBD.
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Affiliation(s)
- Sabina A. Mir
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Department of Agriculture/ARS Children’s Nutrition Research Center, Houston, Texas, United States of America
| | - Dorottya Nagy-Szakal
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Department of Agriculture/ARS Children’s Nutrition Research Center, Houston, Texas, United States of America
| | - Scot E. Dowd
- MR DNA (Molecular Research), Shallowater, Texas, United States of America
| | - Reka G. Szigeti
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
| | - C. Wayne Smith
- Section of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, Department of Agriculture/ARS Children’s Nutrition Research Center, Houston, Texas, United States of America
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Department of Agriculture/ARS Children’s Nutrition Research Center, Houston, Texas, United States of America
- * E-mail:
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20
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Nagy-Szakal D, Hollister EB, Luna RA, Szigeti R, Tatevian N, Smith CW, Versalovic J, Kellermayer R. Cellulose supplementation early in life ameliorates colitis in adult mice. PLoS One 2013; 8:e56685. [PMID: 23437211 PMCID: PMC3577696 DOI: 10.1371/journal.pone.0056685] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/14/2013] [Indexed: 01/19/2023] Open
Abstract
Decreased consumption of dietary fibers, such as cellulose, has been proposed to promote the emergence of inflammatory bowel diseases (IBD: Crohn disease [CD] and ulcerative colitis [UC]) where intestinal microbes are recognized to play an etiologic role. However, it is not known if transient fiber consumption during critical developmental periods may prevent consecutive intestinal inflammation. The incidence of IBD peaks in young adulthood indicating that pediatric environmental exposures may be important in the etiology of this disease group. We studied the effects of transient dietary cellulose supplementation on dextran sulfate sodium (DSS) colitis susceptibility during the pediatric period in mice. Cellulose supplementation stimulated substantial shifts in the colonic mucosal microbiome. Several bacterial taxa decreased in relative abundance (e.g., Coriobacteriaceae [p = 0.001]), and other taxa increased in abundance (e.g., Peptostreptococcaceae [p = 0.008] and Clostridiaceae [p = 0.048]). Some of these shifts persisted for 10 days following the cessation of cellulose supplementation. The changes in the gut microbiome were associated with transient trophic and anticolitic effects 10 days following the cessation of a cellulose-enriched diet, but these changes diminished by 40 days following reversal to a low cellulose diet. These findings emphasize the transient protective effect of dietary cellulose in the mammalian large bowel and highlight the potential role of dietary fibers in amelioration of intestinal inflammation.
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Affiliation(s)
- Dorottya Nagy-Szakal
- Section of Pediatric Gastroenterology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- USDA/ARS Children's Nutrition Research Center, Houston, Texas, United States of America
| | - Emily B. Hollister
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Ruth Ann Luna
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Reka Szigeti
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nina Tatevian
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - C. Wayne Smith
- USDA/ARS Children's Nutrition Research Center, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - James Versalovic
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- USDA/ARS Children's Nutrition Research Center, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
- * E-mail:
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21
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Abstract
Metastable epialleles (MEs) are mammalian genomic loci where epigenetic patterning occurs before gastrulation in a stochastic fashion leading to systematic interindividual variation within one species. Importantly, periconceptual nutritional influences may modulate the establishment of epigenetic changes, such as DNA methylation at MEs. Based on these characteristics, we exploited Infinium HumanMethylation450 BeadChip kits in a 2-tissue parallel screen on peripheral blood leukocyte and colonic mucosal DNA from 10 children without identifiable large intestinal disease. This approach led to the delineation of 1776 CpG sites meeting our criteria for MEs, which associated with 1013 genes. The list of ME candidates exhibited overlaps with recently identified human genes (including CYP2E1 and MGMT, where methylation has been associated with Parkinson disease and glioblastoma, respectively) in which perinatal DNA methylation levels where linked to maternal periconceptual nutrition. One hundred 18 (11.6%) of the ME candidates overlapped with genes where DNA methylation correlated (r > 0.871; p < 0.055) with expression in the colon mucosa of 5 independent control children. Genes involved in homophilic cell adhesion (including cadherin-associated genes) and developmental processes were significantly overrepresented in association with MEs. Additional filtering of gene expression-correlated MEs defined 35 genes, associated with 2 or more CpG sites within a 10 kb genomic region, fulfilling the ME criteria. DNA methylation changes at a number of these genes have been linked to various forms of human disease, including cancers, such as asthma and acute myeloid leukemia (ALOX12), gastric cancer (EBF3), breast cancer (NAV1), colon cancer and acute lymphoid leukemia (KCNK15), Wilms tumor (protocadherin gene cluster; PCDHAs) and colorectal cancer (TCERG1L), suggesting a potential etiologic role for MEs in tumorigenesis and underscoring the possible developmental origins of these malignancies. The presented compendium of ME candidates may accelerate our understanding of the epigenetic origins of common human disorders.
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Affiliation(s)
- R Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Harris RA, Nagy-Szakal D, Pedersen N, Opekun A, Bronsky J, Munkholm P, Jespersgaard C, Andersen PS, Melegh B, Ferry G, Jess T, Kellermayer R. Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases. Inflamm Bowel Dis 2012; 18:2334-41. [PMID: 22467598 PMCID: PMC3812910 DOI: 10.1002/ibd.22956] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 02/22/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Crohn's disease (CD) and ulcerative colitis (UC) are common forms of inflammatory bowel disease (IBD). Monozygotic (MZ) twin discordance rates and epidemiologic data implicate that environmental changes and epigenetic factors may play a pathogenic role in IBD. DNA methylation (the methylation of cytosines within CpG dinucleotides) is an epigenetic modification, which can respond to environmental influences. We investigated whether DNA methylation might be connected with IBD in peripheral blood leukocyte (PBL) DNA by utilizing genome-wide microarrays. METHODS Two different high-throughput microarray-based methods for genome-wide DNA methylation analysis were employed. First, DNA isolated from MZ twin pairs concordant (CD: 4; UC: 3) and discordant (CD: 4; UC: 7) for IBD was interrogated by a custom-made methylation-specific amplification microarray (MSAM). Second, the recently developed Illumina Infinium HumanMethylation450 BeadChip arrays were used on 48 samples of PBL DNA from discordant MZ twin pairs (CD: 3; UC: 3) and treatment-naive pediatric cases of IBD (CD: 14; UC: 8), as well as controls (n = 14). The microarrays were validated with bisulfite pyrosequencing. RESULTS The MSAMs did not yield significant IBD associations. The Methylation BeadChip approach identified a single DNA methylation association of IBD at TEPP (testis, prostate and placenta-expressed protein) when DNA isolated selectively from peripheral blood mononuclear cells was analyzed (8.6% increase in methylation between CD and control, FDR = 0.0065). CONCLUSIONS Microarray interrogation of IBD-dependent DNA methylation from PBLs appears to have limited ability to detect significant disease associations. More detailed and/or selective approaches may be useful for the elucidation of connections between the DNA methylome and IBD in the future.
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Affiliation(s)
- R. Alan. Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dorottya Nagy-Szakal
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA,USDA/ARS Children’s Nutrition Research Center, Houston, TX, USA
| | - Natalia Pedersen
- Gastroenterology Unit, Herlev University Hospital, Herlev, Denmark
| | - Antone Opekun
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA,Department of Gasteonterology-TMC Digestive Disease Center, Baylor College of Medicine
| | - Jiri Bronsky
- Department of Pediatrics, Second Medical Faculty, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pia Munkholm
- Gastroenterology Unit, Herlev University Hospital, Herlev, Denmark
| | - Cathrine Jespersgaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Bela Melegh
- Department of Medical Genetics, University of Pecs, Hungary
| | - George Ferry
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA
| | - Tine Jess
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Richard Kellermayer
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA,USDA/ARS Children’s Nutrition Research Center, Houston, TX, USA
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Nagy-Szakal D, Ross MC, Dowd SE, Mir SA, Schaible TD, Petrosino JF, Kellermayer R. Maternal micronutrients can modify colonic mucosal microbiota maturation in murine offspring. Gut Microbes 2012; 3:426-33. [PMID: 22713270 PMCID: PMC3679229 DOI: 10.4161/gmic.20697] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Epidemiologic data suggest that early nutritional exposures may inflict persistent changes in the developing mammalian "super-organism" (i.e., the host and its residing microbiota). Such persistent modifications could predispose young adults to inflammatory bowel diseases (IBD). We recently observed that the dietary supplementation of four micronutrients to dams augmented colitis susceptibility in murine offspring in association with mucosal microbiota composition changes. In this study the effects of the four micronutrients on the microbiota of dams and female mice was examined. Additionally, age dependent microbiota composition shifts during pediatric development were delineated from the previous offspring data sets. Maternal and adult female microbiota did not separate secondary to the nutritional intervention. Significant microbiota composition changes occurred from postnatal day 30 (P30) to P90 at the level of 1 phylum and 15 genera. Most of these changes were absent or opposite in the maternally supplemented offspring. Nutritionally induced alterations in mucosal microbiota maturation may be contributors to colitis susceptibility in mammals.
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Affiliation(s)
- Dorottya Nagy-Szakal
- Section of Pediatric Gastroenterology; Baylor College of Medicine; Texas Children's Hospital; Houston, TX USA
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research Center, Houston, TX USA
| | - Scot E. Dowd
- MR DNA Molecular Research LP, Shallowater, TX USA
| | - Sabina A.V. Mir
- Section of Pediatric Gastroenterology; Baylor College of Medicine; Texas Children's Hospital; Houston, TX USA
| | - Tiffany D. Schaible
- Section of Pediatric Gastroenterology; Baylor College of Medicine; Texas Children's Hospital; Houston, TX USA
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research Center, Houston, TX USA,Department of Molecular Virology and Microbiology; Baylor College of Medicine; Houston, TX, USA,Human Genome Sequencing Center; Houston, TX, USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology; Baylor College of Medicine; Texas Children's Hospital; Houston, TX USA,Correspondence to: Richard Kellermayer,
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Szigeti R, Pangas SA, Nagy-Szakal D, Dowd SE, Shulman RJ, Olive AP, Popek EJ, Finegold MJ, Kellermayer R. SMAD4 haploinsufficiency associates with augmented colonic inflammation in select humans and mice. Ann Clin Lab Sci 2012; 42:401-408. [PMID: 23090737 PMCID: PMC3875295] [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] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
SMAD4 is a common mediator of the TGF-beta signaling pathway. One of the members of this pathway, TGF-beta 1, has an important role in controlling gut inflammation in relation to the continuous stimulation of the intestinal microbiota. SMAD4 haploinsufficiency in humans has been linked to juvenile polyposis hereditary hemorrhagic telangiectasia syndrome (JP/HHT; OMIM#17505). Hematochezia and colonic mucosal inflammation suggestive of inflammatory bowel diseases (IBD) have been reported in JP/HHT. Stimulated by recent experience with two affected pediatric patients presented here, we explored the potential role of Smad4 haploinsufficiency in a murine model of colonic inflammation. Smad4(+/-) mice were maintained on a mixed C57/129SvEv background. Chronic colitis was induced with repeated administration of dextran sulfate sodium (DSS) in drinking water. The colonic mucosal microbiota was interrogated by massively parallel pyrosequencing of the bacterial 16S rRNA gene. 66.7% of Smad4(+/-) mice were sensitive to DSS colitis compared to 14.3% of wild type (Chi-Square p=0.036). The augmented colitis was associated with microbiota separation in the Smad4(+/-) mice. Enterococcus and Enterococcus faecalis specifically was increased in abundance in the colitis-prone animals. Smad4 haploinsufficiency can associate with increased susceptibility to large bowel inflammation in mammals with variable penetrance in association with the colonic mucosal microbiota. These findings may reveal implications not only towards colonic inflammation in the setting of SMAD4 haploinsufficiency, but for colorectal cancer as well.
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Affiliation(s)
- Reka Szigeti
- Department of Pathology and Immunology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Stephanie A. Pangas
- Department of Pathology and Immunology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Dorottya Nagy-Szakal
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Scot E. Dowd
- MR DNA Molecular Research LP, Shallowater, TX, USA
| | - Robert J. Shulman
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Anthony P. Olive
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Edwina J. Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Milton J. Finegold
- Department of Pathology and Immunology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX
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Abstract
The stunning complexity of the resident microbiota and the intricate pathways of microbial and host interactions provide a massive adaptive capacity for mammals. In this addendum we reflect on our recent publication on Toll-like receptor 2 deficiency related colonic mucosal epigenetic, immunologic and microbiomic changes. Our findings underscored the tremendous flexibility of the gut and its microbiota. This flexibility can provide means to overcome significant environmental or genetic challenges. In the meantime, the challenged intestinal system may become vulnerable to otherwise tolerable insults. In such instances, the fine-tuned mutualistic balance between the gut and its microflora may collapse leading to dysbiosis and disease. The ultimate challenge for biomedical research in these cases is to find optimal means for the restoration and maintenance of healthy host physiology.
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Affiliation(s)
- Dorottya Nagy-Szakal
- Section of Pediatric Gastroenterology; Department of Pediatrics; Baylor College of Medicine; Houston, TX USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology; Department of Pediatrics; Baylor College of Medicine; Houston, TX USA,Texas Children's Hospital; Houston, TX USA
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