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Selmin OI, Papoutsis AJ, Hazan S, Smith C, Greenfield N, Donovan MG, Wren SN, Doetschman TC, Snider JM, Snider AJ, Chow SHH, Romagnolo DF. n-6 High Fat Diet Induces Gut Microbiome Dysbiosis and Colonic Inflammation. Int J Mol Sci 2021; 22:ijms22136919. [PMID: 34203196 PMCID: PMC8269411 DOI: 10.3390/ijms22136919] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Concerns are emerging that a high-fat diet rich in n-6 PUFA (n-6HFD) may alter gut microbiome and increase the risk of intestinal disorders. Research is needed to model the relationships between consumption of an n-6HFD starting at weaning and development of gut dysbiosis and colonic inflammation in adulthood. We used a C57BL/6J mouse model to compare the effects of exposure to a typical American Western diet (WD) providing 58.4%, 27.8%, and 13.7% energy (%E) from carbohydrates, fat, and protein, respectively, with those of an isocaloric and isoproteic soybean oil-rich n-6HFD providing 50%E and 35.9%E from total fat and carbohydrates, respectively on gut inflammation and microbiome profile. Methods: At weaning, male offspring were assigned to either the WD or n-6HFD through 10-16 weeks of age. The WD included fat exclusively from palm oil whereas the n-6HFD contained fat exclusively from soybean oil. We recorded changes in body weight, cyclooxygenase-2 (COX-2) expression, colon histopathology, and gut microbiome profile. Results: Compared to the WD, the n-6HFD increased plasma levels of n-6 fatty acids; colonic expression of COX-2; and the number of colonic inflammatory and hyperplastic lesions. At 16 weeks of age, the n-6HFD caused a marked reduction in the gut presence of Firmicutes, Clostridia, and Lachnospiraceae, and induced growth of Bacteroidetes and Deferribacteraceae. At the species level, the n-6HFD sustains the gut growth of proinflammatory Mucispirillum schaedleri and Lactobacillus murinus. Conclusions: An n-6HFD consumed from weaning to adulthood induces a shift in gut bacterial profile associated with colonic inflammation.
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Affiliation(s)
- Ornella I. Selmin
- Department of Nutritional Sciences, The University of Arizona, Tucson, AZ 85721, USA; (O.I.S.); (S.N.W.); (J.M.S.); (A.J.S.)
- The University of Arizona Cancer Center, Tucson, AZ 85724, USA;
| | | | - Sabine Hazan
- ProgenomaBiome, Ventura, CA 93003, USA; (A.J.P.); (S.H.)
| | | | | | - Micah G. Donovan
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85724, USA;
| | - Spencer N. Wren
- Department of Nutritional Sciences, The University of Arizona, Tucson, AZ 85721, USA; (O.I.S.); (S.N.W.); (J.M.S.); (A.J.S.)
| | - Thomas C. Doetschman
- Department of Molecular and Cellular Medicine, The University of Arizona, Tucson, AZ 85724, USA;
| | - Justin M. Snider
- Department of Nutritional Sciences, The University of Arizona, Tucson, AZ 85721, USA; (O.I.S.); (S.N.W.); (J.M.S.); (A.J.S.)
| | - Ashley J. Snider
- Department of Nutritional Sciences, The University of Arizona, Tucson, AZ 85721, USA; (O.I.S.); (S.N.W.); (J.M.S.); (A.J.S.)
| | - Sherry H.-H. Chow
- The University of Arizona Cancer Center, Tucson, AZ 85724, USA;
- Department of Medicine, The University of Arizona, Tucson, AZ 85724, USA
| | - Donato F. Romagnolo
- Department of Nutritional Sciences, The University of Arizona, Tucson, AZ 85721, USA; (O.I.S.); (S.N.W.); (J.M.S.); (A.J.S.)
- The University of Arizona Cancer Center, Tucson, AZ 85724, USA;
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85724, USA;
- Correspondence:
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McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE. Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol 2019; 20:72. [PMID: 30953547 PMCID: PMC6450011 DOI: 10.1186/s13059-019-1687-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 11/10/2022] Open
Abstract
Following publication of the original article [1], the authors would like to highlight the following two corrections.
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Affiliation(s)
- Alexa B R McIntyre
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA.,School of Medicine, New York Medical College, Valhalla, NY, 10595, USA
| | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA, 95120, USA
| | - Elizabeth Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Samuel S Minot
- One Codex, Reference Genomics, San Francisco, CA, 94103, USA
| | - David Danko
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT, 05405, USA
| | - Nur A Hasan
- CosmosID, Inc, Rockville, MD, 20850, USA.,Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies (UMIACS), College Park, MD, 20742, USA
| | | | | | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Nick Greenfield
- One Codex, Reference Genomics, San Francisco, CA, 94103, USA
| | - Rita R Colwell
- CosmosID, Inc, Rockville, MD, 20850, USA.,Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gail L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, 19104, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA. .,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA. .,The Feil Family Brain and Mind Research Institute, New York, NY, 10065, USA.
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3
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McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol 2017; 18:182. [PMID: 28934964 PMCID: PMC5609029 DOI: 10.1186/s13059-017-1299-7] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [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: 02/07/2017] [Accepted: 08/16/2017] [Indexed: 12/25/2022] Open
Abstract
Background One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. Results In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. Conclusions This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1299-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexa B R McIntyre
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA.,School of Medicine, New York Medical College, Valhalla, NY, 10595, USA
| | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA, 95120, USA
| | - Elizabeth Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Samuel S Minot
- One Codex, Reference Genomics, San Francisco, CA, 94103, USA
| | - David Danko
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT, 05405, USA
| | - Nur A Hasan
- CosmosID, Inc, Rockville, MD, 20850, USA.,Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies (UMIACS), College Park, MD, 20742, USA
| | | | | | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Nick Greenfield
- One Codex, Reference Genomics, San Francisco, CA, 94103, USA
| | - Rita R Colwell
- CosmosID, Inc, Rockville, MD, 20850, USA.,Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gail L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, 19104, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA. .,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA. .,The Feil Family Brain and Mind Research Institute, New York, NY, 10065, USA.
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Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE. Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications. J Biomol Tech 2017; 28:46-55. [PMID: 28344519 DOI: 10.7171/jbt.17-2801-008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample. We extracted and sequenced genomic DNA (gDNA) from 8 environmental samples and compared the quality of the sequencing data for the MDA and their corresponding non-MDA samples. The degree of REPLI-g MDA bias was evaluated by sequence metrics, species composition, and cross-validating observed species abundance and species diversity estimates using the One Codex and MetaPhlAn taxonomic classification tools. Here, we provide evidence of the overall efficacy of REPLI-g MDA on retaining sequencing data quality and species abundance measurements while providing increased yields of high-fidelity DNA. We find that species abundance estimates are largely consistent across samples, even with REPLI-g amplification, as demonstrated by the Spearman's rank order coefficient (R2 > 0.8). However, REPLI-g MDA often produced fewer classified reads at the species, genera, and family level, resulting in decreased species diversity. We also observed some areas with the PCR "jackpot effect," with varying input DNA values for the Metagenomics Research Group (MGRG) controls at specific genomic loci. We visualize this effect in whole genome coverage plots and with sequence composition analyses and note these caveats of the MDA method. Despite overall concordance of species abundance between the amplified and unamplified samples, these results demonstrate that amplification of DNA using the REPLI-g method has some limitations. These concerns could be addressed by future improvements in the enzymes or methods for REPLI-g to be considered a >99% robust method for increasing the amount of high-fidelity DNA from low-biomass samples or at the very least, accounted for during computational analysis of MDA samples.
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Affiliation(s)
- Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA;; School of Medicine, New York Medical College, Valhalla, New York, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Mustafa Hakyemezoğlu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA;; Feil Family Brain & Mind Research Institute, New York, New York, USA
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5
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Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gómez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). J Biomol Tech 2017; 28:31-39. [PMID: 28337070 DOI: 10.7171/jbt.17-2801-004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.
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Affiliation(s)
- Scott Tighe
- Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; School of Medicine, New York Medical College, Valhalla, New York, USA
| | - Tara M Rock
- Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - Ken McGrath
- Australian Genome Research Facility, Gehrmann Labs, University of Queensland, St Lucia, QLD, Australia
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Alexa McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois, Chicago, Illinois, USA
| | - Samantha Joye
- Marine Sciences, The University of Georgia, Athens, Georgia, USA
| | | | - Don A Baldwin
- Signal Biology Inc., Philadelphia, Pennsylvania, USA
| | - Nathan Bivens
- DNA Core Facility, University of Missouri, Columbia, Missouri, USA
| | - Nadim Ajami
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph R Carmical
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ian Charold Herriott
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, Maryland, USA
| | - Mohamed Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | | | - Tim Hunter
- Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Jessica Hoffman
- Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Joshua Hyman
- UW Biotechnology Center, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | | | - Diana Krawczyk
- Greenland Institute of Natural Resources, Greenland Climate Research Centre, Nuuk, Greenland
| | - Jodie Lee
- Molecular Diagnostics, Qiagen, Germantown, Maryland, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Natàlia Garcia-Reyero
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, US Army Engineer Research & Development Center, Vicksburg, Mississippi, USA
| | - Matthew Settles
- Genome Center, University of California-Davis, Davis, California, USA
| | - Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Felipe Gómez
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir, Torrejon de Ardoz, Madrid, Spain
| | - Lynn Schriml
- Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nikos Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Jon Penterman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
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Greenfield N, Vijayanathan V, Thomas TJ, Gallo MA, Thomas T. Increase in the stability and helical content of estrogen receptor alpha in the presence of the estrogen response element: analysis by circular dichroism spectroscopy. Biochemistry 2001; 40:6646-52. [PMID: 11380259 DOI: 10.1021/bi002846l] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand-dependent stabilization of the estrogen receptor (ER) is often postulated, with limited support from experimental data. We studied the thermal unfolding of recombinant ERalpha by circular dichroism (CD) spectroscopy. The T(M) of unfolding of ERalpha was 38 +/- 2.4 degrees C, and the van't Hoff enthalpy of unfolding was 31.7 +/- 3.4 kcal/mol in the absence of ligands. Addition of estradiol (E(2)) increased the T(M) to 43.6 +/- 2.3 degrees C, while addition of E(2) and an oligonucleotide harboring the estrogen response element (ERE) increased the T(M) to 47.9 +/- 1.6 degrees C. Addition of the antiestrogen 4-hydroxytamoxifen (HT) alone did not increase the T(M); however, a combination of HT and the ERE increased the T(M) to 48.9 +/- 1.0 degrees C. The ERE alone increased the T(M) to 46.1 +/- 0.9 degrees C. Addition of E(2) alone had no effect on the apparent enthalpy of unfolding; however, the ERE alone increased the apparent enthalpy from 31.7 to 36.1 kcal/mol. ERalpha samples containing the ERE also exhibited an increase in the negative ellipticity at 208 and 222 nm, relative to that of ligand-free ERalpha, suggesting a stabilization of the alpha-helix. CD data analysis further showed that the presence of the ERE caused a large increase in alpha-helical content of ERalpha in both the presence and absence of the ligands. This increase in alpha-helical content of ERalpha was not observed in the presence of a nonspecific oligonucleotide. These results show that the ERE can increase the thermal stability of ERalpha, enhance its alpha-helical content, and facilitate the cooperativity of the folding transition.
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Affiliation(s)
- N Greenfield
- Departments of Neuroscience and Cell Biology, Medicine, and Environmental and Community Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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Kayed R, Bernhagen J, Greenfield N, Sweimeh K, Brunner H, Voelter W, Kapurniotu A. Conformational transitions of islet amyloid polypeptide (IAPP) in amyloid formation in vitro. J Mol Biol 1999; 287:781-96. [PMID: 10191146 DOI: 10.1006/jmbi.1999.2646] [Citation(s) in RCA: 315] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amyloid aggregates have been recognized to be a pathological hallmark of several fatal diseases, including Alzheimer's disease, the prion-related diseases, and type II diabetes. Pancreatic amyloidosis is characterized by the deposition of amyloid consisting of islet amyloid polypeptide (IAPP). We followed the steps preceding IAPP insolubilization and amyloid formation in vitro using a variety of biochemical methods, including a filtration assay, far and near-UV circular dichroism (CD) spectropolarimetry, 1-anilino-8-naphthalenesulfonic acid (ANS) binding, and atomic force (AFM) and electron (EM) microscopy. IAPP insolubilization and amyloid formation followed kinetics that were consistent with the nucleation-dependent polymerization mechanism. Nucleation of IAPP amyloid formation with traces of preformed fibrils induced a rapid conformational transition into beta-sheets that subsequently aggregated into insoluble amyloid fibrils. Transition proceeded via a molten globule-like conformeric state with large contents of secondary structure, fluctuating tertiary and quaternary aromatic interactions, and strongly solvent-exposed hydrophobic patches. In the temperature denaturation pathway at 5 microM peptide, we found that this state was mostly populated at about 45 degrees C, and either aggregated rapidly into amyloid by prolonged exposure to this temperature, or melted into denaturated but still structured IAPP, when heated further to 65 degrees C. The state at 45 degrees C was also found to be populated at 4.25 M GdnHCl at 25 degrees C during GdnHCl-induced equilibrium denaturation, and was stable in solution for several hours before aggregating into amyloid fibrils. Our studies suggested that this amyloidogenic state was a self-associated form of an aggregation-prone, partially folded state of IAPP. We propose that this partially folded population and its self-associated forms are in a concentration-dependent equilibrium with a non-amyloidogenic IAPP conformer and may act as early, soluble precursors of beta-sheet and amyloid formation. Our findings on the molecular mechanism of IAPP amyloid formation in vitro should assist in gaining insight into the pathogenesis and inhibition of pancreatic amyloidosis and other amyloid-related diseases.
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Affiliation(s)
- R Kayed
- University of Tübingen, Tübingen, D-72076, Germany
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Hu G, Vastardis H, Bendall AJ, Wang Z, Logan M, Zhang H, Nelson C, Stein S, Greenfield N, Seidman CE, Seidman JG, Abate-Shen C. Haploinsufficiency of MSX1: a mechanism for selective tooth agenesis. Mol Cell Biol 1998; 18:6044-51. [PMID: 9742121 PMCID: PMC109190 DOI: 10.1128/mcb.18.10.6044] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/1998] [Accepted: 07/16/1998] [Indexed: 11/20/2022] Open
Abstract
Previously, we found that the cause of autosomal dominant selective tooth agenesis in one family is a missense mutation resulting in an arginine-to-proline substitution in the homeodomain of MSX1. To determine whether the tooth agenesis phenotype may result from haploinsufficiency or a dominant-negative mechanism, we have performed biochemical and functional analyses of the mutant protein Msx1(R31P). We show that Msx1(R31P) has perturbed structure and reduced thermostability compared with wild-type Msx1. As a consequence, the biochemical activities of Msx1(R31P) are severely impaired, since it exhibits little or no ability to interact with DNA or other protein factors or to function in transcriptional repression. We also show that Msx1(R31P) is inactive in vivo, since it does not display the activities of wild-type Msx1 in assays of ectopic expression in the limb. Furthermore, Msx1(R31P) does not antagonize the activity of wild-type Msx1 in any of these assays. Because Msx1(R31P) appears to be inactive and does not affect the action of wild-type Msx1, we propose that the phenotype of affected individuals with selective tooth agenesis is due to haploinsufficiency.
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Affiliation(s)
- G Hu
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA
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Kapurniotu A, Bernhagen J, Greenfield N, Al-Abed Y, Teichberg S, Frank RW, Voelter W, Bucala R. Contribution of advanced glycosylation to the amyloidogenicity of islet amyloid polypeptide. Eur J Biochem 1998; 251:208-16. [PMID: 9492286 DOI: 10.1046/j.1432-1327.1998.2510208.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The formation of amyloid within the islets of Langerhans is associated with the development of type II diabetes mellitus and occurs by the aggregation and insolubilization of islet amyloid polypeptide (IAPP). Recent in vitro studies suggest that amyloid formation follows a nucleation-dependent polymerization mechanism, i.e. aggregation is initiated by pre-formed aggregates or nucleation seeds. Modification of the Alzheimer's disease amyloid peptide by advanced glycosylation end products (AGEs), which form spontaneously by the non-enzymatic addition of glucose to protein amino groups, has been shown to enhance peptide aggregation in vitro. To explore the possibility that AGEs contribute to islet amyloid formation, we prepared AGE-modified IAPP (AGE-IAPP) in vitro and studied its properties by biochemical and biophysical techniques. AGE modification induced the formation of high-molecular-mass IAPP aggregates and amyloid formation was demonstrated by Congo red green-gold birefringence and by the presence of a characteristic fibrillar structure by electron microscopy. AGE-IAPP also showed an increase in cytotoxicity toward the astroglioma cell line HTB14. When added to soluble IAPP, AGE-IAPP seeds accelerated IAPP aggregation and abolished the nucleation period required for the polymerization of unseeded IAPP. Circular dichroism spectropolarimetry indicated that AGE-IAPP seeds may act as a template to stabilize the beta-sheet conformation of IAPP, thereby promoting its aggregation. Our studies demonstrate that AGE modification of IAPP results in high-molecular mass, fibrillar amyloid structures that nucleate IAPP amyloid formation and suggest a model for intra-islet amyloid deposition that may occur by the progressive advanced glycosylation of IAPP in vivo.
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Affiliation(s)
- A Kapurniotu
- Abteilung für Physikalische Biochemie, Physiologisch-chemisches Institut der Universität Tübingen, Germany
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Thomas T, Kulkarni GD, Gallo MA, Greenfield N, Lewis JS, Shirahata A, Thomas TJ. Effects of natural and synthetic polyamines on the conformation of an oligodeoxyribonucleotide with the estrogen response element. Nucleic Acids Res 1997; 25:2396-402. [PMID: 9171091 PMCID: PMC146762 DOI: 10.1093/nar/25.12.2396] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We studied the effects of natural and synthetic polyamines on the conformation of an oligodeoxyribonucleotide (ODN1) harboring the estrogen response element (ERE) by circular dichroism (CD) spectroscopy and polyacrylamide gel electrophoresis. Putrescine and spermidine had no marked effect on the CD spectrum of ODN1. In contrast, spermine provoked and stabilized two characteristic changes in the CD spectrum. The first change was indicated by an increase in the intensity of the CD band at 280 nm at 0.5 mM spermine in Tris-HCl buffer containing 50 mM NaCl. This change appears to be related to changes in base tilt and conformational alterations similar to A-DNA. At 1-2 mM spermine, the CD spectrum was characterized by a loss of positive bands at 220 and 270 nm. This change might have contributions from polyamine-induced condensation/aggregation of DNA. Spectral measurements were also conducted in Tris-HCl buffer containing 150 mM NaCl to minimize contributions from condensation and aggregation of ODN1. Under these conditions, CD spectral changes were retained by (ODN1), although the magnitude of the change was diminished. In contrast, a control oligdeoxyribonucleotide (ODN2) having similar base composition did not show any significant change in the CD spectrum in the presence of 150 mM NaCl and 2 mM spermine. The changes in the CD spectrum of ODN1 were highly sensitive to polyamine structure, as evidenced by experiments using spermine analogs with altered number of -CH2- groups separating the amino and imino groups. Electrophoretic mobility shift analysis further showed ODN1 stabilization by spermine and its analogs. These data demonstrate the ability of an ODN containing ERE to undergo conformational transitions in the presence of polyamines and suggest a possible mechanism for polyamine-mediated alterations in the interaction of estrogen receptor with ERE.
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Affiliation(s)
- T Thomas
- Department of Environmental and Community Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
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Greenfield N, Ponticorvo L, Chasalow F, Lieberman S. Activation and inhibition of the adrenal steroid 21-hydroxylation system by cytosolic constituents: influence of glutathione, glutathione reductase, and ascorbate. Arch Biochem Biophys 1980; 200:232-44. [PMID: 6965849 DOI: 10.1016/0003-9861(80)90350-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Ponticorvo L, Greenfield N, Wolfson A, Chasalow F, Lieberman S. The nature of the cytosolic activators of the adrenal steroid 21-hydroxylation system. Arch Biochem Biophys 1980; 200:223-31. [PMID: 6965848 DOI: 10.1016/0003-9861(80)90349-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Greenfield N, Davidson B, Fasman GD. The use of computed optical rotatory dispersion curves for the evaluation of protein conformation. Biochemistry 1967; 6:1630-7. [PMID: 6035904 DOI: 10.1021/bi00858a009] [Citation(s) in RCA: 181] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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