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Oprea TI, Bologa C, Holmes J, Mathias S, Metzger VT, Waller A, Yang JJ, Leach AR, Jensen LJ, Kelleher KJ, Sheils TK, Mathé E, Avram S, Edwards JS. Overview of the Knowledge Management Center for Illuminating the Druggable Genome. Drug Discov Today 2024; 29:103882. [PMID: 38218214 PMCID: PMC10939799 DOI: 10.1016/j.drudis.2024.103882] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) project aims to aggregate, update, and articulate protein-centric data knowledge for the entire human proteome, with emphasis on the understudied proteins from the three IDG protein families. KMC collates and analyzes data from over 70 resources to compile the Target Central Resource Database (TCRD), which is the web-based informatics platform (Pharos). These data include experimental, computational, and text-mined information on protein structures, compound interactions, and disease and phenotype associations. Based on this knowledge, proteins are classified into different Target Development Levels (TDLs) for identification of understudied targets. Additional work by the KMC focuses on enriching target knowledge and producing DrugCentral and other data visualization tools for expanding investigation of understudied targets.
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Affiliation(s)
- Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Cristian Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Stephen Mathias
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Vincent T Metzger
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Anna Waller
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jeremy J Yang
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Keith J Kelleher
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Timothy K Sheils
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Ewy Mathé
- National Center for Advancing Translational Sciences (NCATS), NIH, Bethesda, MD, USA
| | - Sorin Avram
- Coriolan Dragulescu Institute of Chemistry, Timisoara, Romania
| | - Jeremy S Edwards
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA.
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2
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Abok JI, Garver WS, Edwards JS. Bioinformatic analysis of human ZPR1 gene pathogenic exome mutations. bioRxiv 2024:2024.02.27.582196. [PMID: 38464185 PMCID: PMC10925172 DOI: 10.1101/2024.02.27.582196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Advanced sequencing technologies enable rapid detection of sequence variants, aiming to uncover the molecular foundations of human genetic disorders. The challenge lies in interpreting the influence of new exome variants that lead to diverse phenotypes. Our study introduces a detailed, multi-tiered method for assessing the impact of novel variants, particularly focusing on the zinc finger protein 1 (ZPR1) gene. Herein, we employed a combination of variant effect predictors, protein stability analyses, and the American College of Medical Genetics and Association of Molecular Pathology (ACMG/AMP) guidelines. Our structural analysis pinpoints specific amino acid residues in the ZPR1 zinc finger domains that are sensitive to changes, distinguishing between benign and disease-causing coding variants using rigorous in silico tools. We examined 223 germline ZPR1 exome variants, uncovering significant ethnic disparities in the frequency of heterozygous harmful ZPR1 variants, ranging from 0.04% in the Ashkenazi Jewish population to 0.34% in African/African Americans. Additionally, the discovery of three homozygous carriers in European and South Asian groups suggests a higher occurrence of ZPR1 variants in these demographics, meriting further exploration. This research provides insights into the prevalence and implications of amino acid substitutions in the ZPR1 protein.
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Affiliation(s)
- Jeremiah I. Abok
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - William S. Garver
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
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3
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Shimada R, Alden EN, Hoff K, Ding X, Sun J, Halasz AM, Zhou W, Edwards JS. SARS-CoV-2 variant identification using a genome tiling array and genotyping probes. Per Med 2023; 20:13-25. [PMID: 36974726 DOI: 10.2217/pme-2022-0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
With over 5.5 million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. The authors previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome compared with traditional short-read sequencing methods which can be time-consuming and costly. Herein, the addition of genotyping probes to a DNA chip that targets known SARS-CoV-2 variants is presented. The incorporation of genotyping probe sets along with the advent of a moving average filter improved the sequencing coverage and accuracy of the SARS-CoV-2 genome.
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Affiliation(s)
- Ryota Shimada
- Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Emily N Alden
- Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Kendall Hoff
- Centrillion Technologies, Palo Alto, CA 94303, USA
| | - Xun Ding
- Centrillion Technologies, Palo Alto, CA 94303, USA
| | - Jiayi Sun
- Centrillion Technologies, Palo Alto, CA 94303, USA
| | - Adam M Halasz
- Department of Mathematics, West Virginia University, Morgantown, WV 26506, USA
| | - Wei Zhou
- Centrillion Technologies, Palo Alto, CA 94303, USA
| | - Jeremy S Edwards
- Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
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4
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Kerketta R, Erasmus MF, Wilson BS, Halasz AM, Edwards JS. Spatial Stochastic Model of the Pre-B Cell Receptor. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:683-693. [PMID: 35482702 PMCID: PMC10123485 DOI: 10.1109/tcbb.2022.3166149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Survival and proliferation of immature B lymphocytes requires expression and tonic signaling of the pre-B cell receptor (pre-BCR). This low level, ligand-independent signaling is likely achieved through frequent, but short-lived, homo interactions. Tonic signaling is also central in the pathology of precursor B acute lymphoblastic leukemia (B-ALL). In order to understand how repeated, transient events can lead to sustained signaling and to assess the impact of receptor accumulation induced by the membrane landscape, we developed a spatial stochastic model of receptor aggregation and downstream signaling events. Our rule- and agent-based model builds on previous mature BCR signaling models and incorporates novel parameters derived from single particle tracking of pre-BCR on surfaces of two different B-ALL cell lines, 697 and Nalm6. Live cell tracking of receptors on the two cell lines revealed characteristic differences in their dimer dissociation rates and diffusion coefficients. We report here that these differences affect pre-BCR aggregation and consequent signal initiation events. Receptors on Nalm6 cells, which have a lower off-rate and lower diffusion coefficient, more frequently form higher order oligomers than pre-BCR on 697 cells, resulting in higher levels of downstream phosphorylation in the Nalm6 cell line.
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Kim HS, Blazyte A, Jeon S, Yoon C, Kim Y, Kim C, Bolser D, Ahn JH, Edwards JS, Bhak J. LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads. GigaByte 2022; 2022:gigabyte51. [PMID: 36824523 PMCID: PMC9650228 DOI: 10.46471/gigabyte.51] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly, constructed using 57× nanopore long reads and polished using 47× short paired-end reads. We utilized 72 GB of Hi-C chromosomal mapping data for scaffolding, to maximize assembly contiguity and accuracy. The contig assembly of LT1 was 2.73 Gbp in length, comprising 4490 contigs with an NG50 value of 12.0 Mbp. After scaffolding with Hi-C data and manual curation, the final assembly has an NG50 value of 137 Mbp and 4699 scaffolds. Assessment of gene prediction quality using Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 89.3% of the single-copy orthologous genes included in the benchmark. Detailed characterization of LT1 suggests it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,616 short indels, and 12,079 large structural variants. These data may be used as a benchmark for further in-depth genomic analyses of Baltic populations.
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Affiliation(s)
- Hui-Su Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea, Corresponding authors. E-mail: ;
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeonkyung Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changjae Kim
- Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dan Bolser
- Geromics Ltd., Suite 1, Frohock House, 222 Mill Road, Cambridge, CB1 3NF, UK
| | - Ji-Hye Ahn
- Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Geromics Ltd., Suite 1, Frohock House, 222 Mill Road, Cambridge, CB1 3NF, UK, Corresponding authors. E-mail: ;
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6
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Güven E, Wester MJ, Edwards JS, Halász ÁM. Modeling the Cluster Size Distribution of Vascular Endothelial Growth Factor (VEGF) Receptors. Bioinform Biol Insights 2022; 16:11779322221085078. [PMID: 35356495 PMCID: PMC8958695 DOI: 10.1177/11779322221085078] [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] [Received: 12/09/2021] [Accepted: 02/12/2022] [Indexed: 11/15/2022] Open
Abstract
We previously developed a method of defining receptor clusters in the membrane based on mutual distance and applied it to a set of transmission microscopy images of vascular endothelial growth factor receptors. An optimal length parameter was identified, resulting in cluster identification and a procedure that assigned a geometric shape to each cluster. We showed that the observed particle distribution results were consistent with the random placement of receptors within the clusters and, to a lesser extent, the random placement of the clusters on the cell membrane. Here, we develop and validate a stochastic model of clustering, based on a hypothesis of preexisting domains that have a high affinity for receptors. The proximate objective is to clarify the mechanism behind cluster formation and to estimate the effect on signaling. Receptor-enriched domains may significantly impact signaling pathways that rely on ligand-induced dimerization of receptors. We define a simple statistical model, based on the preexisting domain hypothesis, to predict the probability distribution of cluster sizes. The process yielded sets of parameter values that can readily be used in dynamical calculations as the estimates of the quantitative characteristics of the clustering domains.
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Affiliation(s)
- Emine Güven
- Department of Biomedical Engineering, Düzce University, Düzce, Turkey
| | - Michael J Wester
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, USA
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Jeremy S Edwards
- Department of Chemistry and Chemical Biology University of New Mexico, Albuquerque, NM, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ádám M Halász
- Mathematics, West Virginia University, Morgantown, WV, USA
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7
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Shimada R, Alden EN, Hoff K, Ding X, Sun J, Halasz AM, Zhou W, Edwards JS. SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes. bioRxiv 2021:2021.05.11.443659. [PMID: 34013279 PMCID: PMC8132287 DOI: 10.1101/2021.05.11.443659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With over three million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. We previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome when compared to traditional short read sequencing methods which can be time consuming and costly. Herein we present the addition of genotyping probes to our DNA chip which target known SARS-CoV-2 variants. The incorporation of the genotyping probe sets along with the advent of a moving average filter have improved our sequencing coverage and accuracy of the SARS-CoV-2 genome.
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8
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Hoff K, Ding X, Carter L, Duque J, Lin JY, Dung S, Singh P, Sun J, Crnogorac F, Swaminathan R, Alden EN, Zhu X, Shimada R, Posavi M, Hull N, Dinwiddie D, Halasz AM, McGall G, Zhou W, Edwards JS. Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples. Langmuir 2021; 37:4763-4771. [PMID: 33848173 PMCID: PMC8056606 DOI: 10.1021/acs.langmuir.0c02927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/31/2021] [Indexed: 06/02/2023]
Abstract
SARS-CoV-2 has infected over 128 million people worldwide, and until a vaccine is developed and widely disseminated, vigilant testing and contact tracing are the most effective ways to slow the spread of COVID-19. Typical clinical testing only confirms the presence or absence of the virus, but rather, a simple and rapid testing procedure that sequences the entire genome would be impactful and allow for tracing the spread of the virus and variants, as well as the appearance of new variants. However, traditional short read sequencing methods are time consuming and expensive. Herein, we describe a tiled genome array that we developed for rapid and inexpensive full viral genome resequencing, and we have applied our SARS-CoV-2-specific genome tiling array to rapidly and accurately resequence the viral genome from eight clinical samples. We have resequenced eight samples acquired from patients in Wyoming that tested positive for SARS-CoV-2. We were ultimately able to sequence over 95% of the genome of each sample with greater than 99.9% average accuracy.
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Affiliation(s)
| | - Xun Ding
- Centrillion Technologies, Palo Alto, CA 94303
| | | | - John Duque
- Centrillion Technologies, Palo Alto, CA 94303
| | - Ju-Yu Lin
- Centrillion Technologies, Palo Alto, CA 94303
| | | | | | - Jiayi Sun
- Centrillion Technologies, Palo Alto, CA 94303
| | | | - Radha Swaminathan
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Emily N Alden
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Xuechen Zhu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Ryota Shimada
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Marijan Posavi
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Noah Hull
- Wyoming Public Health Laboratory, Wyoming Department of Health, Cheyenne, WY 82007
| | - Darrell Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
| | - Adam M. Halasz
- Department of Mathematics, West Virginia University, Morgantown, WV, 26506
| | | | - Wei Zhou
- Centrillion Technologies, Palo Alto, CA 94303
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
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9
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Jeon Y, Jeon S, Blazyte A, Kim YJ, Lee JJ, Bhak Y, Cho YS, Park Y, Noh EK, Manica A, Edwards JS, Bolser D, Kim S, Lee Y, Yoon C, Lee S, Kim BC, Park NH, Bhak J. Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling. Front Genet 2021; 12:633731. [PMID: 33633791 PMCID: PMC7900555 DOI: 10.3389/fgene.2021.633731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/27/2020] [Accepted: 01/20/2021] [Indexed: 12/27/2022] Open
Abstract
The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016 in the Ulsan Metropolitan City as the first large-scale genome project with public participation in Korea. The project produced a set of genetic materials, genotype information, clinical data, and lifestyle survey answers from participants aged 20–96. As compensation, the participants received a free general health check-up on 110 clinical traits, accompanied by a genetic report of their genotypes followed by genetic counseling. In a follow-up survey, 91.0% of the participants indicated that their genetic reports motivated them to improve their health. Overall, WGP expanded not only the general awareness of genomics, DNA sequencing technologies, bioinformatics, and bioethics regulations among all the parties involved, but also the general public’s understanding of how genome projects can indirectly benefit their health and lifestyle management. WGP established a data construction framework for not only scientific research but also the welfare of participants. In the future, the WGP framework can help lay the groundwork for a new personalized healthcare system that is seamlessly integrated with existing public medical infrastructure.
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Affiliation(s)
- Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | | | - Jasmin Junseo Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Human Biology Program, Faculty of Arts and Sciences, University of Toronto, Toronto, ON, Canada
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | | | - Yeshin Park
- Clinomics Inc., Ulsan, South Korea.,Department of Medical Sciences, Graduate School of Ajou University School, Suwon, South Korea
| | - Eui-Kyu Noh
- Department of Hematology and Oncology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, South Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Jeremy S Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, United States
| | - Dan Bolser
- Geromics Ltd., Cambridge, United Kingdom
| | - Sukyeon Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Yuji Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | | | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, South Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Clinomics Inc., Ulsan, South Korea.,Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong, South Korea
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10
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Jeon S, Bhak Y, Choi Y, Jeon Y, Kim S, Jang J, Jang J, Blazyte A, Kim C, Kim Y, Shim J, Kim N, Kim YJ, Park SG, Kim J, Cho YS, Park Y, Kim HM, Kim BC, Park NH, Shin ES, Kim BC, Bolser D, Manica A, Edwards JS, Church G, Lee S, Bhak J. Korean Genome Project: 1094 Korean personal genomes with clinical information. Sci Adv 2020; 6:eaaz7835. [PMID: 32766443 PMCID: PMC7385432 DOI: 10.1126/sciadv.aaz7835] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/19/2020] [Indexed: 05/30/2023]
Abstract
We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonsong Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Seunghoon Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jaeyoung Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jinho Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changjae Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonkyung Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungae Shim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Nayeong Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeo Jin Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seung Gu Park
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
| | | | - Yeshin Park
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | | | - Neung-Hwa Park
- Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
- Biomedical Research Center, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan 44686, Republic of Korea
| | | | - Dan Bolser
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico and University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87106, USA
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
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11
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Hoff K, Halpain M, Garbagnati G, Edwards JS, Zhou W. Enzymatic Synthesis of Designer DNA Using Cyclic Reversible Termination and a Universal Template. ACS Synth Biol 2020; 9:283-293. [PMID: 31895546 DOI: 10.1021/acssynbio.9b00315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 02/08/2023]
Abstract
Phosphoramidite chemistry remains the industry standard for DNA synthesis despite significant limitations on the length and yield of the oligonucleotide, time restrictions, and hazardous waste production. Herein, we demonstrate the synthesis of single-stranded oligos on a solid surface by DNA polymerases and reverse transcriptases. We report the extension of surface-bound oligonucleotides enabled by transient hybridization of as few as two bases to a neighboring strand. When multiple hybridization structures are possible, each templating a different base, a DNA polymerase or reverse transcriptase can extend the oligonucleotide with any of the complementary bases. Therefore, the sequence of the newly synthesized fragment can be controlled by adding only the desired base as a substrate to the reaction solution. We used this enzymatic approach to synthesize a 20 base oligonucleotide by incorporating reversible terminator dNTPs through a two-step cyclic reversible termination process with a corrected stepwise efficiency over 98%. In our approach, a nascent DNA strand that serves as both primer and template is extended through polymerase-controlled sequential addition of 3'-reversibly blocked nucleotides followed by subsequent cleavage of the 3'-capping group. This process enables oligonucleotide synthesis in an environment not permitted by traditional phosphoramidite methods, eliminates the need for hazardous chemicals, has the potential to provide faster and higher yield results, and synthesizes DNA on a solid support with a free 3' end.
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Affiliation(s)
- Kendall Hoff
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
| | - Michelle Halpain
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
| | - Giancarlo Garbagnati
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
| | - Jeremy S. Edwards
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
- Chemistry and Chemical Biology and Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico 87131, United States
| | - Wei Zhou
- Department of Advanced Research and Development, Centrillion Biosciences, Palo Alto, California 94303, United States
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12
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Lee H, Kim J, Weber JA, Chung O, Cho YS, Jho S, Jun J, Kim HM, Lim J, Choi JP, Jeon S, Blazyte A, Edwards JS, Paek WK, Bhak J. Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity. Mol Cells 2020; 43:86-95. [PMID: 31940721 PMCID: PMC6999708 DOI: 10.14348/molcells.2019.0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane's long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified redcrowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH , RPA1, PHAX, HNMT , HS2ST1 , PPCDC , PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species.
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Affiliation(s)
- HyeJin Lee
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Jungeun Kim
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Jessica A. Weber
- Department of Genetics, Harvard Medical School, Boston, MA 02115,
USA
| | | | | | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | | | - Hak-Min Kim
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Jeongheui Lim
- National Science Museum, Ministry of Science and ICT, Daejeon 34143,
Korea
| | - Jae-Pil Choi
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Sungwon Jeon
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Asta Blazyte
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Jeremy S. Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131,
USA
| | - Woon Kee Paek
- National Science Museum, Ministry of Science and ICT, Daejeon 34143,
Korea
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
- Clinomics, Ulsan 44919,
Korea
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
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13
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Cho YS, Jun JH, Kim JA, Kim HM, Chung O, Kang SG, Park JY, Kim HJ, Kim S, Kim HJ, Jang JH, Na KJ, Kim J, Park SG, Lee HY, Manica A, Mindell DP, Fuchs J, Edwards JS, Weber JA, Witt CC, Yeo JH, Kim S, Bhak J. Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles. Genome Biol 2019; 20:181. [PMID: 31464627 PMCID: PMC6714440 DOI: 10.1186/s13059-019-1793-1] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 08/13/2019] [Indexed: 01/11/2023] Open
Abstract
Background Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. Results Here, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identify common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems, such as loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems that are convergent with other nocturnal avian orders. Additionally, we find that a suite of genes associated with vision and circadian rhythm are differentially expressed in blood tissue between nocturnal and diurnal raptors, possibly indicating adaptive expression change during the transition to nocturnality. Conclusions Overall, raptor genomes show genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators. Electronic supplementary material The online version of this article (10.1186/s13059-019-1793-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Jung A Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Hak-Min Kim
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | | | - Seung-Gu Kang
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Jin-Young Park
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Hwa-Jung Kim
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Sunghyun Kim
- Strategic Planning Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Hee-Jong Kim
- Chungnam Wild Animal Rescue Center, Kongju National University, Yesan, Republic of Korea
| | - Jin-Ho Jang
- Chungnam Wild Animal Rescue Center, Kongju National University, Yesan, Republic of Korea
| | - Ki-Jeong Na
- College of veterinary medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Jeongho Kim
- Medical care team, Cheongju Zoo, Cheongju, Republic of Korea
| | - Seung Gu Park
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | | | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - David P Mindell
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Jérôme Fuchs
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Jessica A Weber
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Joo-Hong Yeo
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Soonok Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea.
| | - Jong Bhak
- Clinomics Inc, Ulsan, Republic of Korea. .,Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea. .,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
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14
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Kim HM, Weber JA, Lee N, Park SG, Cho YS, Bhak Y, Lee N, Jeon Y, Jeon S, Luria V, Karger A, Kirschner MW, Jo YJ, Woo S, Shin K, Chung O, Ryu JC, Yim HS, Lee JH, Edwards JS, Manica A, Bhak J, Yum S. The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation. BMC Biol 2019; 17:28. [PMID: 30925871 PMCID: PMC6441219 DOI: 10.1186/s12915-019-0643-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 01/08/2019] [Accepted: 02/28/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. RESULTS We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura's jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). CONCLUSIONS Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.
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Affiliation(s)
- Hak-Min Kim
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jessica A Weber
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nayoung Lee
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Seung Gu Park
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yun Sung Cho
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Clinomics Inc., Ulsan, 44919, Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Nayun Lee
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Victor Luria
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Amir Karger
- IT - Research Computing, Harvard Medical School, Boston, MA, 02115, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ye Jin Jo
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Seonock Woo
- Faculty of Marine Environmental Science, University of Science and Technology (UST), Geoje, 53201, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Kyoungsoon Shin
- Ballast Water Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea
| | - Oksung Chung
- Clinomics Inc., Ulsan, 44919, Republic of Korea
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Jae-Chun Ryu
- Cellular and Molecular Toxicology Laboratory, Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Hyung-Soon Yim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Jong Bhak
- Korean Genomics Industrialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Clinomics Inc., Ulsan, 44919, Republic of Korea.
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
| | - Seungshic Yum
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea.
- Faculty of Marine Environmental Science, University of Science and Technology (UST), Geoje, 53201, Republic of Korea.
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15
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Pallikkuth S, Martin C, Farzam F, Edwards JS, Lakin MR, Lidke DS, Lidke KA. Sequential super-resolution imaging using DNA strand displacement. PLoS One 2018; 13:e0203291. [PMID: 30169528 PMCID: PMC6118358 DOI: 10.1371/journal.pone.0203291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022] Open
Abstract
Sequential labeling and imaging in fluorescence microscopy allows the imaging of multiple structures in the same cell using a single fluorophore species. In super-resolution applications, the optimal dye suited to the method can be chosen, the optical setup can be simpler and there are no chromatic aberrations between images of different structures. We describe a method based on DNA strand displacement that can be used to quickly and easily perform the labeling and removal of the fluorophores during each sequence. Site-specific tags are conjugated with unique and orthogonal single stranded DNA. Labeling for a particular structure is achieved by hybridization of antibody-bound DNA with a complimentary dye-labeled strand. After imaging, the dye is removed using toehold-mediated strand displacement, in which an invader strand competes off the dye-labeled strand than can be subsequently washed away. Labeling and removal of each DNA-species requires only a few minutes. We demonstrate the concept using sequential dSTORM super-resolution for multiplex imaging of subcellular structures.
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Affiliation(s)
- Sandeep Pallikkuth
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Cheyenne Martin
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Farzin Farzam
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Jeremy S. Edwards
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Matthew R. Lakin
- Department of Computer Science, University of New Mexico, Albuquerque, New Mexico, United States of America
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Diane S. Lidke
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Keith A. Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- * E-mail:
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16
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Abstract
Background Next-generation sequencing (NGS) has revolutionized almost all fields of biology, agriculture and medicine, and is widely utilized to analyse genetic variation. Over the past decade, the NGS pipeline has been steadily improved, and the entire process is currently relatively straightforward. However, NGS instrumentation still requires upfront library preparation, which can be a laborious process, requiring significant hands-on time. Herein, we present a simple but robust approach to streamline library preparation by utilizing surface bound transposases to construct DNA libraries directly on a flowcell surface. Results The surface bound transposases directly fragment genomic DNA while simultaneously attaching the library molecules to the flowcell. We sequenced and analysed a Drosophila genome library generated by this surface tagmentation approach, and we showed that our surface bound library quality was comparable to the quality of the library from a commercial kit. In addition to the time and cost savings, our approach does not require PCR amplification of the library, which eliminates potential problems associated with PCR duplicates. Conclusions We described the first study to construct libraries directly on a flowcell. We believe our technique could be incorporated into the existing Illumina sequencing pipeline to simplify the workflow, reduce costs, and improve data quality.
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Affiliation(s)
- Kuan Feng
- Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Justin Costa
- Special Projects, Centrillion Technologies, Palo Alto, CA, 94303, USA
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA. .,Internal Medicine, Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA. .,University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87131, USA. .,University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
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17
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Kim J, Weber JA, Jho S, Jang J, Jun J, Cho YS, Kim HM, Kim H, Kim Y, Chung O, Kim CG, Lee H, Kim BC, Han K, Koh I, Chae KS, Lee S, Edwards JS, Bhak J. KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses. Sci Rep 2018; 8:5677. [PMID: 29618732 PMCID: PMC5885007 DOI: 10.1038/s41598-018-23837-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 09/22/2017] [Accepted: 03/16/2018] [Indexed: 01/05/2023] Open
Abstract
High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. We report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project when prioritizing disease-causing variants. KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.
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Affiliation(s)
- Jungeun Kim
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
| | - Jessica A Weber
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
| | - Jinho Jang
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - JeHoon Jun
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
- Geromics, Ulsan, 44919, Republic of Korea
| | | | - Hak-Min Kim
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan, 44919, Republic of Korea
| | - Yumi Kim
- Geromics, Ulsan, 44919, Republic of Korea
| | - OkSung Chung
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
- Geromics, Ulsan, 44919, Republic of Korea
| | - Chang Geun Kim
- National Standard Reference Center, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea
| | - HyeJin Lee
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
| | | | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - InSong Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Kyun Shik Chae
- National Standard Reference Center, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea.
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Geromics, Ulsan, 44919, Republic of Korea.
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18
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Lidke DS, Martin C, Farzam F, Edwards JS, Lakin M, Pallikkuth S, Lidke KA. Multi-Structure Super-Resolution Imaging using DNA Strand Displacement. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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19
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Kim S, Cho YS, Kim HM, Chung O, Kim H, Jho S, Seomun H, Kim J, Bang WY, Kim C, An J, Bae CH, Bhak Y, Jeon S, Yoon H, Kim Y, Jun J, Lee H, Cho S, Uphyrkina O, Kostyria A, Goodrich J, Miquelle D, Roelke M, Lewis J, Yurchenko A, Bankevich A, Cho J, Lee S, Edwards JS, Weber JA, Cook J, Kim S, Lee H, Manica A, Lee I, O'Brien SJ, Bhak J, Yeo JH. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Genome Biol 2016; 17:211. [PMID: 27802837 PMCID: PMC5090899 DOI: 10.1186/s13059-016-1071-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [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: 07/05/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. RESULTS We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. CONCLUSIONS Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.
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Affiliation(s)
- Soonok Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Yun Sung Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Hak-Min Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Oksung Chung
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan, 44919, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Hong Seomun
- Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Jeongho Kim
- Cheongju Zoo, Cheongju, 28311, Republic of Korea
| | - Woo Young Bang
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Changmu Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Chang Hwan Bae
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyejun Yoon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yumi Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - JeHoon Jun
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.,Geromics, Ulsan, 44919, Republic of Korea
| | - HyeJin Lee
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.,Geromics, Ulsan, 44919, Republic of Korea
| | - Suan Cho
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.,Geromics, Ulsan, 44919, Republic of Korea
| | - Olga Uphyrkina
- Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Aleksey Kostyria
- Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | | | - Dale Miquelle
- Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY, 10460, USA.,Department of Ecology, Far Eastern Federal University, Ayaks, Russki Island, Vladivostok, 690950, Russia
| | - Melody Roelke
- Laboratory of Animal Sciences Program, Leídos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, 21702, USA
| | - John Lewis
- International Zoo Veterinary Group (UK) IZVG LLP, Station House, Parkwood Street, Keighley, BD21 4NQ, UK
| | - Andrey Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia
| | - Anton Bankevich
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Juok Cho
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Semin Lee
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jessica A Weber
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jo Cook
- Zoological Society of London, London, NW1 4RY, UK
| | - Sangsoo Kim
- Department of Bioinformatics & Life Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Ilbeum Lee
- Daejeon O-World, Daejeon, 35073, Republic of Korea
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia. .,Oceanographic Center 8000 N. Ocean Drive, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA.
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea. .,Geromics, Ulsan, 44919, Republic of Korea.
| | - Joo-Hong Yeo
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
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20
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Kerketta R, Halász ÁM, Steinkamp MP, Wilson BS, Edwards JS. Effect of Spatial Inhomogeneities on the Membrane Surface on Receptor Dimerization and Signal Initiation. Front Cell Dev Biol 2016; 4:81. [PMID: 27570763 PMCID: PMC4981600 DOI: 10.3389/fcell.2016.00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/25/2016] [Indexed: 11/23/2022] Open
Abstract
Important signal transduction pathways originate on the plasma membrane, where microdomains may transiently entrap diffusing receptors. This results in a non-random distribution of receptors even in the resting state, which can be visualized as “clusters” by high resolution imaging methods. Here, we explore how spatial in-homogeneities in the plasma membrane might influence the dimerization and phosphorylation status of ErbB2 and ErbB3, two receptor tyrosine kinases that preferentially heterodimerize and are often co-expressed in cancer. This theoretical study is based upon spatial stochastic simulations of the two-dimensional membrane landscape, where variables include differential distributions and overlap of transient confinement zones (“domains”) for the two receptor species. The in silico model is parameterized and validated using data from single particle tracking experiments. We report key differences in signaling output based on the degree of overlap between domains and the relative retention of receptors in such domains, expressed as escape probability. Results predict that a high overlap of domains, which favors transient co-confinement of both receptor species, will enhance the rate of hetero-interactions. Where domains do not overlap, simulations confirm expectations that homo-interactions are favored. Since ErbB3 is uniquely dependent on ErbB2 interactions for activation of its catalytic activity, variations in domain overlap or escape probability markedly alter the predicted patterns and time course of ErbB3 and ErbB2 phosphorylation. Taken together, these results implicate membrane domain organization as an important modulator of signal initiation, motivating the design of novel experimental approaches to measure these important parameters across a wider range of receptor systems.
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Affiliation(s)
- Romica Kerketta
- Department of Pathology, University of New Mexico Health Sciences Center Albuquerque, NM, USA
| | - Ádám M Halász
- Department of Mathematics and Mary Babb Randolph Cancer Center, West Virginia University Morgantown, WV, USA
| | - Mara P Steinkamp
- Department of Pathology, University of New Mexico Health Sciences CenterAlbuquerque, NM, USA; Cancer Center, University of New Mexico Health Sciences CenterAlbuquerque, NM, USA
| | - Bridget S Wilson
- Department of Pathology, University of New Mexico Health Sciences CenterAlbuquerque, NM, USA; Cancer Center, University of New Mexico Health Sciences CenterAlbuquerque, NM, USA
| | - Jeremy S Edwards
- Cancer Center, University of New Mexico Health Sciences CenterAlbuquerque, NM, USA; Department of Chemical and Biological Engineering, University of New MexicoAlbuquerque, NM, USA; Department of Chemistry and Chemical Biology, University of New MexicoAlbuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New MexicoAlbuquerque, NM, USA
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21
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McCabe Pryor M, Steinkamp MP, Halasz AM, Chen Y, Yang S, Smith MS, Zahoransky-Kohalmi G, Swift M, Xu XP, Hanein D, Volkmann N, Lidke DS, Edwards JS, Wilson BS. Orchestration of ErbB3 signaling through heterointeractions and homointeractions. Mol Biol Cell 2015; 26:4109-23. [PMID: 26378253 PMCID: PMC4710241 DOI: 10.1091/mbc.e14-06-1114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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] [Received: 06/16/2014] [Accepted: 09/09/2015] [Indexed: 12/27/2022] Open
Abstract
Members of the ErbB family of receptor tyrosine kinases are capable of both homointeractions and heterointeractions. Because each receptor has a unique set of binding sites for downstream signaling partners and differential catalytic activity, subtle shifts in their combinatorial interplay may have a large effect on signaling outcomes. The overexpression and mutation of ErbB family members are common in numerous human cancers and shift the balance of activation within the signaling network. Here we report the development of a spatial stochastic model that addresses the dynamics of ErbB3 homodimerization and heterodimerization with ErbB2. The model is based on experimental measures for diffusion, dimer off-rates, kinase activity, and dephosphorylation. We also report computational analysis of ErbB3 mutations, generating the prediction that activating mutations in the intracellular and extracellular domains may be subdivided into classes with distinct underlying mechanisms. We show experimental evidence for an ErbB3 gain-of-function point mutation located in the C-lobe asymmetric dimerization interface, which shows enhanced phosphorylation at low ligand dose associated with increased kinase activity.
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Affiliation(s)
- Meghan McCabe Pryor
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Mara P Steinkamp
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
| | - Adam M Halasz
- Department of Mathematics, West Virginia University, Morgantown, WV 25606
| | - Ye Chen
- Department of Mathematics, West Virginia University, Morgantown, WV 25606
| | - Shujie Yang
- Department of OB/GYN, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | | | | | - Mark Swift
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Xiao-Ping Xu
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Dorit Hanein
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Niels Volkmann
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Diane S Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
| | - Jeremy S Edwards
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131 Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
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22
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Tyler CR, Weber JA, Labrecque M, Hessinger JM, Edwards JS, Allan AM. ChIP-Seq analysis of the adult male mouse brain after developmental exposure to arsenic. Data Brief 2015; 5:248-54. [PMID: 26543888 PMCID: PMC4589800 DOI: 10.1016/j.dib.2015.08.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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] [Received: 07/16/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 01/12/2023] Open
Abstract
Exposure to the common environmental contaminant arsenic impacts the epigenetic landscape, including DNA methylation and histone modifications, of several cell types. Developmental arsenic exposure (DAE) increases acetylation and methylation of histone proteins and the protein expression of several chromatin-modifying enzymes in the dentate gyrus (DG) subregion of the adult male mouse brain [26]. To complement and support these data, ChIP-Seq analysis of DNA associated with trimethylation of histone 3 lysine 4 (H3K4me3) derived from the adult male DG after DAE was performed. DAE induced differential H3K4me3 enrichment on genes in pathways associated with cellular development and growth, cell death and survival, and neurological disorders, particularly as they relate to cancer, in the adult male brain. Comparison of H3K4me3 enrichment in controls revealed mechanisms that are potentially lacking in arsenic-exposed animals, including neurotransmission, neuronal growth and development, hormonal regulation, protein synthesis, and cellular homeostasis. New pathways impacted by arsenic include cytoskeleton organization, cell signaling, and potential disruption of immune function and warrant further investigation using this DAE paradigm in the mouse brain.
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Affiliation(s)
- Christina R Tyler
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jessica A Weber
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Matthew Labrecque
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Justin M Hessinger
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jeremy S Edwards
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, USA ; Department of Chemical & Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA ; Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA ; Cancer Research & Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Andrea M Allan
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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23
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Ruan J, Jin V, Huang Y, Xu H, Edwards JS, Chen Y, Zhao Z. Education, collaboration, and innovation: intelligent biology and medicine in the era of big data. BMC Genomics 2015; 16 Suppl 7:S1. [PMID: 26099197 PMCID: PMC4474420 DOI: 10.1186/1471-2164-16-s7-s1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Here we present a summary of the 2014 International Conference on Intelligent Biology and Medicine (ICIBM 2014) and the editorial report of the supplement to BMC Genomics and BMC Systems Biology that includes 20 research articles selected from ICIBM 2014. The conference was held on December 4-6, 2014 at San Antonio, Texas, USA, and included six scientific sessions, four tutorials, four keynote presentations, nine highlight talks, and a poster session that covered cutting-edge research in bioinformatics, systems biology, and computational medicine.
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24
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Jun J, Cho YS, Hu H, Kim HM, Jho S, Gadhvi P, Park KM, Lim J, Paek WK, Han K, Manica A, Edwards JS, Bhak J. Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. BMC Genomics 2014; 15 Suppl 9:S4. [PMID: 25521865 PMCID: PMC4290615 DOI: 10.1186/1471-2164-15-s9-s4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. Results We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. Conclusions Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.
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25
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Figueiredo J, Mailloux J, Kirov K, Kinna D, Stamp M, Devaux S, Arnoux G, Edwards JS, Stephen AV, McCullen P, Hogben C. An arc control and protection system for the JET lower hybrid antenna based on an imaging system. Rev Sci Instrum 2014; 85:11E806. [PMID: 25430371 DOI: 10.1063/1.4889904] [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] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Arcs are the potentially most dangerous events related to Lower Hybrid (LH) antenna operation. If left uncontrolled they can produce damage and cause plasma disruption by impurity influx. To address this issue an arc real time control and protection imaging system for the Joint European Torus (JET) LH antenna has been implemented. The LH system is one of the additional heating systems at JET. It comprises 24 microwave generators (klystrons, operating at 3.7 GHz) providing up to 5 MW of heating and current drive to the JET plasma. This is done through an antenna composed of an array of waveguides facing the plasma. The protection system presented here is based primarily on an imaging arc detection and real time control system. It has adapted the ITER like wall hotspot protection system using an identical CCD camera and real time image processing unit. A filter has been installed to avoid saturation and spurious system triggers caused by ionization light. The antenna is divided in 24 Regions Of Interest (ROIs) each one corresponding to one klystron. If an arc precursor is detected in a ROI, power is reduced locally with subsequent potential damage and plasma disruption avoided. The power is subsequently reinstated if, during a defined interval of time, arcing is confirmed not to be present by image analysis. This system was successfully commissioned during the restart phase and beginning of the 2013 scientific campaign. Since its installation and commissioning, arcs and related phenomena have been prevented. In this contribution we briefly describe the camera, image processing, and real time control systems. Most importantly, we demonstrate that an LH antenna arc protection system based on CCD camera imaging systems works. Examples of both controlled and uncontrolled LH arc events and their consequences are shown.
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Affiliation(s)
- J Figueiredo
- Associação EURATOM/IST, Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal and EFDA-CSU, Culham Science Centre, Abingdon OX14 3DB, United Kingdom
| | - J Mailloux
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - K Kirov
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - D Kinna
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - M Stamp
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - S Devaux
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - G Arnoux
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - J S Edwards
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - A V Stephen
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - P McCullen
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
| | - C Hogben
- EURATOM/CCFE Fusion Association, Culham Science Center, Abingdon OX14 3DB, United Kingdom
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26
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Edwards JS, Atlas SR, Wilson SM, Cooper CF, Luo L, Stidley CA. Integrated statistical and pathway approach to next-generation sequencing analysis: a family-based study of hypertension. BMC Proc 2014; 8:S104. [PMID: 25519358 PMCID: PMC4143684 DOI: 10.1186/1753-6561-8-s1-s104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Genome wide association studies (GWAS) have been used to search for associations between genetic variants and a phenotypic trait of interest. New technologies, such as next-generation sequencing, hold the potential to revolutionize GWAS. However, millions of polymorphisms are identified with next-generation sequencing technology. Consequently, researchers must be careful when performing such a large number of statistical tests, and corrections are typically made to account for multiple testing. Additionally, for typical GWAS, the p value cutoff is set quite low (approximately <10−8). As a result of this p value stringency, it is likely that there are many true associations that do not meet this threshold. To account for this we have incorporated a priori biological knowledge to help identify true associations that may not have reached statistical significance. We propose the application of a pipelined series of statistical and bioinformatic methods, to enable the assessment of the association of genetic polymorphisms with a disease phenotype--here, hypertension--as well as the identification of statistically significant pathways of genes that may play a role in the disease process.
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Affiliation(s)
- Jeremy S Edwards
- Molecular Genetics and Microbiology, and Chemical and Nuclear Engineering, 1 University of New Mexico, University of New Mexico Cancer Center, Albuquerque, NM 87131, USA
| | - Susan R Atlas
- Physics and Astronomy, Center for Advanced Research Computing, 1 University of New Mexico, University of New Mexico Cancer Center, Albuquerque, NM 87131, USA
| | - Susan M Wilson
- Center for Advanced Research Computing, University of New Mexico Cancer Center, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Candice F Cooper
- Molecular Genetics and Microbiology, and Chemical and Nuclear Engineering, 1 University of New Mexico, University of New Mexico Cancer Center, Albuquerque, NM 87131, USA
| | - Li Luo
- University of New Mexico Cancer Center, Internal Medicine, 1 University of New Mexico, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Christine A Stidley
- University of New Mexico Cancer Center, Internal Medicine, 1 University of New Mexico, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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Pryor MM, Low-Nam ST, Halász AM, Lidke DS, Wilson BS, Edwards JS. Dynamic transition states of ErbB1 phosphorylation predicted by spatial stochastic modeling. Biophys J 2014; 105:1533-43. [PMID: 24048005 DOI: 10.1016/j.bpj.2013.07.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/08/2013] [Accepted: 07/29/2013] [Indexed: 11/25/2022] Open
Abstract
ErbB1 overexpression is strongly linked to carcinogenesis, motivating better understanding of erbB1 dimerization and activation. Recent single-particle-tracking data have provided improved measures of dimer lifetimes and strong evidence that transient receptor coconfinement promotes repeated interactions between erbB1 monomers. Here, spatial stochastic simulations explore the potential impact of these parameters on erbB1 phosphorylation kinetics. This rule-based mathematical model incorporates structural evidence for conformational flux of the erbB1 extracellular domains, as well as asymmetrical orientation of erbB1 cytoplasmic kinase domains during dimerization. The asymmetric dimer model considers the theoretical consequences of restricted transactivation of erbB1 receptors within a dimer, where the N-lobe of one monomer docks with the C-lobe of the second monomer and triggers its catalytic activity. The dynamic nature of the erbB1 phosphorylation state is shown by monitoring activation states of individual monomers as they diffuse, bind, and rebind after ligand addition. The model reveals the complex interplay between interacting liganded and nonliganded species and the influence of their distribution and abundance within features of the membrane landscape.
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Affiliation(s)
- Meghan McCabe Pryor
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico
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Halász ÁM, Lai HJ, McCabe MM, Radhakrishnan K, Edwards JS. Analytical solution of steady-state equations for chemical reaction networks with bilinear rate laws. IEEE/ACM Trans Comput Biol Bioinform 2013; 10:957-69. [PMID: 24334389 PMCID: PMC4090023 DOI: 10.1109/tcbb.2013.41] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
True steady states are a rare occurrence in living organisms, yet their knowledge is essential for quasi-steady-state approximations, multistability analysis, and other important tools in the investigation of chemical reaction networks (CRN) used to describe molecular processes on the cellular level. Here, we present an approach that can provide closed form steady-state solutions to complex systems, resulting from CRN with binary reactions and mass-action rate laws. We map the nonlinear algebraic problem of finding steady states onto a linear problem in a higher-dimensional space. We show that the linearized version of the steady-state equations obeys the linear conservation laws of the original CRN. We identify two classes of problems for which complete, minimally parameterized solutions may be obtained using only the machinery of linear systems and a judicious choice of the variables used as free parameters. We exemplify our method, providing explicit formulae, on CRN describing signal initiation of two important types of RTK receptor-ligand systems, VEGF and EGF-ErbB1.
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Affiliation(s)
- Ádám M. Halász
- Department of Mathematics, West Virginia University, Morgantown, WV 26506-6310
- corresponding author (, )
| | - Hong-Jian Lai
- Department of Mathematics, West Virginia University, Morgantown, WV 26506-6310
| | - Meghan M. McCabe
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131 ()
| | - Krishnan Radhakrishnan
- Preventive Medicine and Environmental Health, College of Public Health, University of Kentucky, Lexington, KY 40536 ()
| | - Jeremy S. Edwards
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Science Center, Albuquerque, NM 87131 ()
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Chen Y, Short C, Halász ÁM, Edwards JS. The impact of high density receptor clusters on VEGF signaling. Electron Proc Theor Comput Sci 2013; 2013:37-52. [PMID: 25506421 PMCID: PMC4262124 DOI: 10.4204/eptcs.??.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Vascular endothelial growth factor (VEGF) signaling is involved in the process of blood vessel development and maintenance. Signaling is initiated by binding of the bivalent VEGF ligand to the membrane-bound receptors (VEGFR), which in turn stimulates receptor dimerization. Herein, we discuss experimental evidence that VEGF receptors localize in caveloae and other regions of the plasma membrane, and for other receptors, it has been shown that receptor clustering has an impact on dimerization and thus also on signaling. Overall, receptor clustering is part of a complex ecosystem of interactions and how receptor clustering impacts dimerization is not well understood. To address these questions, we have formulated the simplest possible model. We have postulated the existence of a single high affinity region in the cell membrane, which acts as a transient trap for receptors. We have defined an ODE model by introducing high- and low-density receptor variables and introduce the corresponding reactions from a realistic model of VEGF signal initiation. Finally, we use the model to investigate the relation between the degree of VEGFR concentration, ligand availability, and signaling. In conclusion, our simulation results provide a deeper understanding of the role of receptor clustering in cell signaling.
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Affiliation(s)
- Ye Chen
- Department of Mathematics, West Virginia University
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30
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Aragon AD, Torrez-Martinez N, Edwards JS. Genomic analysis of Saccharomyces cerevisiae isolates that grow optimally with glucose as the sole carbon source. Electrophoresis 2012; 33:3514-20. [PMID: 23135695 DOI: 10.1002/elps.201200172] [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] [Received: 03/20/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 11/07/2022]
Abstract
A population of Saccharomyces cerevisiae was cultured for approximately 450 generations in the presence of high glucose to select for genetic variants that grew optimally under these conditions. Using the parental strain BY4741 as the starting population, an evolved culture was obtained after aerobic growth in a high glucose medium for approximately 450 generations. After the evolution period, three single colony isolates were selected for analysis. Next-generation Ion Torrent sequencing was used to evaluate genetic changes. Greater than 100 deletion/insertion changes were found with approximately half of these effecting genes. Additionally, over 180 SNPs were identified with more than one-quarter of these resulting in a nonsynonymous mutation. Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain. It was established that approximately 900 genes demonstrated significantly altered expression in the evolved strains relative to the parental strain. Many of these genes showed similar alterations in their expression in all three evolved strains. Interestingly, genes with altered expression in the three evolved strains included genes with a role in oxidative metabolism. Overall these results are consistent with the physiological observations of optimal growth with glucose as the carbon source. Namely, the decreased ethanol production suggest that the underlying metabolism switched from fermentation to respiration during the selection for optimal growth on glucose.
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Affiliation(s)
- Anthony D Aragon
- UNM Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, USA
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Radhakrishnan K, Halász Á, McCabe MM, Edwards JS, Wilson BS. Mathematical simulation of membrane protein clustering for efficient signal transduction. Ann Biomed Eng 2012; 40:2307-18. [PMID: 22669501 PMCID: PMC3822010 DOI: 10.1007/s10439-012-0599-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/17/2012] [Indexed: 12/13/2022]
Abstract
Initiation and propagation of cell signaling depend on productive interactions among signaling proteins at the plasma membrane. These diffusion-limited interactions can be influenced by features of the membrane that introduce barriers, such as cytoskeletal corrals, or microdomains that transiently confine both transmembrane receptors and membrane-tethered peripheral proteins. Membrane topographical features can lead to clustering of receptors and other membrane components, even under very dynamic conditions. This review considers the experimental and mathematical evidence that protein clustering impacts cell signaling in complex ways. Simulation approaches used to consider these stochastic processes are discussed.
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Affiliation(s)
| | - Ádám Halász
- Dept. of Mathematics, West Virginia University, Morgantown, WV
| | - Meghan M. McCabe
- Dept. of Chemical Engineering, University of New Mexico, Albuquerque, N M
| | - Jeremy S. Edwards
- Dept. of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, N M
- Dept. of Chemical Engineering, University of New Mexico, Albuquerque, N M
- Cancer Center, University of New Mexico, Albuquerque, N M
| | - Bridget S. Wilson
- Dept. of Pathology, University of New Mexico, Albuquerque, N M
- Cancer Center, University of New Mexico, Albuquerque, N M
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32
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Singh AP, Andries E, Edwards JS, Steinberg S. The shuttling scaffold model for prevention of yeast pheromone pathway misactivation. Bull Math Biol 2012; 74:2861-74. [PMID: 23104201 DOI: 10.1007/s11538-012-9785-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 10/15/2012] [Indexed: 11/30/2022]
Abstract
The molecular scaffold in the yeast pheromone pathway, Ste5, shuttles continuously between the nucleus and the cytoplasm. Ste5 undergoes oligomerization reaction in the nucleus. Upon pheromone stimulation, the Ste5 dimer is rapidly exported out of the nucleus and recruited to the plasma membrane for pathway activation. This clever device on part of the yeast cell is thought to prevent pathway misactivation at high enough levels of Ste5 in the absence of pheromone. We have built a spatiotemporal model of signaling in this pathway to describe its regulation. Our present work underscores the importance of spatial modeling of cell signaling networks to understand their control and functioning.
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Halasz AM, Brundage K, Fortney J, Zwartz GJ, Lidke D, Radhakrishnan K, Wilson BS, Gibson L, Edwards JS. Abstract 3970: Model-driven investigation of VEGF binding to endothelial cells and implications of the spatial organization of the cell membrane. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-3970] [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: 11/16/2022]
Abstract
Abstract
VEGF signaling plays an important role in the development and maintenance of blood vessels and it has received much attention due to its role in tumor development and other pathologies. Recent developments in therapeutics have highlighted the complex and often contradictory features of cell signaling mediated by the VEGF ligand and receptor family. The aim of this study is to constrain the effective parameters of a minimal mathematical model [1] of the first steps in VEGF signaling, namely, the molecular transformations that occur from the presentation of VEGF ligand in the extracellular space to the formation of activated ligand-receptor complexes on the cell membrane. This study addresses unique properties of VEGF due to its bivalent nature. Bivalence complicates signal initiation, which requires the formation of a complex of two receptors cross-linked by a ligand. Unlike the initial capture of ligand from the surrounding volume, the second binding step occurs between proteins bound to the cell membrane, and is therefore modulated by the lateral mobility of the receptors, which in turn reflects the limitations to free movement due to various features of the cell membrane. The kinetics of cross-linking are reflected in (i) the degree of reversibility of VEGF binding to the cell, and (ii) the phenomenon of high dose inhibition. Thus, the empirically derived kinetics that defines the well mixed model [1] help integrate binding data with high resolution imaging and single particle tracking studies of the cell membrane, two classes of experimental information that are hard to compare directly. The binding of VEGF to human umbilical vascular endothelial cells (HUVEC) has been well studied in the literature, and was the basis of the original parameterization of the model [1]. However, those experiments did not pursue the distinction between the two different binding steps, and the kinetics of cross-linking was not well determined. To address this, we use a synthetic compound, single-chain VEGF [2], conjugated to a fluorescent tag (scVEGF-Cy5.5). This ligand has two functional binding sites and its binding affinity and physiological effect on cells expressing VEGFR-2 closely reproduce those of VEGF165. We used flow cytometry to quantify the binding of scVEGF-Cy5.5 to HUVEC in vitro. We obtained dose response curves and time courses for total binding in solution, for incubation times from 30 - 120 minutes and ligand concentrations from 0.1 - 200 nM. The data show possible signs of high dose inhibition in the 100 nM range, and allow us to estimate a range for the characteristic time of cross-linking. Subsequent experiments will directly probe this time range, based on use of this versatile probe for imaging studies of receptor localization and mobility in the cell membrane. References: [1] MacGabhann F and Popel AS, Biophys.Chem. 128:125-139 (2007) [2] Backer MV et al, Nat.Med. 13:504-509 (2007)
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3970. doi:1538-7445.AM2012-3970
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Archuleta MN, McDermott JE, Edwards JS, Resat H. An adaptive coarse graining method for signal transduction in three dimensions. Fundam Inform 2012; 118:10.3233/FI-2012-720. [PMID: 24357890 PMCID: PMC3865981 DOI: 10.3233/fi-2012-720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The spatio-temporal landscape of the plasma membrane regulates activation and signal transduction of membrane bound receptors by restricting their two-dimensional mobility and by inducing receptor clustering. This regulation also extends to complex formation between receptors and adaptor proteins, which are the intermediate signaling molecules involved in cellular signaling that relay the received cues from cell surface to cytoplasm and eventually to the nucleus. Although their investigation poses challenging technical difficulties, there is a crucial need to understand the impact of the receptor diffusivity, clustering, and spatial heterogeneity, and of receptor-adaptor protein complex formation on the cellular signal transduction patterns. Building upon our earlier studies, we have developed an adaptive coarse-grained Monte Carlo method that can be used to investigate the role of diffusion, clustering and membrane corralling on receptor association and receptor-adaptor protein complex formation dynamics in three dimensions. The new Monte Carlo lattice based approach allowed us to introduce spatial resolution on the 2-D plasma membrane and to model the cytoplasm in three-dimensions. Being a multi-resolution approach, our new method makes it possible to represent various parts of the cellular system at different levels of detail and enabled us to utilize the locally homogeneous assumption when justified (e.g., cytoplasmic region away from the cell membrane) and avoid its use when high spatial resolution is needed (e.g., cell membrane and cytoplasmic region near the membrane) while keeping the required computational complexity manageable. Our results have shown that diffusion has a significant impact on receptor-receptor dimerization and receptor-adaptor protein complex formation kinetics. We have observed an "adaptor protein hopping" mechanism where the receptor binding proteins may hop between receptors to form short-lived transient complexes. This increased residence time of the adaptor proteins near cell membrane and their ability to frequently change signaling partners may explain the increase in signaling efficiency when receptors are clustered. We also hypothesize that the adaptor protein hopping mechanism can cause concurrent or sequential activation of multiple signaling pathways, thus leading to crosstalk between diverse biological functions.
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Affiliation(s)
- Michelle N Archuleta
- Chemical and Nuclear Engineering Department, University of New Mexico, Albuquerque, NM 87131, USA
| | - Jason E McDermott
- Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jeremy S Edwards
- Molecular Genetics and Microbiology Department, UNM Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Haluk Resat
- Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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35
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Zhou YE, O'Rourke JP, Edwards JS, Ness SA. Single molecule analysis of c-myb alternative splicing reveals novel classifiers for precursor B-ALL. PLoS One 2011; 6:e22880. [PMID: 21853052 PMCID: PMC3154906 DOI: 10.1371/journal.pone.0022880] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/06/2011] [Indexed: 11/18/2022] Open
Abstract
The c-Myb transcription factor, a key regulator of proliferation and differentiation in hematopoietic and other cell types, has an N-terminal DNA binding domain and a large C-terminal domain responsible for transcriptional activation, negative regulation and determining target gene specificity. Overexpression and rearrangement of the c-myb gene (MYB) has been reported in some patients with leukemias and other types of cancers, implicating activated alleles of c-myb in the development of human tumors. Alternative RNA splicing can produce variants of c-myb with qualitatively distinct transcriptional activities that may be involved in transformation and leukemogenesis. Here, by performing a detailed, single molecule assay we found that c-myb alternative RNA splicing was elevated and much more complex in leukemia samples than in cell lines or CD34+ hematopoietic progenitor cells from normal donors. The results revealed that leukemia samples express more than 60 different c-myb splice variants, most of which have multiple alternative splicing events and were not detectable by conventional microarray or PCR approaches. For example, the single molecule assay detected 21 and 22 splice variants containing the 9B and 9S exons, respectively, most of which encoded unexpected variant forms of c-Myb protein. Furthermore, the detailed analysis identified some splice variants whose expression correlated with poor survival in a small cohort of precursor B-ALL samples. Our findings indicate that single molecule assays can reveal complexities in c-myb alternative splicing that have potential as novel biomarkers and could help explain the role of c-Myb variants in the development of human leukemia.
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Affiliation(s)
- Ye E. Zhou
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - John P. O'Rourke
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Jeremy S. Edwards
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Scott A. Ness
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- * E-mail:
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Radhakrishnan K, Edwards JS, Lidke DS, Jovin TM, Wilson BS, Oliver JM. Sensitivity analysis predicts that the ERK-pMEK interaction regulates ERK nuclear translocation. IET Syst Biol 2011; 3:329-41. [PMID: 21028924 DOI: 10.1049/iet-syb.2009.0010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Following phosphorylation, nuclear translocation of the mitogen-activated protein kinases (MAPKs), ERK1 and ERK2, is critical for both gene expression and DNA replication induced by growth factors. ERK nuclear translocation has therefore been studied extensively, but many details remain unresolved, including whether or not ERK dimerisation is required for translocation. Here, we simulate ERK nuclear translocation with a compartmental computational model that includes systematic sensitivity analysis. The governing ordinary differential equations are solved with the backward differentiation formula and decoupled direct methods. To better understand the regulation of ERK nuclear translocation, we use this model in conjunction with a previously published model of the ERK pathway that does not include an ERK dimer species and with experimental measurements of nuclear translocation of wild-type ERK and a mutant form, ERK1-4, which is unable to dimerise. Sensitivity analysis reveals that the delayed nuclear uptake of ERK1-4 compared to that of wild-type ERK1 can be explained by the altered interaction of ERK1-4 with phosphorylated MEK (MAPK/ERK kinase), and so may be independent of dimerisation. Our study also identifies biological experiments that can verify this explanation.
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Affiliation(s)
- K Radhakrishnan
- University of New Mexico School of Medicine, Department of Pathology and Cancer Center, Albuquerque, NM, USA.
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37
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Nichols JW, Breen M, Denver RJ, Distefano JJ, Edwards JS, Hoke RA, Volz DC, Zhang X. Predicting chemical impacts on vertebrate endocrine systems. Environ Toxicol Chem 2011; 30:39-51. [PMID: 20963851 DOI: 10.1002/etc.376] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Animals have evolved diverse protective mechanisms for responding to toxic chemicals of both natural and anthropogenic origin. From a governmental regulatory perspective, these protective responses complicate efforts to establish acceptable levels of chemical exposure. To explore this issue, we considered vertebrate endocrine systems as potential targets for environmental contaminants. Using the hypothalamic-pituitary-thyroid (HPT), hypothalamic-pituitary-gonad (HPG), and hypothalamic-pituitary-adrenal (HPA) axes as case examples, we identified features of these systems that allow them to accommodate and recover from chemical insults. In doing so, a distinction was made between effects on adults and those on developing organisms. This distinction was required because endocrine system disruption in early life stages may alter development of organs and organ systems, resulting in permanent changes in phenotypic expression later in life. Risk assessments of chemicals that impact highly regulated systems must consider the dynamics of these systems in relation to complex environmental exposures. A largely unanswered question is whether successful accommodation to a toxic insult exerts a fitness cost on individual animals, resulting in adverse consequences for populations. Mechanistically based mathematical models of endocrine systems provide a means for better understanding accommodation and recovery. In the short term, these models can be used to design experiments and interpret study findings. Over the long term, a set of validated models could be used to extrapolate limited in vitro and in vivo testing data to a broader range of untested chemicals, species, and exposure scenarios. With appropriate modification, Tier 2 assays developed in support of the U.S. Environmental Protection Agency's Endocrine Disruptor Screening Program could be used to assess the potential for accommodation and recovery and inform the development of mechanistically based models.
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Affiliation(s)
- John W Nichols
- U.S. Environmental Protection Agency, Duluth, Minnesota, USA.
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38
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Costa MN, Radhakrishnan K, Edwards JS. Monte Carlo simulations of plasma membrane corral-induced EGFR clustering. J Biotechnol 2010; 151:261-70. [PMID: 21167222 DOI: 10.1016/j.jbiotec.2010.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 11/30/2010] [Accepted: 12/04/2010] [Indexed: 11/26/2022]
Abstract
Experimental evidence suggests that the cell membrane is a highly organized structure that is compartmentalized by the underlying membrane cytoskeleton (MSK). The interaction between the cell membrane and the cytoskeleton led to the "picket-fence" model, which was proposed to explain certain aspects of membrane compartmentalization. This model assumes that the MSK hinders and confines the motion of receptors and lipids to compartments in the membrane. However, the impact of the MSK on receptor clustering, aggregation, and downstream signaling remains unclear. For example, some evidence suggests that the MSK enhances dimerization, while other evidence suggests decreased dimerization and signaling. Herein, we use computational Monte Carlo simulations to examine the effects of MSK density and receptor concentration on receptor dimerization and clustering. Preliminary results suggest that the MSK may have the potential to induce receptor clustering, which is a function of both picket-fence density and receptor concentration.
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Affiliation(s)
- Michelle N Costa
- Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, United States
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39
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Radhakrishnan K, Halász A, Vlachos D, Edwards JS. Quantitative understanding of cell signaling: the importance of membrane organization. Curr Opin Biotechnol 2010; 21:677-82. [PMID: 20829029 DOI: 10.1016/j.copbio.2010.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [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: 08/09/2010] [Accepted: 08/09/2010] [Indexed: 12/13/2022]
Abstract
Systems biology modeling of signal transduction pathways traditionally employs ordinary differential equations, deterministic models based on the assumptions of spatial homogeneity. However, this can be a poor approximation for certain aspects of signal transduction, especially its initial steps: the cell membrane exhibits significant spatial organization, with diffusion rates approximately two orders of magnitude slower than those in the cytosol. Thus, to unravel the complexities of signaling pathways, quantitative models must consider spatial organization as an important feature of cell signaling. Furthermore, spatial separation limits the number of molecules that can physically interact, requiring stochastic simulation methods that account for individual molecules. Herein, we discuss the need for mathematical models and experiments that appreciate the importance of spatial organization in the membrane.
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Affiliation(s)
- Krishnan Radhakrishnan
- Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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40
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Hsieh MY, Yang S, Raymond-Stinz MA, Edwards JS, Wilson BS. Spatio-temporal modeling of signaling protein recruitment to EGFR. BMC Syst Biol 2010; 4:57. [PMID: 20459599 PMCID: PMC2877007 DOI: 10.1186/1752-0509-4-57] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 05/06/2010] [Indexed: 12/31/2022]
Abstract
Background A stochastic simulator was implemented to study EGFR signal initiation in 3D with single molecule detail. The model considers previously unexplored contributions to receptor-adaptor coupling, such as receptor clustering and diffusive properties of both receptors and binding partners. The agent-based and rule-based approach permits consideration of combinatorial complexity, a problem associated with multiple phosphorylation sites and the potential for simultaneous binding of adaptors. Results The model was used to simulate recruitment of four different signaling molecules (Grb2, PLCγ1, Stat5, Shc) to the phosphorylated EGFR tail, with rules based on coarse-grained prediction of spatial constraints. Parameters were derived in part from quantitative immunoblotting, immunoprecipitation and electron microscopy data. Results demonstrate that receptor clustering increases the efficiency of individual adaptor retainment on activated EGFR, an effect that is overridden if crowding is imposed by receptor overexpression. Simultaneous docking of multiple proteins is highly dependent on receptor-adaptor stability and independent of clustering. Conclusions Overall, we propose that receptor density, reaction kinetics and membrane spatial organization all contribute to signaling efficiency and influence the carcinogenesis process.
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Affiliation(s)
- Ming-yu Hsieh
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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41
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Ogunnaike BA, Gelmi CA, Edwards JS. A probabilistic framework for microarray data analysis: Fundamental probability models and statistical inference. J Theor Biol 2010; 264:211-22. [DOI: 10.1016/j.jtbi.2010.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 12/07/2009] [Accepted: 02/12/2010] [Indexed: 11/29/2022]
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42
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Costa MN, Radhakrishnan K, Wilson BS, Vlachos DG, Edwards JS. Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction. PLoS One 2009; 4:e6316. [PMID: 19626123 PMCID: PMC2710010 DOI: 10.1371/journal.pone.0006316] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [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: 02/10/2009] [Accepted: 06/17/2009] [Indexed: 01/24/2023] Open
Abstract
Background The ErbB family of receptors activates intracellular signaling pathways that control cellular proliferation, growth, differentiation and apoptosis. Given these central roles, it is not surprising that overexpression of the ErbB receptors is often associated with carcinogenesis. Therefore, extensive laboratory studies have been devoted to understanding the signaling events associated with ErbB activation. Methodology/Principal Findings Systems biology has contributed significantly to our current understanding of ErbB signaling networks. However, although computational models have grown in complexity over the years, little work has been done to consider the spatial-temporal dynamics of receptor interactions and to evaluate how spatial organization of membrane receptors influences signaling transduction. Herein, we explore the impact of spatial organization of the epidermal growth factor receptor (ErbB1/EGFR) on the initiation of downstream signaling. We describe the development of an algorithm that couples a spatial stochastic model of membrane receptors with a nonspatial stochastic model of the reactions and interactions in the cytosol. This novel algorithm provides a computationally efficient method to evaluate the effects of spatial heterogeneity on the coupling of receptors to cytosolic signaling partners. Conclusions/Significance Mathematical models of signal transduction rarely consider the contributions of spatial organization due to high computational costs. A hybrid stochastic approach simplifies analyses of the spatio-temporal aspects of cell signaling and, as an example, demonstrates that receptor clustering contributes significantly to the efficiency of signal propagation from ligand-engaged growth factor receptors.
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Affiliation(s)
- Michelle N. Costa
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Krishnan Radhakrishnan
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Bridget S. Wilson
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Dionisios G. Vlachos
- Department of Chemical Engineering, University of Delaware, Newark, Delaware, United States of America
| | - Jeremy S. Edwards
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico, United States of America
- Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- * E-mail:
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Abstract
The binding of effector to an allosteric protein exhibits a non-Michaelis-Menten behavior, resulting in either ultrasensitive or subsensitive response. In the present work, a modular approach has been developed to determine the response curve for allosteric systems at higher concentration of allosteric enzyme than that of effector (zero-order sensitivity, as observed in enzyme cascades) by equilibrium analysis. The analysis shows that, in an allosteric system, the zero-order effect can make the response ultrasensitive or subsensitive with respect to the enzyme concentration. The response is dependent on the number of binding sites, cooperativity, and the total effector concentration. The framework was further applied to a well studied allosteric protein, the Escherichia coli aspartate transcarbamoylase. The predictions are found to be consistent with the reported experimental data.
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Affiliation(s)
- Vivek K Mutalik
- Department of Chemical Engineering, Indian Institute of Technology, Powai, Mumbai, India
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44
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Hsieh MY, Yang S, Raymond-Stinz MA, Steinberg S, Vlachos DG, Shu W, Wilson B, Edwards JS. Stochastic simulations of ErbB homo and heterodimerisation: potential impacts of receptor conformational state and spatial segregation. IET Syst Biol 2009; 2:256-72. [PMID: 19045821 DOI: 10.1049/iet-syb:20070073] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ErbB overexpression is linked to carcinogenesis. It is hypothesised that this is due to increased receptor density and receptor clustering, leading to increased receptor dimerisation and activation. Herein, spatial stochastic simulations have been performed to shed light receptor dimerisation processes. First, ligand-independent homodimerisation, is considered, based upon constitutive oligomerisation estimates (14%) in A431 cells that overexpress epidermal growth factor receptor (EGFR). When autocrine stimulation is blocked, ligand-independent EGFR activation is demonstrated by persistent, low levels of phosphorylation. The possibility that ligand-independent signalling is due to the fluctuation of EGFR conformation is considered. The agent-based model predicts the frequency (expressed as a probability) that uniformly distributed receptors would need to flux to the open conformation to reach 14% EGFR dimers at high receptor density. Simulations suggest that ligand-independent EGFR homodimerisation is highly density dependent, since collisions between 'open', dimerisation-competent receptors are a rare event at low receptor levels. Simulations that incorporate receptor clustering lower the threshold for homodimerisation of unoccupied receptors as well as the estimate of the probability for fluxing to the dimer-competent conformation. The impact of ErbB receptor clustering patterns on hetero and homodimerisation rates is also considered, using immunoelectron microscopy data derived from SKBR3 breast cancer cells that express ErbB2>>EGFR>ErbB3. Partial spatial segregation of ErbB receptors has a profound effect on simulated heterodimerisation rates. Despite the general assumption that ErbB2 is a preferred heterodimerising partner for other ErbBs, it is predicted that most ErbB2 will form homodimers. Overall, it is proposed that both receptor density and membrane spatial organisation contribute to the carcinogenesis process.
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Affiliation(s)
- M-Y Hsieh
- University of New Mexico, Department of Electrical and Computer Engineering, Albuquerque, NM, USA
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45
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Affiliation(s)
- Jeremy S Edwards
- Molecular Genetics and Microbiology, Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM, USA
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46
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Mayawala K, Vlachos DG, Edwards JS. The role of reaction engineering in cancer biology: Bio-imaging informatics reveals implications of the plasma membrane heterogeneities. Chem Eng Sci 2007. [DOI: 10.1016/j.ces.2007.01.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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47
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Mayawala K, Vlachos DG, Edwards JS. Spatial modeling of dimerization reaction dynamics in the plasma membrane: Monte Carlo vs. continuum differential equations. Biophys Chem 2006; 121:194-208. [PMID: 16504372 DOI: 10.1016/j.bpc.2006.01.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Accepted: 01/19/2006] [Indexed: 12/17/2022]
Abstract
Bimolecular reactions in the plasma membrane, such as receptor dimerization, are a key signaling step for many signaling systems. For receptors to dimerize, they must first diffuse until a collision happens, upon which a dimerization reaction may occur. Therefore, study of the dynamics of cell signaling on the membrane may require the use of a spatial modeling framework. Despite the availability of spatial simulation methods, e.g., stochastic spatial Monte Carlo (MC) simulation and partial differential equation (PDE) based approaches, many biological models invoke well-mixed assumptions without completely evaluating the importance of spatial organization. Whether one is to utilize a spatial or non-spatial simulation framework is therefore an important decision. In order to evaluate the importance of spatial effects a priori, i.e., without performing simulations, we have assessed the applicability of a dimensionless number, known as second Damköhler number (Da), defined here as the ratio of time scales of collision and reaction, for 2-dimensional bimolecular reactions. Our study shows that dimerization reactions in the plasma membrane with Da approximately >0.1 (tested in the receptor density range of 10(2)-10(5)/microm(2)) require spatial modeling. We also evaluated the effective reaction rate constants of MC and simple deterministic PDEs. Our simulations show that the effective reaction rate constant decreases with time due to time dependent changes in the spatial distribution of receptors. As a result, the effective reaction rate constant of simple PDEs can differ from that of MC by up to two orders of magnitude. Furthermore, we show that the fluctuations in the number of copies of signaling proteins (noise) may also depend on the diffusion properties of the system. Finally, we used the spatial MC model to explore the effect of plasma membrane heterogeneities, such as receptor localization and reduced diffusivity, on the dimerization rate. Interestingly, our simulations show that localization of epidermal growth factor receptor (EGFR) can cause the diffusion limited dimerization rate to be up to two orders of magnitude higher at higher average receptor densities reported for cancer cells, as compared to a normal cell.
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Affiliation(s)
- Kapil Mayawala
- Department of Chemical Engineering, 150 Academy Street, University of Delaware, Newark, DE 19716, USA
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48
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Kauffman KJ, Ogunnaike BA, Edwards JS. Designing experiments that aid in the identification of regulatory networks. Brief Funct Genomic Proteomic 2006; 4:331-42. [PMID: 17202124 DOI: 10.1093/bfgp/eli004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Predictive mathematical models of the interactions of a genetic network can provide insight into the mechanisms of gene regulation, the role of various genes within a network and how multiple genes interact leading to complex traits. However, identification of the parameters and interactions is currently a limiting step in the development of such models. This work reviews the state of the art for design of experiments in biological systems and demonstrates the need for improved design of experiments through the use of a model system. Appropriate design of experiments has a profound impact on the ability to identify a model and on the quality of resulting identified model. Key issues include the selection of appropriate input sequences (e.g. random, independent multivariate inputs) and the selection of the sampling frequencies. This work demonstrates that these issues are especially important in the identification of biochemical networks and that the traditional biochemical approach is incapable of truly identifying the behavior present in such networks.
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Mayawala K, Vlachos DG, Edwards JS. Computational modeling reveals molecular details of epidermal growth factor binding. BMC Cell Biol 2005; 6:41. [PMID: 16318625 PMCID: PMC1322221 DOI: 10.1186/1471-2121-6-41] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [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: 08/02/2005] [Accepted: 11/30/2005] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ErbB family of receptors are dysregulated in a number of cancers, and the signaling pathway of this receptor family is a critical target for several anti-cancer drugs. Therefore a detailed understanding of the mechanisms of receptor activation is critical. However, despite a plethora of biochemical studies and recent single particle tracking experiments, the early molecular mechanisms involving epidermal growth factor (EGF) binding and EGF receptor (EGFR) dimerization are not as well understood. Herein, we describe a spatially distributed Monte Carlo based simulation framework to enable the simulation of in vivo receptor diffusion and dimerization. RESULTS Our simulation results are in agreement with the data from single particle tracking and biochemical experiments on EGFR. Furthermore, the simulations reveal that the sequence of receptor-receptor and ligand-receptor reaction events depends on the ligand concentration, receptor density and receptor mobility. CONCLUSION Our computer simulations reveal the mechanism of EGF binding on EGFR. Overall, we show that spatial simulation of receptor dynamics can be used to gain a mechanistic understanding of receptor activation which may in turn enable improved cancer treatments in the future.
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Affiliation(s)
- Kapil Mayawala
- Department of Chemical Engineering, University of Delaware, Newark, DE, USA
| | | | - Jeremy S Edwards
- Molecular Genetics and Microbiology, Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM, USA
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Mayawala K, Vlachos DG, Edwards JS. Heterogeneities in EGF receptor density at the cell surface can lead to concave up scatchard plot of EGF binding. FEBS Lett 2005; 579:3043-7. [PMID: 15896781 DOI: 10.1016/j.febslet.2005.04.059] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 03/30/2005] [Accepted: 04/12/2005] [Indexed: 11/18/2022]
Abstract
The mechanism responsible for the concave up nature of the Scatchard plot of epidermal growth factor (EGF) binding on EGF receptor (EGFR) has been a controversial issue for more than a decade. Past efforts to mechanistically simulate the concave up nature of the Scatchard plot of EGF binding have shown that negative cooperativity in EGF binding on an EGFR dimer or inclusion of some external site or binding event can describe this behavior. However, herein we show that heterogeneity in the density of EGFR due to localization in certain regions of the plasma membrane, which has been experimentally reported, can also lead to concave up shape of the Scatchard plot of the EGF binding on EGFR.
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Affiliation(s)
- Kapil Mayawala
- Department of Chemical Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
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