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Suo R, Wang Q, Tan Y, Han Q. An innovative MGM-BPNN-ARIMA model for China's energy consumption structure forecasting from the perspective of compositional data. Sci Rep 2024; 14:8494. [PMID: 38605041 PMCID: PMC11009293 DOI: 10.1038/s41598-024-58966-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Effective forecasting of energy consumption structure is vital for China to reach its "dual carbon" objective. However, little attention has been paid to existing studies on the holistic nature and internal properties of energy consumption structure. Therefore, this paper incorporates the theory of compositional data into the study of energy consumption structure, which not only takes into account the specificity of the internal features of the structure, but also digs deeper into the relative information. Meanwhile, based on the minimization theory of squares of the Aitchison distance in the compositional data, a combined model based on the three single models, namely the metabolism grey model (MGM), back-propagation neural network (BPNN) model, and autoregressive integrated moving average (ARIMA) model, is structured in this paper. The forecast results of the energy consumption structure in 2023-2040 indicate that the future energy consumption structure of China will evolve towards a more diversified pattern, but the proportion of natural gas and non-fossil energy has yet to meet the policy goals set by the government. This paper not only suggests that compositional data from joint prediction models have a high applicability value in the energy sector, but also has some theoretical significance for adapting and improving the energy consumption structure in China.
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Affiliation(s)
- Ruixia Suo
- College of Management, Xi'an University of Science and Technology, Xi'an, 710054, China.
| | - Qi Wang
- College of Management, Xi'an University of Science and Technology, Xi'an, 710054, China
| | - Yuanyuan Tan
- College of Management, Xi'an University of Science and Technology, Xi'an, 710054, China
| | - Qiutong Han
- College of Management, Xi'an University of Science and Technology, Xi'an, 710054, China
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2
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Eslami M, Chen YP, Nicholson AC, Weston M, Bell M, McQuiston JR, Samuel J, van Schaik EJ, de Figueiredo P. Neural network based integration of assays to assess pathogenic potential. Sci Rep 2023; 13:6021. [PMID: 37055450 PMCID: PMC10102301 DOI: 10.1038/s41598-023-32950-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/05/2023] [Indexed: 04/15/2023] Open
Abstract
Limited data significantly hinders our capability of biothreat assessment of novel bacterial strains. Integration of data from additional sources that can provide context about the strain can address this challenge. Datasets from different sources, however, are generated with a specific objective and which makes integration challenging. Here, we developed a deep learning-based approach called the neural network embedding model (NNEM) that integrates data from conventional assays designed to classify species with new assays that interrogate hallmarks of pathogenicity for biothreat assessment. We used a dataset of metabolic characteristics from a de-identified set of known bacterial strains that the Special Bacteriology Reference Laboratory (SBRL) of the Centers for Disease Control and Prevention (CDC) has curated for use in species identification. The NNEM transformed results from SBRL assays into vectors to supplement unrelated pathogenicity assays from de-identified microbes. The enrichment resulted in a significant improvement in accuracy of 9% for biothreat. Importantly, the dataset used in our analysis is large, but noisy. Therefore, the performance of our system is expected to improve as additional types of pathogenicity assays are developed and deployed. The proposed NNEM strategy thus provides a generalizable framework for enrichment of datasets with previously collected assays indicative of species.
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Affiliation(s)
- Mohammed Eslami
- Netrias, LLC, 1162 Gateway Drive, Annapolis, MD, 21409, USA.
| | - Yi-Pei Chen
- Netrias, LLC, 1162 Gateway Drive, Annapolis, MD, 21409, USA
| | - Ainsley C Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Mark Weston
- Netrias, LLC, 1162 Gateway Drive, Annapolis, MD, 21409, USA
| | - Melissa Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - John R McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - James Samuel
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA
| | - Erin J van Schaik
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA.
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, 77843, USA.
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3
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Hyeon DY, Nam D, Han Y, Kim DK, Kim G, Kim D, Bae J, Back S, Mun DG, Madar IH, Lee H, Kim SJ, Kim H, Hyun S, Kim CR, Choi SA, Kim YR, Jeong J, Jeon S, Choo YW, Lee KB, Kwon W, Choi S, Goo T, Park T, Suh YA, Kim H, Ku JL, Kim MS, Paek E, Park D, Jung K, Baek SH, Jang JY, Hwang D, Lee SW. Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes. Nat Cancer 2023; 4:290-307. [PMID: 36550235 DOI: 10.1038/s43018-022-00479-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
We report a proteogenomic analysis of pancreatic ductal adenocarcinoma (PDAC). Mutation-phosphorylation correlations identified signaling pathways associated with somatic mutations in significantly mutated genes. Messenger RNA-protein abundance correlations revealed potential prognostic biomarkers correlated with patient survival. Integrated clustering of mRNA, protein and phosphorylation data identified six PDAC subtypes. Cellular pathways represented by mRNA and protein signatures, defining the subtypes and compositions of cell types in the subtypes, characterized them as classical progenitor (TS1), squamous (TS2-4), immunogenic progenitor (IS1) and exocrine-like (IS2) subtypes. Compared with the mRNA data, protein and phosphorylation data further classified the squamous subtypes into activated stroma-enriched (TS2), invasive (TS3) and invasive-proliferative (TS4) squamous subtypes. Orthotopic mouse PDAC models revealed a higher number of pro-tumorigenic immune cells in TS4, inhibiting T cell proliferation. Our proteogenomic analysis provides significantly mutated genes/biomarkers, cellular pathways and cell types as potential therapeutic targets to improve stratification of patients with PDAC.
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Affiliation(s)
- Do Young Hyeon
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dowoon Nam
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Youngmin Han
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Duk Ki Kim
- Department of Anatomy and Cell Biology and Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Seoul, Republic of Korea
| | - Gibeom Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul, Republic of Korea
| | - Daeun Kim
- Department of Biological Sciences, College of Natural Sciences and Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Jingi Bae
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Seunghoon Back
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Dong-Gi Mun
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Inamul Hasan Madar
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Hangyeore Lee
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Su-Jin Kim
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Hokeun Kim
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea
| | - Sangyeop Hyun
- Department of Biological Sciences, College of Natural Sciences and Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Chang Rok Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul, Republic of Korea
| | - Seon Ah Choi
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul, Republic of Korea
| | - Yong Ryoul Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul, Republic of Korea
| | - Juhee Jeong
- Department of Anatomy and Cell Biology and Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Suwan Jeon
- Department of Anatomy and Cell Biology and Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yeon Woong Choo
- Department of Anatomy and Cell Biology and Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung Bun Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Wooil Kwon
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seunghyuk Choi
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
| | - Taewan Goo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Young-Ah Suh
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hongbeom Kim
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Eunok Paek
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences and Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea.
| | - Keehoon Jung
- Department of Anatomy and Cell Biology and Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, Republic of Korea.
| | - Sung Hee Baek
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. .,Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul, Republic of Korea.
| | - Jin-Young Jang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Sang-Won Lee
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Republic of Korea.
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4
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Jang WE, Park JH, Park G, Bang G, Na CH, Kim JY, Kim KY, Kim KP, Shin CY, An JY, Lee YS, Kim MS. Cntnap2-dependent molecular networks in autism spectrum disorder revealed through an integrative multi-omics analysis. Mol Psychiatry 2023; 28:810-21. [PMID: 36253443 DOI: 10.1038/s41380-022-01822-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/28/2022]
Abstract
Autism spectrum disorder (ASD) is a major neurodevelopmental disorder in which patients present with core symptoms of social communication impairment, restricted interest, and repetitive behaviors. Although various studies have been performed to identify ASD-related mechanisms, ASD pathology is still poorly understood. CNTNAP2 genetic variants have been found that represent ASD genetic risk factors, and disruption of Cntnap2 expression has been associated with ASD phenotypes in mice. In this study, we performed an integrative multi-omics analysis by combining quantitative proteometabolomic data obtained with Cntnap2 knockout (KO) mice with multi-omics data obtained from ASD patients and forebrain organoids to elucidate Cntnap2-dependent molecular networks in ASD. To this end, a mass spectrometry-based proteometabolomic analysis of the medial prefrontal cortex in Cntnap2 KO mice led to the identification of Cntnap2-associated molecular features, and these features were assessed in combination with multi-omics data obtained on the prefrontal cortex in ASD patients to identify bona fide ASD cellular processes. Furthermore, a reanalysis of single-cell RNA sequencing data obtained from forebrain organoids derived from patients with CNTNAP2-associated ASD revealed that the aforementioned identified ASD processes were mainly linked to excitatory neurons. On the basis of these data, we constructed Cntnap2-associated ASD network models showing mitochondrial dysfunction, axonal impairment, and synaptic activity. Our results may shed light on the Cntnap2-dependent molecular networks in ASD.
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Park SJ, Park S, Kim Y, Hyeon DY, Park H, Jeong J, Jeong U, Yoon YS, You D, Kwak J, Timilsina R, Hwang D, Kim J, Woo HR. Ethylene responsive factor34 mediates stress-induced leaf senescence by regulating salt stress-responsive genes. Plant Cell Environ 2022; 45:1719-1733. [PMID: 35312081 DOI: 10.1111/pce.14317] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/29/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Leaf senescence proceeds with age but is modulated by various environmental stresses and hormones. Salt stress is one of the most well-known environmental stresses that accelerate leaf senescence. However, the molecular mechanisms that integrate salt stress signalling with leaf senescence programmes remain elusive. In this study, we characterised the role of ETHYLENE RESPONSIVE FACTOR34 (ERF34), an Arabidopsis APETALA2 (AP2)/ERF family transcription factor, in leaf senescence. ERF34 was differentially expressed under various leaf senescence-inducing conditions, and negatively regulated leaf senescence induced by age, dark, and salt stress. ERF34 also promoted salt stress tolerance at different stages of the plant life cycle such as seed germination and vegetative growth. Transcriptome analysis revealed that the overexpression of ERF34 increased the transcript levels of salt stress-responsive genes including COLD-REGULATED15A (COR15A), EARLY RESPONSIVE TO DEHYDRATION10 (ERD10), and RESPONSIVE TO DESICCATION29A (RD29A). Moreover, ERF34 directly bound to ERD10 and RD29A promoters and activated their expression. Our findings indicate that ERF34 plays a key role in the convergence of the salt stress response with the leaf senescence programmes, and is a potential candidate for crop improvement, particularly by enhancing salt stress tolerance.
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Affiliation(s)
- Sung-Jin Park
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Korea
| | - Sanghoon Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Yongmin Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, Korea
| | - Do Young Hyeon
- School of Biological Science, Seoul National University, Seoul, Korea
| | - Hyunsoo Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Junyong Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon, Korea
| | - Ukcheol Jeong
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Yeong Seon Yoon
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Daesang You
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Junmin Kwak
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Rupak Timilsina
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Daehee Hwang
- School of Biological Science, Seoul National University, Seoul, Korea
| | - Jeongsik Kim
- Faculty of Science Education and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
- New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
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6
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Park S, Park JH, Kang UB, Choi SK, Elfadl A, Ullah HMA, Chung MJ, Son JY, Yun HH, Park JM, Yim JH, Jung SJ, Kim SH, Choi YC, Kim DS, Shin JH, Park JS, Hur K, Lee SH, Lee EJ, Hwang D, Jeong KS. Nogo-A regulates myogenesis via interacting with Filamin-C. Cell Death Discov 2021; 7:1. [PMID: 33414425 PMCID: PMC7791112 DOI: 10.1038/s41420-020-00384-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/02/2020] [Revised: 11/22/2020] [Accepted: 11/28/2020] [Indexed: 12/23/2022] Open
Abstract
Among the three isoforms encoded by Rtn4, Nogo-A has been intensely investigated as a central nervous system inhibitor. Although Nogo-A expression is increased in muscles of patients with amyotrophic lateral sclerosis, its role in muscle homeostasis and regeneration is not well elucidated. In this study, we discovered a significant increase in Nogo-A expression in various muscle-related pathological conditions. Nogo−/− mice displayed dystrophic muscle structure, dysregulated muscle regeneration following injury, and altered gene expression involving lipid storage and muscle cell differentiation. We hypothesized that increased Nogo-A levels might regulate muscle regeneration. Differentiating myoblasts exhibited Nogo-A upregulation and silencing Nogo-A abrogated myoblast differentiation. Nogo-A interacted with filamin-C, suggesting a role for Nogo-A in cytoskeletal arrangement during myogenesis. In conclusion, Nogo-A maintains muscle homeostasis and integrity, and pathologically altered Nogo-A expression mediates muscle regeneration, suggesting Nogo-A as a novel target for the treatment of myopathies in clinical settings.
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Affiliation(s)
- SunYoung Park
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.,Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ji-Hwan Park
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Un-Beom Kang
- R&D Division, BERTIS, Inc., Seongnam-si, Gyeonggi-do, 13605, Republic of Korea
| | - Seong-Kyoon Choi
- Division of Biotechnology, DGIST, Daegu, 42988, Republic of Korea.,Core Protein Resources Center, DGIST, Daegu, 42988, Republic of Korea
| | - Ahmed Elfadl
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - H M Arif Ullah
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Myung-Jin Chung
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ji-Yoon Son
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyun Ho Yun
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Min Park
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Hyuk Yim
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Jun Jung
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sang-Hyup Kim
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Young-Chul Choi
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06058, Republic of Korea
| | - Dae-Seong Kim
- Department of Neurology, Pusan National University Yangsan Hospital, Yangsan, 50612, Republic of Korea
| | - Jin-Hong Shin
- Department of Neurology, Pusan National University Yangsan Hospital, Yangsan, 50612, Republic of Korea
| | - Jin-Sung Park
- Department of Neurology, Kyungpook National University School of Medicine, Daegu, 41944, Republic of Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, 41944, Republic of Korea
| | - Sang-Han Lee
- Department of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Eun-Joo Lee
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Daehee Hwang
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyu-Shik Jeong
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea.
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7
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Lyu JI, Kim JH, Chu H, Taylor MA, Jung S, Baek SH, Woo HR, Lim PO, Kim J. Natural allelic variation of GVS1 confers diversity in the regulation of leaf senescence in Arabidopsis. New Phytol 2019; 221:2320-2334. [PMID: 30266040 DOI: 10.1111/nph.15501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Leaf senescence affects plant fitness. Plants that evolve in different environments are expected to acquire distinct regulations of leaf senescence. However, the adaptive and evolutionary roles of leaf senescence are largely unknown. We investigated leaf senescence in 259 natural accessions of Arabidopsis by quantitatively assaying dark-induced senescence responses using a high-throughput chlorophyll fluorescence imaging system. A meta-analysis of our data with phenotypic and climatic information demonstrated biological and environmental links with leaf senescence. We further performed genome-wide association mapping to identify the genetic loci underlying the diversity of leaf senescence responses. We uncovered a new locus, Genetic Variants in leaf Senescence (GVS1), with high similarity to reductase, where a single nonsynonymous nucleotide substitution at GVS1 mediates the diversity of the senescence trait. Loss-of-function mutations of GVS1 in Columbia-0 delayed leaf senescence and increased sensitivity to oxidative stress, suggesting that this GVS1 variant promotes optimal responses to developmental and environmental signals. Intriguingly, gvs1 loss-of-function mutants display allele- and accession-dependent phenotypes, revealing the functional diversity of GVS1 alleles not only in leaf senescence, but also oxidative stress. Our discovery of GVS1 as the genetic basis of natural variation in senescence programs reinforces its adaptive potential in modulating life histories across diverse environments.
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Affiliation(s)
- Jae Il Lyu
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Hyosub Chu
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Mark A Taylor
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Sukjoon Jung
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Seung Hee Baek
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
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8
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Mun DG, Bhin J, Kim S, Kim H, Jung JH, Jung Y, Jang YE, Park JM, Kim H, Jung Y, Lee H, Bae J, Back S, Kim SJ, Kim J, Park H, Li H, Hwang KB, Park YS, Yook JH, Kim BS, Kwon SY, Ryu SW, Park DY, Jeon TY, Kim DH, Lee JH, Han SU, Song KS, Park D, Park JW, Rodriguez H, Kim J, Lee H, Kim KP, Yang EG, Kim HK, Paek E, Lee S, Lee SW, Hwang D. Proteogenomic Characterization of Human Early-Onset Gastric Cancer. Cancer Cell 2019; 35:111-124.e10. [PMID: 30645970 DOI: 10.1016/j.ccell.2018.12.003] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/22/2018] [Accepted: 12/10/2018] [Indexed: 02/08/2023]
Abstract
We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.
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Affiliation(s)
- Dong-Gi Mun
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Jinhyuk Bhin
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea; Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Sangok Kim
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hyunwoo Kim
- Department of Computer Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea; Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon 34141, Republic of Korea
| | - Jae Hun Jung
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in 446-701, Republic of Korea
| | - Yeonjoo Jung
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Ye Eun Jang
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jong Moon Park
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Hokeun Kim
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Yeonhwa Jung
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hangyeore Lee
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Jingi Bae
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Seunghoon Back
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Su-Jin Kim
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Jieun Kim
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Heejin Park
- Department of Computer Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Honglan Li
- School of Computer Science and Engineering, Soongsil University, Seoul 156-743, Republic of Korea
| | - Kyu-Baek Hwang
- School of Computer Science and Engineering, Soongsil University, Seoul 156-743, Republic of Korea
| | - Young Soo Park
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
| | - Jeong Hwan Yook
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
| | - Byung Sik Kim
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
| | - Sun Young Kwon
- Department of Surgery, Keimyung University School of Medicine, Daegu 700-712, Republic of Korea
| | - Seung Wan Ryu
- Department of Surgery, Keimyung University School of Medicine, Daegu 700-712, Republic of Korea
| | - Do Youn Park
- Department of Pathology, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
| | - Tae Yong Jeon
- Department of Surgery, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
| | - Dae Hwan Kim
- Department of Surgery, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
| | - Jae-Hyuck Lee
- Department of Pathology, Chonnam National University Medical School, Gwangju 501-746, Republic of Korea
| | - Sang-Uk Han
- Department of Surgery, Ajou University School of Medicine, Suwon 443-380 Republic of Korea
| | - Kyu Sang Song
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon 301-747 Republic of Korea
| | - Dongmin Park
- National Cancer Center, Goyang 410-769, Republic of Korea
| | - Jun Won Park
- National Cancer Center, Goyang 410-769, Republic of Korea
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jaesang Kim
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hookeun Lee
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in 446-701, Republic of Korea
| | - Eun Gyeong Yang
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea.
| | - Hark Kyun Kim
- National Cancer Center, Goyang 410-769, Republic of Korea.
| | - Eunok Paek
- Department of Computer Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea.
| | - Sanghyuk Lee
- Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Sang-Won Lee
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea.
| | - Daehee Hwang
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea.
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9
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Huang H, Lee SH, Sousa-Lima I, Kim SS, Hwang WM, Dagon Y, Yang WM, Cho S, Kang MC, Seo JA, Shibata M, Cho H, Belew GD, Bhin J, Desai BN, Ryu MJ, Shong M, Li P, Meng H, Chung BH, Hwang D, Kim MS, Park KS, Macedo MP, White M, Jones J, Kim YB. Rho-kinase/AMPK axis regulates hepatic lipogenesis during overnutrition. J Clin Invest 2018; 128:5335-5350. [PMID: 30226474 DOI: 10.1172/jci63562] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Obesity is a major risk factor for developing nonalcoholic fatty liver disease (NAFLD). NAFLD is the most common form of chronic liver disease and is closely associated with insulin resistance, ultimately leading to cirrhosis and hepatocellular carcinoma. However, knowledge of the intracellular regulators of obesity-linked fatty liver disease remains incomplete. Here we showed that hepatic Rho-kinase 1 (ROCK1) drives obesity-induced steatosis in mice through stimulation of de novo lipogenesis. Mice lacking ROCK1 in the liver were resistant to diet-induced obesity owing to increased energy expenditure and thermogenic gene expression. Constitutive expression of hepatic ROCK1 was sufficient to promote adiposity, insulin resistance, and hepatic lipid accumulation in mice fed a high-fat diet. Correspondingly, liver-specific ROCK1 deletion prevented the development of severe hepatic steatosis and reduced hyperglycemia in obese diabetic (ob/ob) mice. Of pathophysiological significance, hepatic ROCK1 was markedly upregulated in humans with fatty liver disease and correlated with risk factors clustering around NAFLD and insulin resistance. Mechanistically, we found that hepatic ROCK1 suppresses AMPK activity and a ROCK1/AMPK pathway is necessary to mediate cannabinoid-induced lipogenesis in the liver. Furthermore, treatment with metformin, the most widely used antidiabetes drug, reduced hepatic lipid accumulation by inactivating ROCK1, resulting in activation of AMPK downstream signaling. Taken together, our findings establish a ROCK1/AMPK signaling axis that regulates de novo lipogenesis, providing a unique target for treating obesity-related metabolic disorders such as NAFLD.
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Affiliation(s)
- Hu Huang
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA.,Department of Kinesiology and Physiology, East Carolina University, East Carolina Diabetes and Obesity Institute, Greenville, North Carolina, USA
| | - Seung-Hwan Lee
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA.,Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Inês Sousa-Lima
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA.,Centro de Estudos de Doenҫas Crónicas (CEDOC), Chronic Disease Research Center, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sang Soo Kim
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Won Min Hwang
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Yossi Dagon
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Won-Mo Yang
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Sungman Cho
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Min-Cheol Kang
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Ji A Seo
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA.,Division of Endocrinology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Munehiko Shibata
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Hyunsoo Cho
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Getachew Debas Belew
- Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, Coimbra, Portugal
| | - Jinhyuk Bhin
- Center for Plant Aging Research and Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Korea
| | - Bhavna N Desai
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Min Jeong Ryu
- Department of Endocrinology and Metabolism, Chungnam National University School of Medicine, Daejeon, Korea
| | - Minho Shong
- Department of Endocrinology and Metabolism, Chungnam National University School of Medicine, Daejeon, Korea
| | - Peixin Li
- Department of Kinesiology and Physiology, East Carolina University, East Carolina Diabetes and Obesity Institute, Greenville, North Carolina, USA.,Department of Comprehensive Surgery Medical and Health Center Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hua Meng
- Department of Comprehensive Surgery Medical and Health Center Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Byung-Hong Chung
- Department of Nutrition Science, Diabetes Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Daehee Hwang
- Center for Plant Aging Research and Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Korea
| | - Min Seon Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan, College of Medicine, Seoul, Korea
| | - Kyong Soo Park
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Maria Paula Macedo
- Centro de Estudos de Doenҫas Crónicas (CEDOC), Chronic Disease Research Center, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Morris White
- Department of Endocrinology, Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - John Jones
- Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, Coimbra, Portugal
| | - Young-Bum Kim
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
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10
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Yeon A, You S, Kim M, Gupta A, Park MH, Weisenberger DJ, Liang G, Kim J. Rewiring of cisplatin-resistant bladder cancer cells through epigenetic regulation of genes involved in amino acid metabolism. Am J Cancer Res 2018; 8:4520-4534. [PMID: 30214636 PMCID: PMC6134931 DOI: 10.7150/thno.25130] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/23/2018] [Indexed: 12/26/2022] Open
Abstract
Alterations in DNA methylation are important epigenetic markers in bladder cancer (BC). These epigenome modifications may drive the mechanisms of aggressive chemo-resistant BC. Clinicopathological biomarkers that indicate chemotherapeutic resistance are critical for better assessing treatment strategies for individual patients. Thus, in this study, we aimed to determine whether DNA methylation of certain metabolic enzymes is significantly altered in cisplatin-resistant BC cells. Methods: To characterize CpG methylation and nucleosome accessibility in cisplatin-resistant BC cells, the Illumina Infinium HM450 DNA methylation assay was performed. Perturbed gene expression was found to be associated with cisplatin resistance, and the biological roles of spermidine/spermine N1-acetyltransferase (SAT1) and argininosuccinate synthase 1 (ASS1) were further studied using qRT-PCR analysis and various cell biology assays, including western blot. Results:ASS1 and SAT1, genes for amino acid and polyamine metabolism catalysts, respectively, were found to be vastly hypermethylated, resulting in greatly downregulated expression. ASS1 expression is of particular interest because prior studies have demonstrated its potential association with BC stage and recurrence. In regard to chemoresistance, we found that aberrant expression or induced stimulation of SAT1 restored cisplatin sensitivity in the cell culture system. We also found that the addition of exogenous arginine deiminase through administration of ADI-PEG 20 (pegylated arginine deiminase) increased ASS1 expression and enhanced cisplatin's apoptotic effects. Conclusions: Our study demonstrates a novel mechanistic link between the epigenetic perturbation of SAT1 and ASS1 and cancer metabolism in cisplatin-resistant bladder cancer cells. These findings suggest potential utility of SAT1 and ASS1 as predictive biomarkers in re-sensitizing bladder cancer to chemotherapy and personalizing therapy.
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11
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Zhao M, Chen L, Yang J, Han D, Fang D, Qiu X, Yang X, Qiao Z, Ma J, Wang L, Jiang S, Song X, Zhou J, Zhang J, Chen M, Qi D, Yang Y, Pan H. BDNF Val66Met polymorphism, life stress and depression: A meta-analysis of gene-environment interaction. J Affect Disord 2018; 227:226-35. [PMID: 29102837 DOI: 10.1016/j.jad.2017.10.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 09/25/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Depression is thought to be multifactorial in etiology, including genetic and environmental components. While a number of gene-environment interaction studies have been carried out, meta-analyses are scarce. The present meta-analysis aimed to quantify evidence on the interaction between brain-derived neurotrophic factor (BDNF) Val66Met polymorphism and stress in depression. METHODS Included were 31 peer-reviewed with a pooled total of 21060 participants published before October 2016 and literature searches were conducted using PubMed, Wolters Kluwer, Web of Science, EBSCO, Elsevier Science Direct and Baidu Scholar databases. RESULTS The results indicated that the Met allele of BDNF Val66Met polymorphism significantly moderated the relationship between stress and depression (Z=2.666, p = 0.003). The results of subgroup analysis concluded that stressful life events and childhood adversity separately interacted with the Met allele of BDNF Val66Met polymorphism in depression (Z = 2.552, p = 0.005; Z = 1.775, p = 0.03). LIMITATIONS The results could be affected by errors or bias in primary studies which had small sample sizes with relatively lower statistic power. We could not estimate how strong the interaction effect between gene and environment was. CONCLUSIONS We found evidence that supported the hypothesis that BDNF Val66Met polymorphism moderated the relationship between stress and depression, despite the fact that many included individual studies did not show this effect.
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12
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Abstract
Mathematical models of cancer stem cells are useful in translational cancer research for facilitating the understanding of tumor growth dynamics and for predicting treatment response and resistance to combined targeted therapies. In this chapter, we describe appealing aspects of different methods used in mathematical oncology and discuss compelling questions in oncology that can be addressed with these modeling techniques. We describe a simplified version of a model of the breast cancer stem cell niche, illustrate the visualization of the model, and apply stochastic simulation to generate full distributions and average trajectories of cell type populations over time. We further discuss the advent of single-cell data in studying cancer stem cell heterogeneity and how these data can be integrated with modeling to advance understanding of the dynamics of invasive and proliferative populations during cancer progression and response to therapy.
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Affiliation(s)
- Mary E Sehl
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Max S Wicha
- Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, USA.
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13
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Zuck M, Austin LS, Danziger SA, Aitchison JD, Kaushansky A. The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria. Front Microbiol 2017; 8:2183. [PMID: 29201016 PMCID: PMC5696578 DOI: 10.3389/fmicb.2017.02183] [Citation(s) in RCA: 14] [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: 09/10/2017] [Accepted: 10/24/2017] [Indexed: 12/18/2022] Open
Abstract
Despite global eradication efforts over the past century, malaria remains a devastating public health burden, causing almost half a million deaths annually (WHO, 2016). A detailed understanding of the mechanisms that control malaria infection has been hindered by technical challenges of studying a complex parasite life cycle in multiple hosts. While many interventions targeting the parasite have been implemented, the complex biology of Plasmodium poses a major challenge, and must be addressed to enable eradication. New approaches for elucidating key host-parasite interactions, and predicting how the parasite will respond in a variety of biological settings, could dramatically enhance the efficacy and longevity of intervention strategies. The field of systems biology has developed methodologies and principles that are well poised to meet these challenges. In this review, we focus our attention on the Liver Stage of the Plasmodium lifecycle and issue a “call to arms” for using systems biology approaches to forge a new era in malaria research. These approaches will reveal insights into the complex interplay between host and pathogen, and could ultimately lead to novel intervention strategies that contribute to malaria eradication.
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Affiliation(s)
- Meghan Zuck
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, WA, United States
| | - Laura S Austin
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, WA, United States
| | - Samuel A Danziger
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, WA, United States.,Institute for Systems Biology, Seattle, WA, United States
| | - John D Aitchison
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, WA, United States.,Institute for Systems Biology, Seattle, WA, United States
| | - Alexis Kaushansky
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, WA, United States.,Department of Global Health, University of Washington, Seattle, WA, United States
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14
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Bin BH, Bhin J, Takaishi M, Toyoshima KE, Kawamata S, Ito K, Hara T, Watanabe T, Irié T, Takagishi T, Lee SH, Jung HS, Rho S, Seo J, Choi DH, Hwang D, Koseki H, Ohara O, Sano S, Tsuji T, Mishima K, Fukada T. Requirement of zinc transporter ZIP10 for epidermal development: Implication of the ZIP10-p63 axis in epithelial homeostasis. Proc Natl Acad Sci U S A 2017; 114:12243-8. [PMID: 29078349 DOI: 10.1073/pnas.1710726114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Skin tissues, in particular the epidermis, are severely affected by zinc deficiency. However, the zinc-mediated mechanisms that maintain the cells that form the epidermis have not been established. Here, we report that the zinc transporter ZIP10 is highly expressed in the outer root sheath of hair follicles and plays critical roles in epidermal development. We found that ZIP10 marked epidermal progenitor cell subsets and that ablating Zip10 caused significant epidermal hypoplasia accompanied by down-regulation of the transactivation of p63, a master regulator of epidermal progenitor cell proliferation and differentiation. Both ZIP10 and p63 are significantly increased during epidermal development, in which ZIP10-mediated zinc influx promotes p63 transactivation. Collectively, these results indicate that ZIP10 plays important roles in epidermal development via, at least in part, the ZIP10-zinc-p63 signaling axis, thereby highlighting the physiological significance of zinc regulation in the maintenance of skin epidermis.
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15
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Bin BH, Bhin J, Seo J, Kim SY, Lee E, Park K, Choi DH, Takagishi T, Hara T, Hwang D, Koseki H, Asada Y, Shimoda S, Mishima K, Fukada T. Requirement of Zinc Transporter SLC39A7/ZIP7 for Dermal Development to Fine-Tune Endoplasmic Reticulum Function by Regulating Protein Disulfide Isomerase. J Invest Dermatol 2017; 137:1682-1691. [PMID: 28545780 DOI: 10.1016/j.jid.2017.03.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/04/2017] [Accepted: 03/10/2017] [Indexed: 11/30/2022]
Abstract
Skin is the first area that manifests zinc deficiency. However, the molecular mechanisms by which zinc homeostasis affects skin development remain largely unknown. Here, we show that zinc-regulation transporter-/iron-regulation transporter-like protein 7 (ZIP7) localized to the endoplasmic reticulum plays critical roles in connective tissue development. Mice lacking the Slc39a7/Zip7 gene in collagen 1-expressing tissue exhibited dermal dysplasia. Ablation of ZIP7 in mesenchymal stem cells inhibited cell proliferation thereby preventing proper dermis formation, indicating that ZIP7 is required for dermal development. We also found that mesenchymal stem cells lacking ZIP7 accumulated zinc in the endoplasmic reticulum, which triggered zinc-dependent aggregation and inhibition of protein disulfide isomerase, leading to endoplasmic reticulum dysfunction. These results suggest that ZIP7 is necessary for endoplasmic reticulum function in mesenchymal stem cells and, as such, is essential for dermal development.
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Affiliation(s)
- Bum-Ho Bin
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, Tokyo, Japan.
| | - Jinhyuk Bhin
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Juyeon Seo
- Amorepacific R&D Unit, Beauty in Longevity Science Research Division, Beauty Food Research Team, Yongin, Republic of Korea
| | - Se-Young Kim
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Eunyoung Lee
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kyuhee Park
- Gyeonggi Bio Center, Gyeonggi Institute of Science & Technology Promotion, Suwon, Republic of Korea
| | - Dong-Hwa Choi
- Gyeonggi Bio Center, Gyeonggi Institute of Science & Technology Promotion, Suwon, Republic of Korea
| | - Teruhisa Takagishi
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
| | - Takafumi Hara
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
| | - Daehee Hwang
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshinobu Asada
- Department of Pediatric Dentistry, Tsurumi University School of Dental Medicine, Yokohama, Japan
| | - Shinji Shimoda
- Department of Oral Anatomy-1, Tsurumi University School of Dental Medicine, Yokohama, Japan
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, Tokyo, Japan
| | - Toshiyuki Fukada
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, Tokyo, Japan; Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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16
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Jeong HS, Bhin J, Joon Kim H, Hwang D, Ryul Lee D, Kim KS. Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. Exp Mol Med 2017; 49:e315. [PMID: 28408750 PMCID: PMC5420799 DOI: 10.1038/emm.2017.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 10/06/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 12/29/2022] Open
Abstract
Spermatogonial stem cells (SSCs) are germline stem cells located along the basement membrane of seminiferous tubules in testes. Recently, SSCs were shown to be reprogrammed into multipotent SSCs (mSSCs). However, both the key factors and biological networks underlying this reprogramming remain elusive. Here, we present transcriptional regulatory networks (TRNs) that control cellular processes related to the SSC-to-mSSC reprogramming. Previously, we established intermediate SSCs (iSSCs) undergoing the transition to mSSCs and generated gene expression profiles of SSCs, iSSCs and mSSCs. By comparing these profiles, we identified 2643 genes that were up-regulated during the reprogramming process and 15 key transcription factors (TFs) that regulate these genes. Using the TF-target relationships, we developed TRNs describing how these TFs regulate three pluripotency-related processes (cell proliferation, stem cell maintenance and epigenetic regulation) during the reprogramming. The TRNs showed that 4 of the 15 TFs (Oct4/Pou5f1, Cux1, Zfp143 and E2f4) regulated cell proliferation during the early stages of reprogramming, whereas 11 TFs (Oct4/Pou5f1, Foxm1, Cux1, Zfp143, Trp53, E2f4, Esrrb, Nfyb, Nanog, Sox2 and Klf4) regulated the three pluripotency-related processes during the late stages of reprogramming. Our TRNs provide a model for the temporally coordinated transcriptional regulation of pluripotency-related processes during the SSC-to-mSSC reprogramming, which can be further tested in detailed functional studies.
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Affiliation(s)
- Hoe-Su Jeong
- Hanyang University College of Medicine, Graduate School of Biomedical Science and Engineering, Seoul, Republic of Korea
| | - Jinhyuk Bhin
- Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea
| | - Hyung Joon Kim
- Hanyang University College of Medicine, Graduate School of Biomedical Science and Engineering, Seoul, Republic of Korea
| | - Daehee Hwang
- Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea.,Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Dong Ryul Lee
- CHA Stem Cell Institute, CHA University, Seoul, Republic of Korea
| | - Kye-Seong Kim
- Hanyang University College of Medicine, Graduate School of Biomedical Science and Engineering, Seoul, Republic of Korea
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17
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Lee IH, Lee IC, Kim J, Kim JH, Chung EH, Kim HJ, Park SJ, Kim YM, Kang SK, Nam HG, Woo HR, Lim PO. NORE1/SAUL1 integrates temperature-dependent defense programs involving SGT1b and PAD4 pathways and leaf senescence in Arabidopsis. Physiol Plant 2016; 158:180-99. [PMID: 26910207 DOI: 10.1111/ppl.12434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/16/2015] [Accepted: 01/06/2016] [Indexed: 05/06/2023]
Abstract
Leaf senescence is not only primarily governed by developmental age but also influenced by various internal and external factors. Although some genes that control leaf senescence have been identified, the detailed regulatory mechanisms underlying integration of diverse senescence-associated signals into the senescence programs remain to be elucidated. To dissect the regulatory pathways involved in leaf senescence, we isolated the not oresara1-1 (nore1-1) mutant showing accelerated leaf senescence phenotypes from an EMS-mutagenized Arabidopsis thaliana population. We found that altered transcriptional programs in defense response-related processes were associated with the accelerated leaf senescence phenotypes observed in nore1-1 through microarray analysis. The nore1-1 mutation activated defense program, leading to enhanced disease resistance. Intriguingly, high ambient temperature effectively suppresses the early senescence and death phenotypes of nore1-1. The gene responsible for the phenotypes of nore1-1 contains a missense mutation in SENESCENCE-ASSOCIATED E3 UBIQUITIN LIGASE 1 (SAUL1), which was reported as a negative regulator of premature senescence in the light intensity- and PHYTOALEXIN DEFICIENT 4 (PAD4)-dependent manner. Through extensive double mutant analyses, we recently identified suppressor of the G2 Allele of SKP1b (SGT1b), one of the positive regulators for disease resistance conferred by many resistance (R) proteins, as a downstream signaling component in NORE1-mediated senescence and cell death pathways. In conclusion, NORE1/SAUL1 is a key factor integrating signals from temperature-dependent defense programs and leaf senescence in Arabidopsis. These findings provide a new insight that plants might utilize defense response program in regulating leaf senescence process, possibly through recruiting the related genes during the evolution of the leaf senescence program.
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Affiliation(s)
- Il Hwan Lee
- Department of Life Sciences, POSTECH, Pohang, 37673, Republic of Korea
| | - In Chul Lee
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Hyo Jung Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Su Jin Park
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, 37673, Republic of Korea
| | - Yong Min Kim
- Department of Bioscience, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sin Kyu Kang
- Department of Bioscience, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea.
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
| | - Pyung Ok Lim
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
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Abstract
The advances in mass spectrometry-based proteomics technologies have enabled the generation of global proteome data from tissue or body fluid samples collected from a broad spectrum of human diseases. Comparative proteomic analysis of global proteome data identifies and prioritizes the proteins showing altered abundances, called differentially expressed proteins (DEPs), in disease samples, compared to control samples. Protein biomarker candidates that can serve as indicators of disease states are then selected as key molecules among these proteins. Recently, it has been addressed that cellular pathways can provide better indications of disease states than individual molecules and also network analysis of the DEPs enables effective identification of cellular pathways altered in disease conditions and key molecules representing the altered cellular pathways. Accordingly, a number of network-based approaches to identify disease-related pathways and representative molecules of such pathways have been developed. In this review, we summarize analytical platforms for network-based protein biomarker discovery and key components in the platforms.
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Affiliation(s)
- Minhyung Kim
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Korea
| | - Daehee Hwang
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Korea
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Seo M, Seo K, Hwang W, Koo HJ, Hahm JH, Yang JS, Han SK, Hwang D, Kim S, Jang SK, Lee Y, Nam HG, Lee SJV. RNA helicase HEL-1 promotes longevity by specifically activating DAF-16/FOXO transcription factor signaling in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2015; 112:E4246-55. [PMID: 26195740 PMCID: PMC4534234 DOI: 10.1073/pnas.1505451112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The homeostatic maintenance of the genomic DNA is crucial for regulating aging processes. However, the role of RNA homeostasis in aging processes remains unknown. RNA helicases are a large family of enzymes that regulate the biogenesis and homeostasis of RNA. However, the functional significance of RNA helicases in aging has not been explored. Here, we report that a large fraction of RNA helicases regulate the lifespan of Caenorhabditis elegans. In particular, we show that a DEAD-box RNA helicase, helicase 1 (HEL-1), promotes longevity by specifically activating the DAF-16/forkhead box O (FOXO) transcription factor signaling pathway. We find that HEL-1 is required for the longevity conferred by reduced insulin/insulin-like growth factor 1 (IGF-1) signaling (IIS) and is sufficient for extending lifespan. We further show that the expression of HEL-1 in the intestine and neurons contributes to longevity. HEL-1 enhances the induction of a large fraction of DAF-16 target genes. Thus, the RNA helicase HEL-1 appears to promote longevity in response to decreased IIS as a transcription coregulator of DAF-16. Because HEL-1 and IIS are evolutionarily well conserved, a similar mechanism for longevity regulation via an RNA helicase-dependent regulation of FOXO signaling may operate in mammals, including humans.
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Affiliation(s)
- Mihwa Seo
- Center for Plant Aging Research, Institute for Basic Science, Daegu 711-873, Korea; School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Wooseon Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Hee Jung Koo
- Center for Plant Aging Research, Institute for Basic Science, Daegu 711-873, Korea; School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Jeong-Hoon Hahm
- Center for Plant Aging Research, Institute for Basic Science, Daegu 711-873, Korea
| | - Jae-Seong Yang
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Daehee Hwang
- Center for Plant Aging Research, Institute for Basic Science, Daegu 711-873, Korea; Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 711-873, Korea
| | - Sanguk Kim
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology, Pohang 790-784, Korea; Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea; Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 711-873, Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu 711-873, Korea; Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 711-873, Korea;
| | - Seung-Jae V Lee
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology, Pohang 790-784, Korea; Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea; Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang 790-784, Korea
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20
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Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP. IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science 2015; 349:1259425. [PMID: 26160952 DOI: 10.1126/science.1259425] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Immune cells function in an interacting hierarchy that coordinates the activities of various cell types according to genetic and environmental contexts. We developed graphical approaches to construct an extensible immune reference map from mass cytometry data of cells from different organs, incorporating landmark cell populations as flags on the map to compare cells from distinct samples. The maps recapitulated canonical cellular phenotypes and revealed reproducible, tissue-specific deviations. The approach revealed influences of genetic variation and circadian rhythms on immune system structure, enabled direct comparisons of murine and human blood cell phenotypes, and even enabled archival fluorescence-based flow cytometry data to be mapped onto the reference framework. This foundational reference map provides a working definition of systemic immune organization to which new data can be integrated to reveal deviations driven by genetics, environment, or pathology.
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Affiliation(s)
- Matthew H Spitzer
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA.
| | - Pier Federico Gherardini
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Gabriela K Fragiadakis
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | | | - Robert T Yuan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Andrew N Hotson
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Rachel Finck
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Yaron Carmi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Eli R Zunder
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Stanford University, Stanford, CA 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Edgar G Engleman
- Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Garry P Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA.
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Abstract
Recent advances in high-throughput technologies have led to the emergence of systems biology as a holistic science to achieve more precise modeling of complex diseases. Many predict the emergence of personalized medicine in the near future. We are, however, moving from two-tiered health systems to a two-tiered personalized medicine. Omics facilities are restricted to affluent regions, and personalized medicine is likely to widen the growing gap in health systems between high and low-income countries. This is mirrored by an increasing lag between our ability to generate and analyze big data. Several bottlenecks slow-down the transition from conventional to personalized medicine: generation of cost-effective high-throughput data; hybrid education and multidisciplinary teams; data storage and processing; data integration and interpretation; and individual and global economic relevance. This review provides an update of important developments in the analysis of big data and forward strategies to accelerate the global transition to personalized medicine.
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Affiliation(s)
- Akram Alyass
- Department of Clinical Epidemiology and Biostatistics, McMaster University, 1280 Main Street West, Hamilton, ON, Canada.
| | - Michelle Turcotte
- Department of Clinical Epidemiology and Biostatistics, McMaster University, 1280 Main Street West, Hamilton, ON, Canada.
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, 1280 Main Street West, Hamilton, ON, Canada.
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, Canada.
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22
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Hung PC, Yang TH, Liaw HJ, Wu WS. The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast. BMC Genomics 2014; 15 Suppl 9:S5. [PMID: 25522035 PMCID: PMC4290617 DOI: 10.1186/1471-2164-15-s9-s5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Histone modification and remodeling play crucial roles in regulating gene transcription. These post-translational modifications of histones function in a combinatorial fashion and can be recognized by specific histone-binding proteins, thus regulating gene transcription. Therefore, understanding the combinatorial patterns of the histone code is vital to understanding the associated biological processes. However, most of the datasets regarding histone modification and chromatin regulation are scattered across various studies, and no comprehensive search and query tool has yet been made available to retrieve genes bearing specific histone modification patterns and regulatory proteins. Description For this reason, we developed the Yeast Nucleosome Atlas database, or the YNA database, which integrates the available experimental data on nucleosome occupancy, histone modifications, the binding occupancy of regulatory proteins, and gene expression data, and provides the genome-wide gene miner to retrieve genes with a specific combination of these chromatin-related datasets. Moreover, the biological significance analyzer, which analyzes the enrichments of histone modifications, binding occupancy, transcription rate, and functionality of the retrieved genes, was constructed to help researchers to gain insight into the correlation among chromatin regulation and transcription. Conclusions Compared to previously established genome browsing databases, YNA provides a powerful gene mining and retrieval interface, and is an investigation tool that can assist users to generate testable hypotheses for studying chromatin regulation during transcription. YNA is available online at http://cosbi3.ee.ncku.edu.tw/yna/.
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Yang TH, Wang CC, Hung PC, Wu WS. cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. BMC Syst Biol 2014; 8 Suppl 4:S8. [PMID: 25521507 PMCID: PMC4290730 DOI: 10.1186/1752-0509-8-s4-s8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Cis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs. DESCRIPTION It is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality. CONCLUSIONS cisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable hypotheses for the molecular mechanisms of metazoan gene regulation. We believe that the information deposited in cisMEP will greatly facilitate the comparative usage of different CRM prediction tools and will help biologists to study the modular regulatory mechanisms between different TFs and their target genes.
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Bin BH, Bhin J, Yang SH, Choi DH, Park K, Shin DW, Lee AY, Hwang D, Cho EG, Lee TR. Hyperosmotic stress reduces melanin production by altering melanosome formation. PLoS One 2014; 9:e105965. [PMID: 25170965 DOI: 10.1371/journal.pone.0105965] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/29/2014] [Indexed: 01/01/2023] Open
Abstract
Many tissues of the human body encounter hyperosmotic stress. The effect of extracellular osmotic changes on melanin production has not yet been elucidated. In this study, we determined that hyperosmotic stress induced by organic osmolytes results in reduced melanin production in human melanoma MNT-1 cells. Under hyperosmotic stress, few pigmented mature melanosomes were detected, but there was an increase in swollen vacuoles. These vacuoles were stained with an anti-M6PR antibody that recognizes late endosomal components and with anti-TA99 and anti-HMB45 antibodies, implying that melanosome formation was affected by hyperosmotic stress. Electron microscopic analysis revealed that the M6PR-positive swollen vacuoles were multi-layered and contained melanized granules, and they produced melanin when L-DOPA was applied, indicating that these vacuoles were still capable of producing melanin, but the inner conditions were not compatible with melanin production. The vacuolation phenomenon induced by hyperosmotic conditions disappeared with treatment with the PI3K activator 740 Y-P, indicating that the PI3K pathway is affected by hyperosmotic conditions and is responsible for the proper formation and maturation of melanosomes. The microarray analysis showed alterations of the vesicle organization and transport under hyperosmotic stress. Our findings suggest that melanogenesis could be regulated by physiological conditions, such as osmotic pressure.
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Zhou C, Teng WJ, Yang J, Hu ZB, Wang CC, Qin BN, Lv QL, Liu ZW, Sun CG. Construction of a Protein-Protein Interaction Network for Chronic Myelocytic Leukemia and Pathway Prediction of Molecular Complexes. Asian Pac J Cancer Prev 2014; 15:5325-30. [DOI: 10.7314/apjcp.2014.15.13.5325] [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: 11/10/2022] Open
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Choi D, Choi J, Kang B, Lee S, Cho YH, Hwang I, Hwang D. iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis. Mol Plant 2014; 7:792-813. [PMID: 24380880 DOI: 10.1093/mp/sst173] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors (IEFs). However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling (iNID) in Arabidopsis. iNID provides a comprehensive resource of (1) transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and (2) protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of (1) phytohormones and light and (2) phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid (BR)-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs.
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Affiliation(s)
- Daeseok Choi
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 790-784, Pohang, Republic of Korea
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Choi EB, Hong SW, Kim DK, Jeon SG, Kim KR, Cho SH, Gho YS, Jee YK, Kim YK. Decreased diversity of nasal microbiota and their secreted extracellular vesicles in patients with chronic rhinosinusitis based on a metagenomic analysis. Allergy 2014; 69:517-26. [PMID: 24611950 DOI: 10.1111/all.12374] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2014] [Indexed: 01/08/2023]
Abstract
BACKGROUND Chronic rhinosinusitis (CRS) is an inflammatory process in the nasal cavity and paranasal sinuses, and bacteria have been considered to be a cause. Indeed, recent evidence indicates that bacteria-derived extracellular vesicles (EV) appear to be an important causative agent of inflammatory diseases. Here, we aimed to evaluate the diversity of nasal microbiota and their secreted EV in patients with CRS. METHODS Nasal lavage (NAL) fluid samples were obtained from five patients with CRS with polyposis, three patients with CRS without polyposis, and three non-CRS controls. After preparation of bacteria and EV from samples using differential centrifugation, genomic DNA was extracted and 16S-rDNA amplicons were subjected to high-throughput pyrosequencing on a Roche 454 GS-FLX platform. RESULTS Metagenomics showed that bacteria composition was positively correlated with EV composition. Samples from patients with CRS had greater bacterial abundance and lower diversity, both from bacteria and the EV portion of samples, compared with non-CRS samples. At each phylogenetic level, Bacteroidetes decreased while Proteobacteria increased in the CRS group at the phylum level. At the genus level, Prevotella spp. decreased in the CRS group, while Staphylococcus spp. increased from both bacteria and EV. Moreover, Staphylococcus aureus and its secreting EV compositions were higher in samples from CRS with polyps compared with CRS without polyps. CONCLUSIONS These results suggest that patients with CRS have altered nasal microbiota and decreased diversity in bacterial compositions as well as increased S. aureus abundance in those patients with polyps.
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Affiliation(s)
- E.-B. Choi
- Department of Life Sciences; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - S.-W. Hong
- Department of Life Sciences; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - D.-K. Kim
- Department of Life Sciences; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - S. G. Jeon
- Department of Life Sciences; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - K.-R. Kim
- Department of Otorhinolaryngology-Head and Neck Surgery; College of Medicine; Hanyang University; Seoul Korea
| | - S.-H. Cho
- Department of Otorhinolaryngology-Head and Neck Surgery; College of Medicine; Hanyang University; Seoul Korea
| | - Y. S. Gho
- Department of Life Sciences; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - Y.-K. Jee
- Department of Internal Medicine; College of Medicine; Dankook University; Cheonan Korea
| | - Y.-K. Kim
- Department of Life Sciences; Pohang University of Science and Technology (POSTECH); Pohang Korea
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Tomescu OA, Mattanovich D, Thallinger GG. Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data. BMC Syst Biol 2014; 8 Suppl 2:S4. [PMID: 25033389 PMCID: PMC4101701 DOI: 10.1186/1752-0509-8-s2-s4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Technological improvements have shifted the focus from data generation to data analysis. The availability of large amounts of data from transcriptomics, protemics and metabolomics experiments raise new questions concerning suitable integrative analysis methods. We compare three integrative analysis techniques (co-inertia analysis, generalized singular value decomposition and integrative biclustering) by applying them to gene and protein abundance data from the six life cycle stages of Plasmodium falciparum. Co-inertia analysis is an analysis method used to visualize and explore gene and protein data. The generalized singular value decomposition has shown its potential in the analysis of two transcriptome data sets. Integrative Biclustering applies biclustering to gene and protein data. Results Using CIA, we visualize the six life cycle stages of Plasmodium falciparum, as well as GO terms in a 2D plane and interpret the spatial configuration. With GSVD, we decompose the transcriptomic and proteomic data sets into matrices with biologically meaningful interpretations and explore the processes captured by the data sets. IBC identifies groups of genes, proteins, GO Terms and life cycle stages of Plasmodium falciparum. We show method-specific results as well as a network view of the life cycle stages based on the results common to all three methods. Additionally, by combining the results of the three methods, we create a three-fold validated network of life cycle stage specific GO terms: Sporozoites are associated with transcription and transport; merozoites with entry into host cell as well as biosynthetic and metabolic processes; rings with oxidation-reduction processes; trophozoites with glycolysis and energy production; schizonts with antigenic variation and immune response; gametocyctes with DNA packaging and mitochondrial transport. Furthermore, the network connectivity underlines the separation of the intraerythrocytic cycle from the gametocyte and sporozoite stages. Conclusion Using integrative analysis techniques, we can integrate knowledge from different levels and obtain a wider view of the system under study. The overlap between method-specific and common results is considerable, even if the basic mathematical assumptions are very different. The three-fold validated network of life cycle stage characteristics of Plasmodium falciparum could identify a large amount of the known associations from literature in only one study.
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Abstract
Regulatory targets of transcription factors (TFs) can be identified by the TF perturbation experiments, which reveal the expression changes owing to the perturbation (deletion or overexpression) of TFs. But the identified targets of a given TF consist of both direct and indirect regulatory targets. It has been shown that most of the TFPE-identified regulatory targets are indirect, indicating that TF-gene regulation is mainly through transcriptional regulatory pathways (TRPs) consisting of intermediate TFs. Without identification of these TRPs, it is not easy to understand how a TF regulates its indirect targets. Because there is no such database depositing the potential TRPs for Saccharomyces cerevisiae now, this motivates us to construct the YTRP (Yeast Transcriptional Regulatory Pathway) database. For each TF-gene regulatory pair under different experimental conditions, all possible TRPs in two underlying networks (constructed using experimentally verified TF-gene binding pairs and TF-gene regulatory pairs from the literature) for the specified experimental conditions were automatically enumerated by TRP mining procedures developed from the graph theory. The enumerated TRPs of a TF-gene regulatory pair provide experimentally testable hypotheses for the molecular mechanisms behind a TF and its regulatory target. YTRP is available online at http://cosbi3.ee.ncku.edu.tw/YTRP/. We believe that the TRPs deposited in this database will greatly improve the usefulness of TFPE data for yeast biologists to study the regulatory mechanisms between a TF and its knocked-out targets. Database URL: http://cosbi3.ee.ncku.edu.tw/YTRP/
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Affiliation(s)
- Tzu-Hsien Yang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan and Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
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Abstract
Endobiogeny is a global systems approach to human biology that may offer an advancement in clinical medicine based in scientific principles of rigor and experimentation and the humanistic principles of individualization of care and alleviation of suffering with minimization of harm. Endobiogeny is neither a movement away from modern science nor an uncritical embracing of pre-rational methods of inquiry but a synthesis of quantitative and qualitative relationships reflected in a systems-approach to life and based on new mathematical paradigms of pattern recognition.
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Affiliation(s)
- Jean-Claude Lapraz
- Société internationale de médecine endobiogénique et de physiologie intégrative, Paris, France
| | - Kamyar M Hedayat
- American society of endobiogenic medicine and integrative physiology, San Diego, California, United States
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Abstract
Over the last 5 years, the emergence of gene expression profiling using high-density DNA microarrays led to a better understanding of tumor development and identified new prognostic markers. However, high-density microarrays failed to leap from the researcher's bench to the clinical practice due to their cost, data management and lack of standardization. DualChip low-density DNA microarrays were developed as a new flexible tool that is able to reliably quantify the expression of a limited number of genes of clinical relevance. This review will illustrate how DualChip technology can be applied to tumor diagnosis and tumor-acquired drug resistance.
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Chun JN, Lim JM, Kang Y, Kim EH, Shin YC, Kim HG, Jang D, Kwon D, Shin SY, So I, Jeon JH. A network perspective on unraveling the role of TRP channels in biology and disease. Pflugers Arch 2014; 466:173-82. [PMID: 23677537 DOI: 10.1007/s00424-013-1292-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/22/2013] [Accepted: 05/03/2013] [Indexed: 02/08/2023]
Abstract
Transient receptor potential (TRP) channels are a large family of non-selective cation channels that mediate numerous physiological and pathophysiological processes; however, still largely unknown are the underlying molecular mechanisms. With data generated on an unprecedented scale, network-based approaches have been revolutionizing the way in which we understand biology and disease, discover disease genes, and develop therapeutic strategies. These circumstances have created opportunities to encounter TRP channel research to data-intensive science. In this review, we provide an introduction of network-based approaches in biomedical science, describe the current state of TRP channel network biology, and discuss the future direction of TRP channel research. Network perspective will facilitate the discovery of latent roles and underlying mechanisms of TRP channels in biology and disease.
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Ma X, Chen R, Liu X, Xie J, Si K, Duan L. Effects of matrine on JAK-STAT signaling transduction pathways in bleomycin-induced pulmonary fibrosis. Afr J Tradit Complement Altern Med 2013; 10:442-8. [PMID: 24146473 DOI: 10.4314/ajtcam.v10i3.10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The current study aims to investigate the effects of matrine on the JAK-STAT signaling transduction pathways in bleomycin (BLM)-induced pulmonary fibrosis (PF) and to explore its action mechanism. A total of 72 male C57BL/6 mice were randomized into the control, model, and treatment groups. PF models were established by instilling BLM intratracheally. The treatment group was given daily matrine through gastric lavage. Six mice were sacrificed in each group at 3, 7, 14, and 28 days. The lung tissues were observed using hematoxylin-eosin staining. The expression of JAK, STAT1, and STAT3 was observed using immunohistochemistry and then determined using real-time polymerase chain reaction. Alveolitis and PF significantly improved in the treatment group compared with the model group (P < 0.05). The expression of JAK, STAT1, and STAT3 in the model group increased at day 7, peaked at day 14 and then decreased, but the expression was still higher than that in the control group at day 28 (P < 0.05). The three indices in the treatment group were significantly lower than those in the model group at any detection time point (P < 0.05). PF causes high expression of JAK, STAT1, and STAT3. Matrine exerts an anti-PF effect by inhibiting the JAK-STAT signaling transduction pathways.
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Affiliation(s)
- Xiuqin Ma
- Department of Respiratory Disease, Yixing People Hospital, Yixing 214200, China
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Badaoui B, Tuggle CK, Hu Z, Reecy JM, Ait-Ali T, Anselmo A, Botti S. Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: a meta-analysis approach. BMC Genomics 2013; 14:220. [PMID: 23552196 PMCID: PMC3623894 DOI: 10.1186/1471-2164-14-220] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 08/08/2012] [Accepted: 03/22/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The availability of gene expression data that corresponds to pig immune response challenges provides compelling material for the understanding of the host immune system. Meta-analysis offers the opportunity to confirm and expand our knowledge by combining and studying at one time a vast set of independent studies creating large datasets with increased statistical power. In this study, we performed two meta-analyses of porcine transcriptomic data: i) scrutinized the global immune response to different challenges, and ii) determined the specific response to Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection. To gain an in-depth knowledge of the pig response to PRRSV infection, we used an original approach comparing and eliminating the common genes from both meta-analyses in order to identify genes and pathways specifically involved in the PRRSV immune response. The software Pointillist was used to cope with the highly disparate data, circumventing the biases generated by the specific responses linked to single studies. Next, we used the Ingenuity Pathways Analysis (IPA) software to survey the canonical pathways, biological functions and transcription factors found to be significantly involved in the pig immune response. We used 779 chips corresponding to 29 datasets for the pig global immune response and 279 chips obtained from 6 datasets for the pig response to PRRSV infection, respectively. RESULTS The pig global immune response analysis showed interconnected canonical pathways involved in the regulation of translation and mitochondrial energy metabolism. Biological functions revealed in this meta-analysis were centred around translation regulation, which included protein synthesis, RNA-post transcriptional gene expression and cellular growth and proliferation. Furthermore, the oxidative phosphorylation and mitochondria dysfunctions, associated with stress signalling, were highly regulated. Transcription factors such as MYCN, MYC and NFE2L2 were found in this analysis to be potentially involved in the regulation of the immune response. The host specific response to PRRSV infection engendered the activation of well-defined canonical pathways in response to pathogen challenge such as TREM1, toll-like receptor and hyper-cytokinemia/ hyper-chemokinemia signalling. Furthermore, this analysis brought forth the central role of the crosstalk between innate and adaptive immune response and the regulation of anti-inflammatory response. The most significant transcription factor potentially involved in this analysis was HMGB1, which is required for the innate recognition of viral nucleic acids. Other transcription factors like interferon regulatory factors IRF1, IRF3, IRF5 and IRF8 were also involved in the pig specific response to PRRSV infection. CONCLUSIONS This work reveals key genes, canonical pathways and biological functions involved in the pig global immune response to diverse challenges, including PRRSV infection. The powerful statistical approach led us to consolidate previous findings as well as to gain new insights into the pig immune response either to common stimuli or specifically to PRRSV infection.
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Affiliation(s)
- Bouabid Badaoui
- Parco Tecnologico Padano - CERSA, Via Einstein, Lodi, 26900, Italy.
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35
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Li B. Using Systems Biology Approaches to Predict New Players in the Innate Immune System. Bioinformatics 2013:690-724. [DOI: 10.4018/978-1-4666-3604-0.ch037] [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: 09/01/2023] Open
Abstract
Toll-like receptors (TLRs) are critical players in the innate immune response to pathogens. However, transcriptional regulatory mechanisms in the TLR activation pathways are still relatively poorly characterized. To address this question, the author of this chapter applied a systematic approach to predict transcription factors that temporally regulate differentially expressed genes under diverse TLR stimuli. Time-course microarray data were selected from mouse bone marrow-derived macrophages stimulated by six TLR agonists. Differentially regulated genes were clustered on the basis of their dynamic behavior. The author then developed a computational method to identify positional overlapping transcription factor (TF) binding sites in each cluster, so as to predict possible TFs that may regulate these genes. A second microarray dataset, on wild-type, Myd88-/- and Trif-/- macrophages stimulated by lipopolysaccharide (LPS), was used to provide supporting evidence on this combined approach. Overall, the author was able to identify known TLR TFs, as well as to predict new TFs that may be involved in TLR signaling.
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Affiliation(s)
- Bin Li
- Merrimack Pharmaceuticals, USA
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36
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Im SK, Jeong H, Jeong HW, Kim KT, Hwang D, Ikegami M, Kong YY. Disruption of sorting nexin 5 causes respiratory failure associated with undifferentiated alveolar epithelial type I cells in mice. PLoS One 2013; 8:e58511. [PMID: 23526992 PMCID: PMC3602295 DOI: 10.1371/journal.pone.0058511] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/05/2013] [Indexed: 01/16/2023] Open
Abstract
Sorting nexin 5 (Snx5) has been posited to regulate the degradation of epidermal growth factor receptor and the retrograde trafficking of cation-independent mannose 6-phosphate receptor/insulin-like growth factor II receptor. Snx5 has also been suggested to interact with Mind bomb-1, an E3 ubiquitin ligase that regulates the activation of Notch signaling. However, the in vivo functions of Snx5 are largely unknown. Here, we report that disruption of the Snx5 gene in mice (Snx5-/- mice) resulted in partial perinatal lethality; 40% of Snx5-/- mice died shortly after birth due to cyanosis, reduced air space in the lungs, and respiratory failure. Histological analysis revealed that Snx5-/- mice exhibited thickened alveolar walls associated with undifferentiated alveolar epithelial type I cells. In contrast, alveolar epithelial type II cells were intact, exhibiting normal surfactant synthesis and secretion. Although the expression levels of surfactant proteins and saturated phosphatidylcholine in the lungs of Snx5-/- mice were comparable to those of Snx5+/+ mice, the expression levels of T1α, Aqp5, and Rage, markers for distal alveolar epithelial type I cells, were significantly decreased in Snx5-/- mice. These results demonstrate that Snx5 is necessary for the differentiation of alveolar epithelial type I cells, which may underlie the adaptation to air breathing at birth.
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Affiliation(s)
- Sun-Kyoung Im
- School of Biological Science, College of Natural Sciences, Seoul National University, Seoul, South Korea
- Department of Life Science, Division of Molecular and Life Science, POSTECH, Pohang, South Korea
| | - HyoBin Jeong
- School of Interdisciplinary Biosciences and Bioengineering, POSTECH, Pohang, South Korea
| | - Hyun-Woo Jeong
- School of Biological Science, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Kyong-Tai Kim
- Department of Life Science, Division of Molecular and Life Science, POSTECH, Pohang, South Korea
| | - Daehee Hwang
- School of Interdisciplinary Biosciences and Bioengineering, POSTECH, Pohang, South Korea
| | - Machiko Ikegami
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Young-Yun Kong
- School of Biological Science, College of Natural Sciences, Seoul National University, Seoul, South Korea
- * E-mail:
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37
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Asadi B, Maurya M, Subramaniam S, Tartakovsky D. Comparison of statistical and optimisation-based methods for data-driven network reconstruction of biochemical systems. IET Syst Biol 2012; 6:155-63. [DOI: 10.1049/iet-syb.2011.0052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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38
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Sung J, Wang Y, Chandrasekaran S, Witten DM, Price ND. Molecular signatures from omics data: from chaos to consensus. Biotechnol J 2012; 7:946-57. [PMID: 22528809 PMCID: PMC3418428 DOI: 10.1002/biot.201100305] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [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: 12/09/2011] [Revised: 02/14/2012] [Accepted: 03/08/2012] [Indexed: 01/17/2023]
Abstract
In the past 15 years, new "omics" technologies have made it possible to obtain high-resolution molecular snapshots of organisms, tissues, and even individual cells at various disease states and experimental conditions. It is hoped that these developments will usher in a new era of personalized medicine in which an individual's molecular measurements are used to diagnose disease, guide therapy, and perform other tasks more accurately and effectively than is possible using standard approaches. There now exists a vast literature of reported "molecular signatures". However, despite some notable exceptions, many of these signatures have suffered from limited reproducibility in independent datasets, insufficient sensitivity or specificity to meet clinical needs, or other challenges. In this paper, we discuss the process of molecular signature discovery on the basis of omics data. In particular, we highlight potential pitfalls in the discovery process, as well as strategies that can be used to increase the odds of successful discovery. Despite the difficulties that have plagued the field of molecular signature discovery, we remain optimistic about the potential to harness the vast amounts of available omics data in order to substantially impact clinical practice.
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Affiliation(s)
- Jaeyun Sung
- Institute for Systems BiologySeattle, WA, USA
- Department of Chemical and Biomolecular Engineering, University of IllinoisUrbana, IL, USA
| | - Yuliang Wang
- Institute for Systems BiologySeattle, WA, USA
- Department of Chemical and Biomolecular Engineering, University of IllinoisUrbana, IL, USA
| | - Sriram Chandrasekaran
- Institute for Systems BiologySeattle, WA, USA
- Center for Biophysics and Computational Biology, University of IllinoisUrbana, IL, USA
| | - Daniela M Witten
- Department of Biostatistics, University of WashingtonSeattle, WA, USA
| | - Nathan D Price
- Institute for Systems BiologySeattle, WA, USA
- Department of Chemical and Biomolecular Engineering, University of IllinoisUrbana, IL, USA
- Center for Biophysics and Computational Biology, University of IllinoisUrbana, IL, USA
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39
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Choi HJ, Yoon YJ, Kwon YK, Lee YJ, Chae S, Hwang D, Hwang GS, Kwon TH. Patterns of gene and metabolite define the effects of extracellular osmolality on kidney collecting duct. J Proteome Res 2012; 11:3816-28. [PMID: 22686594 DOI: 10.1021/pr300309d] [Citation(s) in RCA: 13] [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] [Indexed: 12/25/2022]
Abstract
To investigate the effects of changes in extracellular osmolality on the function of kidney collecting duct cells, particularly on water and sodium reabsorption in the conditions of diuresis and antidiuresis, we generated transcriptome and metabolome profiles of primary cultured inner medullary collecting duct (IMCD) cells. They were grown in hyperosmolar culture medium (640 mOsm) for 4 days and then exposed to either reduced (300 mOsm) or same osmolality for 1 or 2 days more. Integrated analysis of the transcriptome and metabolome revealed that decreased extracellular osmolality was associated with decreased levels of organic osmolytes, glucose, intermediates of citric acid cycle, and branched-chain amino acids (BCAA) in IMCD cells, along with significantly decreased gene expression and protein abundance of P-type transporters (ATP1B1), ABC transporters (ABCC5 and ABCG1), and insulin signaling pathways (IRS2). Quantitative real-time RT-PCR and semiquantitative immunoblotting confirmed the changes of transcript levels of differentially expressed genes and protein levels. Taken together, integrated analysis of omics data demonstrated that water and sodium reabsorption could be reduced by decreased extracellular osmolality per se, through decreased levels of ABC transporters and IRS2, which play a potential role in the transport of organic osmolytes, BCAA, glucose, and trafficking of epithelial sodium channel.
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Affiliation(s)
- Hyo-Jung Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Taegu, Korea
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40
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Abstract
Mitochondria are the power plant of the heart, burning fat and sugars to supply the muscle with the adenosine triphosphate (ATP) free energy that drives contraction and relaxation during each heart beat. This function was first captured in a mathematical model in 1967. Today, interest in such a model has been rekindled by ongoing in silico integrative physiology efforts such as the Cardiac Physiome project. Here, the status of the field of computational modeling of mitochondrial ATP synthetic function is reviewed.
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Affiliation(s)
- J P J Schmitz
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
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41
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Huang SS, Fraenkel E. Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol 2012; 110:57-80. [PMID: 22482945 DOI: 10.1016/B978-0-12-388403-9.00003-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Signaling and transcription are tightly integrated processes that underlie many cellular responses to the environment. A network of signaling events, often mediated by post-translational modification on proteins, can lead to long-term changes in cellular behavior by altering the activity of specific transcriptional regulators and consequently the expression level of their downstream targets. As many high-throughput, "-omics" methods are now available that can simultaneously measure changes in hundreds of proteins and thousands of transcripts, it should be possible to systematically reconstruct cellular responses to perturbations in order to discover previously unrecognized signaling pathways. This chapter describes a computational method for discovering such pathways that aims to compensate for the varying levels of noise present in these diverse data sources. Based on the concept of constraint optimization on networks, the method seeks to achieve two conflicting aims: (1) to link together many of the signaling proteins and differentially expressed transcripts identified in the experiments "constraints" using previously reported protein-protein and protein-DNA interactions, while (2) keeping the resulting network small and ensuring it is composed of the highest confidence interactions "optimization". A further distinctive feature of this approach is the use of transcriptional data as evidence of upstream signaling events that drive changes in gene expression, rather than as proxies for downstream changes in the levels of the encoded proteins. We recently demonstrated that by applying this method to phosphoproteomic and transcriptional data from the pheromone response in yeast, we were able to recover functionally coherent pathways and to reveal many components of the cellular response that are not readily apparent in the original data. Here, we provide a more detailed description of the method, explore the robustness of the solution to the noise level of input data and discuss the effect of parameter values.
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42
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Piao LS, Hur W, Kim TK, Hong SW, Kim SW, Choi JE, Sung PS, Song MJ, Lee BC, Hwang D, Yoon SK. CD133+ liver cancer stem cells modulate radioresistance in human hepatocellular carcinoma. Cancer Lett 2011; 315:129-37. [PMID: 22079466 DOI: 10.1016/j.canlet.2011.10.012] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 12/15/2022]
Abstract
CD133 is a cancer stem-cell (CSC) marker associated with radioresistance and chemoresistance in various cancers. In the present study, CD133-expressing liver cancer cells following radiation exposure showed higher activation of MAPK/PI3K signaling pathway and reduction in reactive oxygen species levels compared to CD133- cells. The in vivo study with a xenograft model showed increased tumor formation in irradiated CD133+ cell-injected nude mice compared to the CD133- group, suggesting that CD133 contributes to radioresistance in HCC. Therefore, CD133-expressing liver cancer cells have anti-apoptotic and radioresistance properties that may be useful to improve anti-cancer treatments, including chemotherapy/radiotherapy of HCC.
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Affiliation(s)
- Lian Shu Piao
- WHO Collaborating Center of Viral Hepatitis, The Catholic University of Korea, Seoul 137-701, Republic of Korea
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43
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Abstract
A number of mechanistic and predictive genetic regulatory networks (GRNs) comprising dozens of genes have already been characterized at the level of cis-regulatory interactions. Reconstructions of networks of 100's to 1000's of genes and their interactions are currently underway. Understanding the organizational and functional principles underlying these networks is probably the single greatest challenge facing genomics today. We review the current approaches to deciphering large-scale GRNs and discuss some of their limitations. We then propose a bottom-up approach in which large-scale GRNs are first organized in terms of functionally distinct GRN building blocks of one or a few genes. Biological processes may then be viewed as the outcome of functional interactions among these simple, well-characterized functional building blocks. We describe several putative GRN functional building blocks and show that they can be located within GRNs on the basis of their interaction topology and additional, simple and experimentally testable constraints.
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Affiliation(s)
- William Longabaugh
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, USA
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44
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Abstract
Data fusion methods are powerful tools for integrating the different views of an organism provided by various types of experimental data. We describe various methodologies for integrating and drawing inferences from a collection of biomedical data, primarily focusing on protein and gene expression data. Computational experiments performed using biomedical data, including known protein-protein interactions, hydropathy profiles, gene expression data and amino acid sequences, demonstrate the utility of this approach. Overall, studies agree in that methodologies using carefully selected data of various types to predict particular classes, groups and interactions, perform better than when applied to a single type of data.
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Affiliation(s)
- Georgia Tsiliki
- Bioinformatics andMedical Informatics Group, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 115 27, Athens, Greece.
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45
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Ratushny AV, Shmulevich I, Aitchison JD. Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues. PLoS Comput Biol 2011; 7:e1002091. [PMID: 21738459 PMCID: PMC3127798 DOI: 10.1371/journal.pcbi.1002091] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 04/29/2011] [Indexed: 11/27/2022] Open
Abstract
When living systems detect changes in their external environment their response must be measured to balance the need to react appropriately with the need to remain stable, ignoring insignificant signals. Because this is a fundamental challenge of all biological systems that execute programs in response to stimuli, we developed a generalized time-frequency analysis (TFA) framework to systematically explore the dynamical properties of biomolecular networks. Using TFA, we focused on two well-characterized yeast gene regulatory networks responsive to carbon-source shifts and a mammalian innate immune regulatory network responsive to lipopolysaccharides (LPS). The networks are comprised of two different basic architectures. Dual positive and negative feedback loops make up the yeast galactose network; whereas overlapping positive and negative feed-forward loops are common to the yeast fatty-acid response network and the LPS-induced network of macrophages. TFA revealed remarkably distinct network behaviors in terms of trade-offs in responsiveness and noise suppression that are appropriately tuned to each biological response. The wild type galactose network was found to be highly responsive while the oleate network has greater noise suppression ability. The LPS network appeared more balanced, exhibiting less bias toward noise suppression or responsiveness. Exploration of the network parameter space exposed dramatic differences in system behaviors for each network. These studies highlight fundamental structural and dynamical principles that underlie each network, reveal constrained parameters of positive and negative feedback and feed-forward strengths that tune the networks appropriately for their respective biological roles, and demonstrate the general utility of the TFA approach for systems and synthetic biology. Biological systems constantly balance noise suppression with responsiveness. In a fluctuating environment, some changes are insignificant to living cells while others represent cues to which they must respond. These stimuli are interpreted by molecular circuits that enable the cell to strike an appropriate balance between responsiveness and noise suppression. This trade-off is governed by the structure and kinetic parameters of molecular networks, which have been tuned by evolutionary selection for different stimuli and responses. We consider three regulatory circuits (two from yeast and one from mammalian cells), which respond to different environments and involve very different physiological processes. To investigate the responses to a time varying signal, we developed a generalized time-frequency analysis framework for studying such trade-offs using mathematical models of regulatory circuits and explore how the structure and parameters of the circuit affect the trade-offs between noise suppression and responsiveness. The generalized TFA approach represents an effective tool for exploring and analyzing different systems-level dynamical properties. Making use of such properties can facilitate prediction and network control for systems- and synthetic biology applications.
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Affiliation(s)
| | - Ilya Shmulevich
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - John D. Aitchison
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail:
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46
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Abstract
Determining the network of physical protein associations is an important first step in developing mechanistic evidence for elucidating biological pathways. Despite rapid advances in the field of high throughput experiments to determine protein interactions, the majority of associations remain unknown. Here we describe computational methods for significantly expanding protein association networks. We describe methods for integrating multiple independent sources of evidence to obtain higher quality predictions and we compare the major publicly available resources available for experimentalists to use.
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Affiliation(s)
- J G Lees
- Research Department of Structural & Molecular Biology, University College London, London, UK.
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47
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Genini S, Badaoui B, Sclep G, Bishop SC, Waddington D, Pinard van der Laan MH, Klopp C, Cabau C, Seyfert HM, Petzl W, Jensen K, Glass EJ, de Greeff A, Smith HE, Smits MA, Olsaker I, Boman GM, Pisoni G, Moroni P, Castiglioni B, Cremonesi P, Del Corvo M, Foulon E, Foucras G, Rupp R, Giuffra E. Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources. BMC Genomics 2011; 12:225. [PMID: 21569310 PMCID: PMC3118214 DOI: 10.1186/1471-2164-12-225] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [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: 12/03/2010] [Accepted: 05/11/2011] [Indexed: 12/30/2022] Open
Abstract
Background Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland pathogens, including samples from cattle challenged in vivo with S. aureus, E. coli, and S. uberis, samples from goats challenged in vivo with S. aureus, as well as cattle macrophages and ovine dendritic cells infected in vitro with S. aureus. We combined different time points from those studies, testing different responses to mastitis infection: overall (common signature), early stage, late stage, and cattle-specific. Results Ingenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including XBP1 and SREBF1. The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of E. coli and S. aureus infections in cattle in vivo revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that E. coli caused a stronger host response. Conclusions This meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.
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Affiliation(s)
- Sem Genini
- Parco Tecnologico Padano - CERSA, Via Einstein, 26900 Lodi, Italy.
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48
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Li B. Using Systems Biology Approaches to Predict New Players in the Innate Immune System. Handbook of Research on Computational and Systems Biology 2011:428-477. [DOI: 10.4018/978-1-60960-491-2.ch020] [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: 09/01/2023]
Abstract
Toll-like receptors (TLRs) are critical players in the innate immune response to pathogens. However, transcriptional regulatory mechanisms in the TLR activation pathways are still relatively poorly characterized. To address this question, the author of this chapter applied a systematic approach to predict transcription factors that temporally regulate differentially expressed genes under diverse TLR stimuli. Time-course microarray data were selected from mouse bone marrow-derived macrophages stimulated by six TLR agonists. Differentially regulated genes were clustered on the basis of their dynamic behavior. The author then developed a computational method to identify positional overlapping transcription factor (TF) binding sites in each cluster, so as to predict possible TFs that may regulate these genes. A second microarray dataset, on wild-type, Myd88-/- and Trif-/- macrophages stimulated by lipopolysaccharide (LPS), was used to provide supporting evidence on this combined approach. Overall, the author was able to identify known TLR TFs, as well as to predict new TFs that may be involved in TLR signaling.
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Affiliation(s)
- Bin Li
- Merrimack Pharmaceuticals, USA
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49
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Sullivan DE, Gabbard JL, Shukla M, Sobral B. Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned. Chem Biodivers 2010; 7:1124-41. [PMID: 20491070 DOI: 10.1002/cbdv.200900317] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Systems-biology and infectious-disease (host-pathogen-environment) research and development is becoming increasingly dependent on integrating data from diverse and dynamic sources. Maintaining integrated resources over long periods of time presents distinct challenges. This review describes experiences and lessons learned from integrating data in two five-year projects focused on pathosystems biology: the Pathosystems Resource Integration Center (PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures-development communities based on genomics data, and the Resource Center for Biodefense Proteomics Research (RCBPR, http://www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data-integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long-term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include 1) an approach for addressing discrepancies between experiment results and interpreted results, and 2) expanding the range of data-integration techniques to include usability engineering at the presentation level.
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Affiliation(s)
- Daniel E Sullivan
- CyberInfrastructure Section, Virginia Bioinformatics Institute, Washington Street, MC 0477, Virginia Tech, Blacksburg, Virginia 24061, USA.
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50
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Abstract
Network inference, which is the reconstruction of biological networks from high-throughput data, can provide valuable information about the regulation of gene expression in cells. However, it is an underdetermined problem, as the number of interactions that can be inferred exceeds the number of independent measurements. Different state-of-the-art tools for network inference use specific assumptions and simplifications to deal with underdetermination, and these influence the inferences. The outcome of network inference therefore varies between tools and can be highly complementary. Here we categorize the available tools according to the strategies that they use to deal with the problem of underdetermination. Such categorization allows an insight into why a certain tool is more appropriate for the specific research question or data set at hand.
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Affiliation(s)
- Riet De Smet
- Centre of Microbial and Plant Genetics/Bioinformatics, Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Leuven, Belgium
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