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Jin G, Deng Z, Wang H, Zhang Y, Fu R. EpMYB2 positively regulates chicoric acid biosynthesis by activating both primary and specialized metabolic genes in purple coneflower. Plant J 2024. [PMID: 38596892 DOI: 10.1111/tpj.16759] [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] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Chicoric acid is the major active ingredient of the world-popular medicinal plant purple coneflower (Echinacea purpurea (L.) Menoch). It is recognized as the quality index of commercial hot-selling Echinacea products. While the biosynthetic pathway of chicoric acid in purple coneflower has been elucidated recently, its regulatory network remains elusive. Through co-expression and phylogenetic analysis, we found EpMYB2, a typical R2R3-type MYB transcription factor (TF) responsive to methyl jasmonate (MeJA) simulation, is a positive regulator of chicoric acid biosynthesis. In addition to directly regulating chicoric acid biosynthetic genes, EpMYB2 positively regulates genes of the upstream shikimate pathway. We also found that EpMYC2 could activate the expression of EpMYB2 by binding to its G-box site, and the EpMYC2-EpMYB2 module is involved in the MeJA-induced chicoric acid biosynthesis. Overall, we identified an MYB TF that positively regulates the biosynthesis of chicoric acid by activating both primary and specialized metabolic genes. EpMYB2 links the gap between the JA signaling pathway and chicoric acid biosynthesis. This work opens a new direction toward engineering purple coneflower with higher medicinal qualities.
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Affiliation(s)
- Ge Jin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Zongbi Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Hsihua Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Yang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Rao Fu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
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2
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Zhong H, Zhou X, Uhm H, Jiang Y, Cao H, Chen Y, Mak TTW, Lo RMN, Wong BWY, Cheng EYL, Mok KY, Chan ALT, Kwok TCY, Mok VCT, Ip FCF, Hardy J, Fu AKY, Ip NY. Using blood transcriptome analysis for Alzheimer's disease diagnosis and patient stratification. Alzheimers Dement 2024; 20:2469-2484. [PMID: 38323937 PMCID: PMC11032555 DOI: 10.1002/alz.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 02/08/2024]
Abstract
INTRODUCTION Blood protein biomarkers demonstrate potential for Alzheimer's disease (AD) diagnosis. Limited studies examine the molecular changes in AD blood cells. METHODS Bulk RNA-sequencing of blood cells was performed on AD patients of Chinese descent (n = 214 and 26 in the discovery and validation cohorts, respectively) with normal controls (n = 208 and 38 in the discovery and validation cohorts, respectively). Weighted gene co-expression network analysis (WGCNA) and deconvolution analysis identified AD-associated gene modules and blood cell types. Regression and unsupervised clustering analysis identified AD-associated genes, gene modules, cell types, and established AD classification models. RESULTS WGCNA on differentially expressed genes revealed 15 gene modules, with 6 accurately classifying AD (areas under the receiver operating characteristics curve [auROCs] > 0.90). These modules stratified AD patients into subgroups with distinct disease states. Cell-type deconvolution analysis identified specific blood cell types potentially associated with AD pathogenesis. DISCUSSION This study highlights the potential of blood transcriptome for AD diagnosis, patient stratification, and mechanistic studies. HIGHLIGHTS We comprehensively analyze the blood transcriptomes of a well-characterized Alzheimer's disease cohort to identify genes, gene modules, pathways, and specific blood cells associated with the disease. Blood transcriptome analysis accurately classifies and stratifies patients with Alzheimer's disease, with some gene modules achieving classification accuracy comparable to that of the plasma ATN biomarkers. Immune-associated pathways and immune cells, such as neutrophils, have potential roles in the pathogenesis and progression of Alzheimer's disease.
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Affiliation(s)
- Huan Zhong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Xiaopu Zhou
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
| | - Hyebin Uhm
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
| | - Yuanbing Jiang
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Han Cao
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
| | - Yu Chen
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
- The Brain Cognition and Brain Disease InstituteShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen–Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research InstitutionsShenzhenGuangdongChina
| | - Tiffany T. W. Mak
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Ronnie Ming Nok Lo
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
| | - Bonnie Wing Yan Wong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Elaine Yee Ling Cheng
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Kin Y. Mok
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | | | - Timothy C. Y. Kwok
- Therese Pei Fong Chow Research Centre for Prevention of DementiaDivision of GeriatricsDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongHKSARChina
| | - Vincent C. T. Mok
- Lau Tat‐chuen Research Centre of Brain Degenerative Diseases in ChineseTherese Pei Fong Chow Research Centre for Prevention of DementiaGerald Choa Neuroscience InstituteLi Ka Shing Institute of Health SciencesDivision of NeurologyDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongHKSARChina
| | - Fanny C. F. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
| | - John Hardy
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
- Institute for Advanced StudyThe Hong Kong University of Science and TechnologyHKSARChina
| | - Amy K. Y. Fu
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
| | - Nancy Y. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
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Wang D, Quan M, Qin S, Fang Y, Xiao L, Qi W, Jiang Y, Zhou J, Gu M, Guan Y, Du Q, Liu Q, El‐Kassaby YA, Zhang D. Allelic variations of WAK106-E2Fa-DPb1-UGT74E2 module regulate fibre properties in Populus tomentosa. Plant Biotechnol J 2024; 22:970-986. [PMID: 37988335 PMCID: PMC10955495 DOI: 10.1111/pbi.14239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/13/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023]
Abstract
Wood formation, intricately linked to the carbohydrate metabolism pathway, underpins the capacity of trees to produce renewable resources and offer vital ecosystem services. Despite their importance, the genetic regulatory mechanisms governing wood fibre properties in woody plants remain enigmatic. In this study, we identified a pivotal module comprising 158 high-priority core genes implicated in wood formation, drawing upon tissue-specific gene expression profiles from 22 Populus samples. Initially, we conducted a module-based association study in a natural population of 435 Populus tomentosa, pinpointing PtoDPb1 as the key gene contributing to wood formation through the carbohydrate metabolic pathway. Overexpressing PtoDPb1 led to a 52.91% surge in cellulose content, a reduction of 14.34% in fibre length, and an increment of 38.21% in fibre width in transgenic poplar. Moreover, by integrating co-expression patterns, RNA-sequencing analysis, and expression quantitative trait nucleotide (eQTN) mapping, we identified a PtoDPb1-mediated genetic module of PtoWAK106-PtoDPb1-PtoE2Fa-PtoUGT74E2 responsible for fibre properties in Populus. Additionally, we discovered the two PtoDPb1 haplotypes that influenced protein interaction efficiency between PtoE2Fa-PtoDPb1 and PtoDPb1-PtoWAK106, respectively. The transcriptional activation activity of the PtoE2Fa-PtoDPb1 haplotype-1 complex on the promoter of PtoUGT74E2 surpassed that of the PtoE2Fa-PtoDPb1 haplotype-2 complex. Taken together, our findings provide novel insights into the regulatory mechanisms of fibre properties in Populus, orchestrated by PtoDPb1, and offer a practical module for expediting genetic breeding in woody plants via molecular design.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyang Quan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Shitong Qin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuanyuan Fang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Liang Xiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Weina Qi
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yongsen Jiang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jiaxuan Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyue Gu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yicen Guan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qingzhang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qing Liu
- CSIRO Agriculture and FoodBlack MountainCanberraACTAustralia
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences CentreUniversity of British ColumbiaVancouverBCCanada
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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Lieu R, Chao G, Kennedy E, Sauder JM, Narayanasamy P, Pustilnik A, Thangaraju A, Ho C, Pedroza MJ, Ruiz D, Yang X. Difficult-to-express antigen generation through a co-expression and disassociation methodology. Biotechnol Prog 2024; 40:e3416. [PMID: 38093578 DOI: 10.1002/btpr.3416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 04/19/2024]
Abstract
Extracellular domain (ECD) antigens are crucial components for antibody discovery, in vitro assays, and epitope mapping during therapeutical antibody development. Oftentimes, those antigens are difficult to produce while retaining the biologic function/activity upon extracellular secretion in commonly used expression systems. We have developed an effective method to cope with the challenge of generating quality antigen ECDs. In this method, a monoclonal antibody (Mab) or antibody fragment antigen-binding (Fab) region acts as a "chaperone" to stabilize the antigen ECD through forming an antibody:antigen complex. This methodology includes transient co-expression of the complex in Chinese hamster ovary cells and then dissociation of the purified complex into individual components by low pH treatment in the presence of arginine. The antigen is then separated from the chaperone on a preparative size exclusion chromatography (pSEC) followed by an optional affinity chromatography process to remove residual Mab or Fab. We demonstrate this co-expression/disassociation methodology on two difficult-to-express antigen ECDs from cluster-of-differentiation/cytokine family and were successful in producing stable, biologically active antigens when the common methods using Histidine-tagged and/or Fc-fused protein failed. This can be applied as a general approach for antigen production if a Mab or binding partner is available.
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Affiliation(s)
- Ricky Lieu
- Biotechnology Discovery Research, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Grace Chao
- Biotechnology Discovery Research, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Emma Kennedy
- Biotechnology Discovery Research, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - J Michael Sauder
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Prabakaran Narayanasamy
- Biotechnology Discovery Research, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Anna Pustilnik
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Adithi Thangaraju
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Carolyn Ho
- Biotechnology Discovery Research, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Mariah J Pedroza
- Lilly On-site Support, Eurofins Lancaster Laboratories PSS, Lancaster, Pennsylvania, USA
| | - Diana Ruiz
- Biotechnology Discovery Research, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
| | - Xiaomin Yang
- Biotechnology Discovery Research, Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California, USA
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5
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Michno J, Liu J, Jeffers JR, Stupar RM, Myers CL. Identification of nodulation-related genes in Medicago truncatula using genome-wide association studies and co-expression networks. Plant Direct 2020; 4:e00220. [PMID: 32426691 PMCID: PMC7229696 DOI: 10.1002/pld3.220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/04/2020] [Accepted: 02/24/2020] [Indexed: 05/17/2023]
Abstract
Genome-wide association studies (GWAS) have proven to be a valuable approach for identifying genetic intervals associated with phenotypic variation in Medicago truncatula. These intervals can vary in size, depending on the historical local recombination. Typically, significant intervals span numerous gene models, limiting the ability to resolve high-confidence candidate genes underlying the trait of interest. Additional genomic data, including gene co-expression networks, can be combined with the genetic mapping information to successfully identify candidate genes. Co-expression network analysis provides information about the functional relationships of each gene through its similarity of expression patterns to other well-defined clusters of genes. In this study, we integrated data from GWAS and co-expression networks to pinpoint candidate genes that may be associated with nodule-related phenotypes in M. truncatula. We further investigated a subset of these genes and confirmed that several had existing evidence linking them nodulation, including MEDTR2G101090 (PEN3-like), a previously validated gene associated with nodule number.
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Affiliation(s)
- Jean‐Michel Michno
- Bioinformatics and Computational BiologyUniversity of MinnesotaSt. PaulMinnesota
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMinnesota
| | - Junqi Liu
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMinnesota
| | - Joseph R. Jeffers
- Department of Computer Science and EngineeringUniversity of MinnesotaMinneapolisMinnesota
| | - Robert M. Stupar
- Bioinformatics and Computational BiologyUniversity of MinnesotaSt. PaulMinnesota
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMinnesota
| | - Chad L. Myers
- Bioinformatics and Computational BiologyUniversity of MinnesotaSt. PaulMinnesota
- Department of Computer Science and EngineeringUniversity of MinnesotaMinneapolisMinnesota
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Lee S, Zhang C, Liu Z, Klevstig M, Mukhopadhyay B, Bergentall M, Cinar R, Ståhlman M, Sikanic N, Park JK, Deshmukh S, Harzandi AM, Kuijpers T, Grøtli M, Elsässer SJ, Piening BD, Snyder M, Smith U, Nielsen J, Bäckhed F, Kunos G, Uhlen M, Boren J, Mardinoglu A. Network analyses identify liver-specific targets for treating liver diseases. Mol Syst Biol 2017; 13:938. [PMID: 28827398 PMCID: PMC5572395 DOI: 10.15252/msb.20177703] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [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: 04/21/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 01/02/2023] Open
Abstract
We performed integrative network analyses to identify targets that can be used for effectively treating liver diseases with minimal side effects. We first generated co-expression networks (CNs) for 46 human tissues and liver cancer to explore the functional relationships between genes and examined the overlap between functional and physical interactions. Since increased de novo lipogenesis is a characteristic of nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC), we investigated the liver-specific genes co-expressed with fatty acid synthase (FASN). CN analyses predicted that inhibition of these liver-specific genes decreases FASN expression. Experiments in human cancer cell lines, mouse liver samples, and primary human hepatocytes validated our predictions by demonstrating functional relationships between these liver genes, and showing that their inhibition decreases cell growth and liver fat content. In conclusion, we identified liver-specific genes linked to NAFLD pathogenesis, such as pyruvate kinase liver and red blood cell (PKLR), or to HCC pathogenesis, such as PKLR, patatin-like phospholipase domain containing 3 (PNPLA3), and proprotein convertase subtilisin/kexin type 9 (PCSK9), all of which are potential targets for drug development.
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Affiliation(s)
- Sunjae Lee
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Zhengtao Liu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Martina Klevstig
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bani Mukhopadhyay
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Bergentall
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Resat Cinar
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Natasha Sikanic
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Joshua K Park
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Sumit Deshmukh
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Azadeh M Harzandi
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Tim Kuijpers
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Simon J Elsässer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Brian D Piening
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ulf Smith
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jens Nielsen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - George Kunos
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Pramparo T, Lombardo MV, Campbell K, Barnes CC, Marinero S, Solso S, Young J, Mayo M, Dale A, Ahrens-Barbeau C, Murray SS, Lopez L, Lewis N, Pierce K, Courchesne E. Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers. Mol Syst Biol 2015; 11:841. [PMID: 26668231 PMCID: PMC4704485 DOI: 10.15252/msb.20156108] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Genetic mechanisms underlying abnormal early neural development in toddlers with Autism Spectrum Disorder (ASD) remain uncertain due to the impossibility of direct brain gene expression measurement during critical periods of early development. Recent findings from a multi‐tissue study demonstrated high expression of many of the same gene networks between blood and brain tissues, in particular with cell cycle functions. We explored relationships between blood gene expression and total brain volume (TBV) in 142 ASD and control male toddlers. In control toddlers, TBV variation significantly correlated with cell cycle and protein folding gene networks, potentially impacting neuron number and synapse development. In ASD toddlers, their correlations with brain size were lost as a result of considerable changes in network organization, while cell adhesion gene networks significantly correlated with TBV variation. Cell cycle networks detected in blood are highly preserved in the human brain and are upregulated during prenatal states of development. Overall, alterations were more pronounced in bigger brains. We identified 23 candidate genes for brain maldevelopment linked to 32 genes frequently mutated in ASD. The integrated network includes genes that are dysregulated in leukocyte and/or postmortem brain tissue of ASD subjects and belong to signaling pathways regulating cell cycle G1/S and G2/M phase transition. Finally, analyses of the CHD8 subnetwork and altered transcript levels from an independent study of CHD8 suppression further confirmed the central role of genes regulating neurogenesis and cell adhesion processes in ASD brain maldevelopment.
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Affiliation(s)
- Tiziano Pramparo
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Michael V Lombardo
- Department of Psychology, University of Cyprus, Nicosia, Cyprus Center for Applied Neuroscience, University of Cyprus, Nicosia, Cyprus Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Kathleen Campbell
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Cynthia Carter Barnes
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Steven Marinero
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Stephanie Solso
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Julia Young
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Maisi Mayo
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Anders Dale
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Clelia Ahrens-Barbeau
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Sarah S Murray
- Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), La Jolla, CA, USA Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Linda Lopez
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Nathan Lewis
- Novo Nordisk Foundation Center for Biosustainability at the UCSD School of Medicine, and Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Eric Courchesne
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
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Sheen TS, Huang YT, Chang YL, Ko JY, Wu CS, Yu YC, Tsai CH, Hsu MM. Epstein-Barr virus-encoded latent membrane protein 1 co-expresses with epidermal growth factor receptor in nasopharyngeal carcinoma. Jpn J Cancer Res 1999; 90:1285-92. [PMID: 10665644 PMCID: PMC5926033 DOI: 10.1111/j.1349-7006.1999.tb00710.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Latent membrane protein 1 (LMP-1) is the only Epstein-Barr virus (EBV)-encoded oncogenic protein that has been detected in nasopharyngeal carcinoma (NPC), a cancer that is closely associated with EBV. Previous in-vitro studies have demonstrated that LMP-1 can upregulate epidermal growth factor receptor (EGFR) in epithelial cells. It was not established whether this cellular effect exists in NPC. To assess the association between LMP-1 and EGFR in NPC tissues, 60 NPC specimens were examined by immunohistochemistry using anti-LMP-1 antibody (CS 1-4) and anti-EGFR antibodies (EGFR 1, EGFR 1005). The results revealed that 41 (68.3%) specimens were immunopositive for LMP-1 and 44 (73.3%) specimens over-expressed EGFR. Morphologically, the expressions of LMP-1 and EGFR were homogeneously distributed in the tumor nests. In addition, the correlation between LMP-1 and EGFR was statistically significant (P<0.001, chi2 test, d.f. = 1). To elucidate further the correlation between LMP-1 and EGFR in vivo and in situ, an indirect dual immunofluorescence assay was conducted, using secondary antibodies conjugated with fluorescein isothiocyanate (FITC) or indocarbocyanine (Cy3). The results disclosed an intimate co-expression of LMP-1 and EGFR. In summary, the data indicate that over-expression of EGFR is a common phenomenon in NPC, and that EGFR is co-expressed with LMP-1 in NPC. Thus, EBV may play a role in the tumorigenesis of NPC through the effects of LMP-1 and EGFR.
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Affiliation(s)
- T S Sheen
- Department of Otolaryngology, National Taiwan University Hospital, Taipei
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