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Ye C, Guo J, Zhou XQ, Chen DG, Liu J, Peng X, Jaremko M, Jaremko Ł, Guo T, Liu CG, Chen K. The Dsup coordinates grain development and abiotic stress in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108184. [PMID: 37977025 DOI: 10.1016/j.plaphy.2023.108184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
DNA damage is a serious threat to all living organisms and may be induced by environmental stressors. Previous studies have revealed that the tardigrade (Ramazzotius varieornatus) DNA damage suppressor protein Dsup has protective effects in human cells and tobacco. However, whether Dsup provides radiation damage protection more widely in crops is unclear. To explore the effects of Dsup in other crops, stable Dsup overexpression lines through Agrobacterium-mediated transformation were generated and their agronomic traits were deeply investigated. In this study, the overexpression of Dsup not only enhanced the DNA damage resistance at the seeds and seedlings stages, they also exhibited grain size enlargement and starch granule structure and cell size alteration by the scanning electron microscopy observation. Notably, the RNA-seq revealed that the Dsup plants increased radiation-related and abiotic stress-related gene expression in comparison to wild types, suggesting that Dsup is capable to coordinate normal growth and abiotic stress resistance in rice. Immunoprecipitation enrichment with liquid chromatography-tandem mass spectrometry (IP-LC-MS) assays uncovered 21 proteins preferably interacting with Dsup in plants, suggesting that Dsup binds to transcription and translation related proteins to regulate the homeostasis between DNA protection and plant development. In conclusion, our data provide a detailed agronomic analysis of Dsup plants and potential mechanisms of Dsup function in crops. Our findings provide novel insights for the breeding of crop radiation resistance.
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Affiliation(s)
- Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Xin-Qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Da-Gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Juan Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Xin Peng
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Łukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuan-Guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China.
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China.
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2
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Vallejo MC, Sarkar S, Elliott EC, Henry HR, Powell SM, Diaz Ludovico I, You Y, Huang F, Payne SH, Ramanadham S, Sims EK, Metz TO, Mirmira RG, Nakayasu ES. A proteomic meta-analysis refinement of plasma extracellular vesicles. Sci Data 2023; 10:837. [PMID: 38017024 PMCID: PMC10684639 DOI: 10.1038/s41597-023-02748-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Extracellular vesicles play major roles in cell-to-cell communication and are excellent biomarker candidates. However, studying plasma extracellular vesicles is challenging due to contaminants. Here, we performed a proteomics meta-analysis of public data to refine the plasma EV composition by separating EV proteins and contaminants into different clusters. We obtained two clusters with a total of 1717 proteins that were depleted of known contaminants and enriched in EV markers with independently validated 71% true-positive. These clusters had 133 clusters of differentiation (CD) antigens and were enriched with proteins from cell-to-cell communication and signaling. We compared our data with the proteins deposited in PeptideAtlas, making our refined EV protein list a resource for mechanistic and biomarker studies. As a use case example for this resource, we validated the type 1 diabetes biomarker proplatelet basic protein in EVs and showed that it regulates apoptosis of β cells and macrophages, two key players in the disease development. Our approach provides a refinement of the EV composition and a resource for the scientific community.
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Affiliation(s)
- Milene C Vallejo
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Emily C Elliott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Hayden R Henry
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Samantha M Powell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ivo Diaz Ludovico
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Fei Huang
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Sasanka Ramanadham
- Department of Cell, Developmental, and Integrative Biology, and Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Emily K Sims
- Department of Pediatrics, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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3
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Chen C, Khanthiyong B, Thaweetee-Sukjai B, Charoenlappanit S, Roytrakul S, Thanoi S, Reynolds GP, Nudmamud-Thanoi S. Proteomic association with age-dependent sex differences in Wisconsin Card Sorting Test performance in healthy Thai subjects. Sci Rep 2023; 13:20238. [PMID: 37981639 PMCID: PMC10658079 DOI: 10.1038/s41598-023-46750-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/04/2023] [Indexed: 11/21/2023] Open
Abstract
Sex differences in cognitive function exist, but they are not stable and undergo dynamic change during the lifespan. However, our understanding of how sex-related neural information transmission evolves with age is still in its infancy. This study utilized the Wisconsin Card Sorting Test (WCST) and the label-free proteomics method with bioinformatic analysis to investigate the molecular mechanisms underlying age-related sex differences in cognitive performance in 199 healthy Thai subjects (aged 20-70 years), as well as explore the sex-dependent protein complexes for predicting cognitive aging. The results showed that males outperformed females in two of the five WCST sub-scores: %Corrects and %Errors. Sex differences in these scores were related to aging, becoming noticeable in those over 60. At the molecular level, differently expressed individual proteins and protein complexes between both sexes are associated with the potential N-methyl-D-aspartate type glutamate receptor (NMDAR)-mediated excitotoxicity, with the NMDAR complex being enriched exclusively in elderly female samples. These findings provided a preliminary indication that healthy Thai females might be more susceptible to such neurotoxicity, as evidenced by their cognitive performance. NMDAR protein complex enrichment in serum could be proposed as a potential indication for predicting cognitive aging in healthy Thai females.
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Affiliation(s)
- Chen Chen
- Medical Science Graduate Program, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | | | | | - Sawanya Charoenlappanit
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Samur Thanoi
- School of Medical Sciences, University of Phayao, Phayao, Thailand.
| | - Gavin P Reynolds
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sutisa Nudmamud-Thanoi
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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4
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Chen DG, Guo J, Chen K, Ye CJ, Liu J, Chen YD, Zhou XQ, Liu CG. Pyramiding Breeding of Low-Glutelin-Content Indica Rice with Good Quality and Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:3763. [PMID: 37960119 PMCID: PMC10647759 DOI: 10.3390/plants12213763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
Low-glutelin-content rice, a type of functional rice with glutelin levels below 4%, is an essential dietary supplement for chronic kidney disease (CKD) patients. Developing low-glutelin-content rice varieties is crucial to catering to the growing CKD population. In this study, we aimed to create a new low-glutelin indica rice variety with excellent agronomic traits. To achieve this, we employed a combination of molecular-marker-assisted selection and traditional breeding techniques. The cultivars W3660, Wushansimiao (WSSM), and Nantaixiangzhan (NTXZ) were crossbred, incorporating the Lgc-1, Pi-2, Xa23, and fgr alleles into a single line. The result of this breeding effort was "Yishenxiangsimiao", a new indica rice variety that inherits the desirable characteristics of its parent lines. Yishenxiangsimiao (YSXSM) possesses not only a low glutelin content but also dual resistance to blast and bacterial blight (BB). It exhibits high-quality grains with a fragrant aroma. This new low-glutelin indica cultivar not only ensures a stable food supply for CKD patients but also serves as a healthy dietary option for the general public. We also performed RNA-seq of these rice varieties to investigate their internal gene expression differences. The YSXSM exhibited a higher biotic-resistance gene expression in comparison to NTXZ. In summary, we successfully developed a novel low-glutelin indica rice variety, "Yishenxiangsimiao", with superior agronomic traits. This rice variety addresses the dietary needs of CKD patients and offers a nutritious choice for all consumers.
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Affiliation(s)
- Da-Gang Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Jie Guo
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Chan-Juan Ye
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Juan Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - You-Ding Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xin-Qiao Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Chuan-Guang Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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5
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Chen C, Khanthiyong B, Charoenlappanit S, Roytrakul S, Reynolds GP, Thanoi S, Nudmamud-Thanoi S. Cholinergic-estrogen interaction is associated with the effect of education on attenuating cognitive sex differences in a Thai healthy population. PLoS One 2023; 18:e0278080. [PMID: 37471329 PMCID: PMC10358962 DOI: 10.1371/journal.pone.0278080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/30/2023] [Indexed: 07/22/2023] Open
Abstract
The development of human brain is shaped by both genetic and environmental factors. Sex differences in cognitive function have been found in humans as a result of sexual dimorphism in neural information transmission. Numerous studies have reported the positive effects of education on cognitive functions. However, little work has investigated the effect of education on attenuating cognitive sex differences and the neural mechanisms behind it based on healthy population. In this study, the Wisconsin Card Sorting Test (WCST) was employed to examine sex differences in cognitive function in 135 Thai healthy subjects, and label-free quantitative proteomic method and bioinformatic analysis were used to study sex-specific neurotransmission-related protein expression profiles. The results showed sex differences in two WCST sub-scores: percentage of Total corrects and Total errors in the primary education group (Bayes factor>100) with males performed better, while such differences eliminated in secondary and tertiary education levels. Moreover, 11 differentially expressed proteins (DEPs) between men and women (FDR<0.1) were presented in both education groups, with majority of them upregulated in females. Half of those DEPs interacted directly with nAChR3, whereas the other DEPs were indirectly connected to the cholinergic pathways through interaction with estrogen. These findings provided a preliminary indication that a cholinergic-estrogen interaction relates to, and might underpin, the effect of education on attenuating cognitive sex differences in a Thai healthy population.
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Affiliation(s)
- Chen Chen
- Medical Science Graduate Program, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | | | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Gavin P. Reynolds
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom
| | - Samur Thanoi
- School of Medical Sciences, University of Phayao, Mae Ka, Phayao, Thailand
| | - Sutisa Nudmamud-Thanoi
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
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6
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Otsuka T, Le HT, Thein ZL, Ihara H, Sato F, Nakao T, Kohsaka A. Deficiency of the circadian clock gene Rev-erbα induces mood disorder-like behaviours and dysregulation of the serotonergic system in mice. Physiol Behav 2022; 256:113960. [PMID: 36115382 DOI: 10.1016/j.physbeh.2022.113960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 10/31/2022]
Abstract
Mood disorders such as depression, anxiety, and bipolar disorder are highly associated with disrupted daily rhythms of activity, which are often observed in shift work and sleep disturbance in humans. Recent studies have proposed the REV-ERBα protein as a key circadian nuclear receptor that links behavioural rhythms to mood regulation. However, how the Rev-erbα gene participates in the regulation of mood remains poorly understood. Here, we show that the regulation of the serotonergic (5-HTergic) system, which plays a central role in stress-induced mood behaviours, is markedly disrupted in Rev-erbα-/- mice. Rev-erbα-/- mice exhibit both negative and positive behavioural phenotypes, including anxiety-like and mania-like behaviours, when subjected to a stressful environment. Importantly, Rev-erbα-/- mice show a significant decrease in the expression of a gene that encodes the rate-limiting enzyme of serotonin (5-HT) synthesis in the raphe nuclei (RN). In addition, 5-HT levels in Rev-erbα-/- mice are significantly reduced in the prefrontal cortex, which receives strong inputs from the RN and controls stress-related behaviours. Our findings indicate that Rev-erbα plays an important role in controlling the 5-HTergic system and thus regulates mood and behaviour.
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Affiliation(s)
- Tsuyoshi Otsuka
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan; The Second Department of Physiology, Wakayama Medical University, Wakayama 641-8509, Japan.
| | - Hue Thi Le
- The Second Department of Physiology, Wakayama Medical University, Wakayama 641-8509, Japan; Department of Biomedical Engineering, National Cerebral and Cardiovascular Center, Osaka, 564-8565, Japan
| | - Zaw Lin Thein
- The Second Department of Physiology, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Hayato Ihara
- The Department of Radioisotope Laboratory Center, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Fuyuki Sato
- Department of Diagnostic Pathology, Shizuoka Cancer Center, Suntogun, Shizuoka 411-8777, Japan; The Departments of Pathology, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Tomomi Nakao
- The Second Department of Physiology, Wakayama Medical University, Wakayama 641-8509, Japan; The First Department of Internal Medicine, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Akira Kohsaka
- The Second Department of Physiology, Wakayama Medical University, Wakayama 641-8509, Japan
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7
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Hephzibah Cathryn R, Udhaya Kumar S, Younes S, Zayed H, George Priya Doss C. A review of bioinformatics tools and web servers in different microarray platforms used in cancer research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:85-164. [PMID: 35871897 DOI: 10.1016/bs.apcsb.2022.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Over the past decade, conventional lab work strategies have gradually shifted from being limited to a laboratory setting towards a bioinformatics era to help manage and process the vast amounts of data generated by omics technologies. The present work outlines the latest contributions of bioinformatics in analyzing microarray data and their application to cancer. We dissect different microarray platforms and their use in gene expression in cancer models. We highlight how computational advances empowered the microarray technology in gene expression analysis. The study on protein-protein interaction databases classified into primary, derived, meta-database, and prediction databases describes the strategies to curate and predict novel interaction networks in silico. In addition, we summarize the areas of bioinformatics where neural graph networks are currently being used, such as protein functions, protein interaction prediction, and in silico drug discovery and development. We also discuss the role of deep learning as a potential tool in the prognosis, diagnosis, and treatment of cancer. Integrating these resources efficiently, practically, and ethically is likely to be the most challenging task for the healthcare industry over the next decade; however, we believe that it is achievable in the long term.
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Affiliation(s)
- R Hephzibah Cathryn
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Salma Younes
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
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8
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Yin R, Yang L, Hao Y, Yang Z, Lu T, Jin W, Dan M, Peng L, Zhang Y, Wei Y, Li R, Ma H, Shi Y, Fan P. Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection. J Neuroinflammation 2022; 19:77. [PMID: 35379280 PMCID: PMC8981687 DOI: 10.1186/s12974-022-02439-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 03/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cognitive impairment is one of the primary sequelae affecting the quality of life of patients with Japanese encephalitis (JE). The clinical treatment is mainly focused on life support, lacking of targeted treatment strategy. METHODS A cerebrospinal fluid (CSF) proteomic profiling study was performed including 26 patients with JE in Gansu province of China from June 2017 to October 2018 and 33 other concurrent hospitalized patients who were excluded central nervous system (CNS) organic or CNS infection diseases. The clinical and proteomics data of patients with JE were undergoing combined analysis for the first time. RESULTS Two subtypes of JE associated with significantly different prognoses were identified. Compared to JE1, the JE2 subtype is associated with lower overall survival rate and a higher risk of cognitive impairment. The percentages of neutrophils (N%), lymphocyte (L%), and monocytes (M%) decreased in JE2 significantly. CONCLUSIONS The differences in proteomic landscape between JE subgroups have specificity for the prognosis of cognitive impairment. The data also provided some potential target proteins for treatment of cognitive impairments caused by JE. Trial registration ChiCTR, ChiCTR2000030499. Registered 1st June 2017, http://www.medresman.org.cn/pub/cn/proj/projectshow.aspx?proj=6333.
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Affiliation(s)
- Rong Yin
- Department of Neurology, Lanzhou General Hospital, Lanzhou, 730050, China.,Department of Neurology, Gansu Province Central Hospital, Lanzhou, 730070, China
| | - Linpeng Yang
- Department of Pharmacy, Lanzhou General Hospital, Lanzhou, 730050, China.,The Fourth Department of Research, Center for Gansu Provincial Vaccine Engineering Research, Lanzhou, 730046, China
| | - Ying Hao
- Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, 10065, USA
| | - Zhiqi Yang
- Department of Neurology, Lanzhou General Hospital, Lanzhou, 730050, China.,Department of Neurology, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Tao Lu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Wanjun Jin
- Department of Pharmacy, Lanzhou General Hospital, Lanzhou, 730050, China
| | - Meiling Dan
- Department of Neurology, Lanzhou General Hospital, Lanzhou, 730050, China.,Department of Neurology, Chongqing University Fuling Hospital, Chongqing, 408000, China
| | - Liang Peng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yingjie Zhang
- Department of Neurology, Lanzhou General Hospital, Lanzhou, 730050, China.,The First Clinical Medical School, Gansu University of Chinese Medicine, Lanzhou, 730030, China
| | - Yaxuan Wei
- Department of Neurology, Gansu Province Central Hospital, Lanzhou, 730070, China
| | - Rong Li
- Department of Neurology, Lanzhou General Hospital, Lanzhou, 730050, China.,Department of Neurology, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Huiping Ma
- Department of Pharmacy, Lanzhou General Hospital, Lanzhou, 730050, China
| | - Yuanyuan Shi
- Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen, 518118, China.
| | - Pengcheng Fan
- Department of Pharmacy, Lanzhou General Hospital, Lanzhou, 730050, China. .,State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, 102206, China.
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9
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Raul B, Bhattacharjee O, Ghosh A, Upadhyay P, Tembhare K, Singh A, Shaheen T, Ghosh AK, Torres-Jerez I, Krom N, Clevenger J, Udvardi M, Scheffler BE, Ozias-Akins P, Sharma RD, Bandyopadhyay K, Gaur V, Kumar S, Sinharoy S. Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:131-145. [PMID: 34689599 DOI: 10.1094/mpmi-05-21-0122-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step toward understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin-derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen-scavenging mechanisms in the Papilionoid family. Finally, the absence of cysteine-rich motif-1-containing nodule-specific cysteine-rich peptide (NCR) genes but the recruitment of defensin-like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobia symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Bikash Raul
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Oindrila Bhattacharjee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Amit Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priya Upadhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kunal Tembhare
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ajeet Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tarannum Shaheen
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Asim Kumar Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Nick Krom
- Noble Research Institute, 2510 Sam Noble Pkwy, Ardmore, OK 73401, U.S.A
| | - Josh Clevenger
- University of Georgia, Institute of Plant Breeding, Genetics and Genomics and Department of Horticulture, Tifton, GA 31793, U.S.A
| | - Michael Udvardi
- Noble Research Institute, 2510 Sam Noble Pkwy, Ardmore, OK 73401, U.S.A
| | - Brian E Scheffler
- United States Department of Agriculture-Agricultural Research Service Jamie Whitten Delta States Research Center (JWDSRC) Stoneville, JWDSRC, Bldg.1, Room 229, Experiment Station Road, PO Box 36, Stoneville, MS 38776-0036, U.S.A
| | - Peggy Ozias-Akins
- University of Georgia, Institute of Plant Breeding, Genetics and Genomics and Department of Horticulture, Tifton, GA 31793, U.S.A
| | - Ravi Datta Sharma
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Kaustav Bandyopadhyay
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Vineet Gaur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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10
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Long T, Xu B, Hu Y, Wang Y, Mao C, Wang Y, Zhang J, Liu H, Huang H, Liu Y, Yu G, Zhao C, Li Y, Huang Y. Genome-wide identification of ZmSnRK2 genes and functional analysis of ZmSnRK2.10 in ABA signaling pathway in maize (Zea mays L). BMC PLANT BIOLOGY 2021; 21:309. [PMID: 34210268 PMCID: PMC8246669 DOI: 10.1186/s12870-021-03064-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 05/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Phytohormone abscisic acid (ABA) is involved in the regulation of a wide range of biological processes. In Arabidopsis, it has been well-known that SnRK2s are the central components of the ABA signaling pathway that control the balance between plant growth and stress response, but the functions of ZmSnRK2 in maize are rarely reported. Therefore, the study of ZmSnRK2 is of great importance to understand the ABA signaling pathways in maize. RESULTS In this study, 14 ZmSnRK2 genes were identified in the latest version of maize genome database. Phylogenetic analysis revealed that ZmSnRK2s are divided into three subclasses based on their diversity of C-terminal domains. The exon-intron structures, phylogenetic, synteny and collinearity analysis indicated that SnRK2s, especially the subclass III of SnRK2, are evolutionally conserved in maize, rice and Arabidopsis. Subcellular localization showed that ZmSnRK2 proteins are localized in the nucleus and cytoplasm. The RNA-Seq datasets and qRT-PCR analysis showed that ZmSnRK2 genes exhibit spatial and temporal expression patterns during the growth and development of different maize tissues, and the transcript levels of some ZmSnRK2 genes in kernel are significantly induced by ABA and sucrose treatment. In addition, we found that ZmSnRK2.10, which belongs to subclass III, is highly expressed in kernel and activated by ABA. Overexpression of ZmSnRK2.10 partially rescued the ABA-insensitive phenotype of snrk2.2/2.3 double and snrk2.2/2.3/2.6 triple mutants and led to delaying plant flowering in Arabidopsis. CONCLUSION The SnRK2 gene family exhibits a high evolutionary conservation and has expanded with whole-genome duplication events in plants. The ZmSnRK2s expanded in maize with whole-genome and segmental duplication, not tandem duplication. The expression pattern analysis of ZmSnRK2s in maize offers important information to study their functions. Study of the functions of ZmSnRK.10 in Arabidopsis suggests that the ABA-dependent members of SnRK2s are evolutionarily conserved in plants. Our study elucidated the structure and evolution of SnRK2 genes in plants and provided a basis for the functional study of ZmSnRK2s protein in maize.
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Affiliation(s)
- Tiandan Long
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130 Sichuan China
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Binjie Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yufeng Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130 Sichuan China
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Yayun Wang
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Changqing Mao
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Yongbin Wang
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya’an, 625014 Sichuan China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural University, Ya’an, 625014 Sichuan China
| | - Huanhuan Huang
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Yangping Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130 Sichuan China
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
| | - Yubi Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130 Sichuan China
- College of Agronomy, Sichuan Agricultural University, No.211 Huimin Rd., Wenjiang Dist, Chengdu, 611130 Sichuan China
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11
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Oocyte-specific linker histone H1foo interacts with Esrrb to induce chromatin decondensation at specific gene loci. Biochem Biophys Res Commun 2021; 561:165-171. [PMID: 34023782 DOI: 10.1016/j.bbrc.2021.05.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 11/21/2022]
Abstract
Linker histone H1 is mainly localized in the linker DNA region, between two nucleosome cores, and regulates chromatin structures linking gene expression. Mammalian oocytes contain the histone H1foo, a distinct member with low sequence similarity to other members in the H1 histone family. Although, from various previous studies, evidence related to H1foo function in chromatin structures is being accumulated, the distribution of H1foo at the target gene loci in a genome-wide manner and the molecular mechanism of H1foo-dependent chromatin architecture remain unclear. In this study, we aimed to identify the target loci and the physiological factor bound to H1foo at the loci. Chromatin immunoprecipitation sequencing analysis of H1foo-overexpressing mouse embryonic stem cells showed that H1foo is enriched around the transcriptional start sites of genes such as oocyte-specific genes and that the chromatin structures at these regions were relaxed. We demonstrated that H1foo was physiologically bound to the nuclear receptor estrogen-related receptor beta (Esrrb), and Esrrb was necessary for H1foo activity of chromatin decondensation at the target loci. The specific localization and interaction with Esrrb were validated in endogenous H1foo of oocytes. Overall, H1foo induces chromatin decondensation in a locus-specific manner and this function is achieved by interacting with Esrrb.
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12
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Jia L, Li J, Li P, Liu D, Li J, Shen J, Zhu B, Ma C, Zhao T, Lan R, Dang L, Li W, Sun S. Site-specific glycoproteomic analysis revealing increased core-fucosylation on FOLR1 enhances folate uptake capacity of HCC cells to promote EMT. Am J Cancer Res 2021; 11:6905-6921. [PMID: 34093861 PMCID: PMC8171077 DOI: 10.7150/thno.56882] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/14/2021] [Indexed: 12/24/2022] Open
Abstract
Rationale: Epithelial-mesenchymal transition (EMT) has been recognized as an important step toward high invasion and metastasis of many cancers including hepatocellular carcinoma (HCC), while the mechanism for EMT promotion is still ambiguous. Methods: The dynamic alterations of site-specific glycosylation during HGF/TGF-β1-induced EMT process of three HCC cell lines were systematically investigated using precision glycoproteomic methods. The possible roles of EMT-related glycoproteins and site-specific glycans were further confirmed by various molecular biological approaches. Results: Using mass spectrometry-based glycoproteomic methods, we totally identified 2306 unique intact glycopeptides from SMMC-7721 and HepG2 cell lines, and found that core-fucosylated glycans were accounted for the largest proportion of complex N-glycans. Through quantification analysis of intact glycopeptides, we found that the majority of core-fucosylated intact glycopeptides from folate receptor α (FOLR1) were up-regulated in the three HGF-treated cell lines. Similarly, core-fucosylation of FOLR1 were up-regulated in SMMC-7721 and Hep3B cells with TGF-β1 treatment. Using molecular approaches, we further demonstrated that FUT8 was a driver for HGF/TGF-β1-induced EMT. The silencing of FUT8 reduced core-fucosylation and partially blocked the progress of HGF-induced EMT. Finally, we confirmed that the level of core-fucosylation on FOLR1 especially at the glycosite Asn-201 positively regulated the cellular uptake capacity of folates, and enhanced uptake of folates could promote the EMT of HCC cells. Conclusions: Based on the results, we proposed a potential pathway for HGF or TGF-β1-induced EMT of HCC cells: HGF or TGF-β1 treatment of HCC cells can increase the expression of glycosyltransferase FUT8 to up-regulate the core-fucosylation of N-glycans on glycoproteins including the FOLR1; core-fucosylation on FOLR1 can then enhance the folate uptake capacity to finally promote the EMT progress of HCC cells.
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13
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Wang H, Wu X, Zhang X, Hou X, Liang T, Wang D, Teng F, Dai J, Duan H, Guo S, Li Y, Yu X. SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution. ACS CENTRAL SCIENCE 2020; 6:2238-2249. [PMID: 33372199 PMCID: PMC7586461 DOI: 10.1021/acscentsci.0c00742] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Indexed: 05/07/2023]
Abstract
Comprehensive profiling of humoral antibody response to severe acute respiratory syndrome (SARS) coronavirus-2 (CoV-2) proteins is essential in understanding the host immunity and in developing diagnostic tests and vaccines. To address this concern, we developed a SARS-CoV-2 proteome peptide microarray to analyze antibody interactions at the amino acid resolution. With the array, we demonstrate the feasibility of employing SARS-CoV-1 antibodies to detect the SARS-CoV-2 nucleocapsid phosphoprotein. The first landscape of B-cell epitopes for SARS-CoV-2 IgM and IgG antibodies in the serum of 10 coronavirus disease of 2019 (COVID-19) patients with early infection is also constructed. With array data and structural analysis, a peptide epitope for neutralizing antibodies within the SARS-CoV-2 spike receptor-binding domain's interaction interface with the angiotensin-converting enzyme 2 receptor was predicted. All the results demonstrate the utility of our microarray as a platform to determine the changes of antibody responses in COVID-19 patients and animal models as well as to identify potential targets for diagnosis and treatment.
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Affiliation(s)
- Hongye Wang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xian Wu
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union
Medical College, Beijing 100730, China
| | - Xiaomei Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xin Hou
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union
Medical College, Beijing 100730, China
| | - Te Liang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Dan Wang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fei Teng
- Department
of Emergency Medicine, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary
Cerebral Resuscitation, Beijing 100020, China
| | - Jiayu Dai
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hu Duan
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Shubin Guo
- Department
of Emergency Medicine, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary
Cerebral Resuscitation, Beijing 100020, China
| | - Yongzhe Li
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union
Medical College, Beijing 100730, China
- (Y.L.)
| | - Xiaobo Yu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- (X.Y.)
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14
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Gho YS, Choi H, Moon S, Song MY, Park HE, Kim DH, Ha SH, Jung KH. Phosphate-Starvation-Inducible S-Like RNase Genes in Rice Are Involved in Phosphate Source Recycling by RNA Decay. FRONTIERS IN PLANT SCIENCE 2020; 11:585561. [PMID: 33424882 PMCID: PMC7793952 DOI: 10.3389/fpls.2020.585561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/02/2020] [Indexed: 05/16/2023]
Abstract
The fine-tuning of inorganic phosphate (Pi) for enhanced use efficiency has long been a challenging subject in agriculture, particularly in regard to rice as a major crop plant. Among ribonucleases (RNases), the RNase T2 family is broadly distributed across kingdoms, but little has been known on its substrate specificity compared to RNase A and RNase T1 families. Class I and class II of the RNase T2 family are defined as the S-like RNase (RNS) family and have showed the connection to Pi recycling in Arabidopsis. In this study, we first carried out a phylogenetic analysis of eight rice and five Arabidopsis RNS genes and identified mono-specific class I and dicot-specific class I RNS genes, suggesting the possibility of functional diversity between class I RNS family members in monocot and dicot species through evolution. We then compared the in silico expression patterns of all RNS genes in rice and Arabidopsis under normal and Pi-deficient conditions and further confirmed the expression patterns of rice RNS genes via qRT-PCR analysis. Subsequently, we found that most of the OsRNS genes were differentially regulated under Pi-deficient treatment. Association of Pi recycling by RNase activity in rice was confirmed by measuring total RNA concentration and ribonuclease activity of shoot and root samples under Pi-sufficient or Pi-deficient treatment during 21 days. The total RNA concentrations were decreased by < 60% in shoots and < 80% in roots under Pi starvation, respectively, while ribonuclease activity increased correspondingly. We further elucidate the signaling pathway of Pi starvation through upregulation of the OsRNS genes. The 2-kb promoter region of all OsRNS genes with inducible expression patterns under Pi deficiency contains a high frequency of P1BS cis-acting regulatory element (CRE) known as the OsPHR2 binding site, suggesting that the OsRNS family is likely to be controlled by OsPHR2. Finally, the dynamic transcriptional regulation of OsRNS genes by overexpression of OsPHR2, ospho2 mutant, and overexpression of OsPT1 lines involved in Pi signaling pathway suggests the molecular basis of OsRNS family in Pi recycling via RNA decay under Pi starvation.
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Affiliation(s)
- Yun-Shil Gho
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Heebak Choi
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Sunok Moon
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Min Yeong Song
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Ha Eun Park
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Doh-Hoon Kim
- Department of Life Science, College of Life Science and Natural Resources, Dong-A University, Busan, South Korea
| | - Sun-Hwa Ha
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
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15
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Hou X, Zhang X, Wu X, Lu M, Wang D, Xu M, Wang H, Liang T, Dai J, Duan H, Xu Y, Yu X, Li Y. Serum Protein Profiling Reveals a Landscape of Inflammation and Immune Signaling in Early-stage COVID-19 Infection. Mol Cell Proteomics 2020; 19:1749-1759. [PMID: 32788344 PMCID: PMC7664125 DOI: 10.1074/mcp.rp120.002128] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious infection and threating the human lives in the world. The elevation of cytokines in blood is crucial to induce cytokine storm and immunosuppression in the transition of severity in COVID-19 patients. However, the comprehensive changes of serum proteins in COVID-19 patients throughout the SARS-CoV-2 infection is unknown. In this work, we developed a high-density antibody microarray and performed an in-depth proteomics analysis of serum samples collected from early COVID-19 (n = 15) and influenza (n = 13) patients. We identified a large set of differentially expressed proteins (n = 132) that participate in a landscape of inflammation and immune signaling related to the SARS-CoV-2 infection. Furthermore, the significant correlations of neutrophil and lymphocyte with the CCL2 and CXCL10 mediated cytokine signaling pathways was identified. These information are valuable for the understanding of COVID-19 pathogenesis, identification of biomarkers and development of the optimal anti-inflammation therapy.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Betacoronavirus/pathogenicity
- Blood Proteins/genetics
- Blood Proteins/immunology
- COVID-19
- Child
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/physiopathology
- Coronavirus Infections/virology
- Cough/genetics
- Cough/immunology
- Cough/physiopathology
- Cough/virology
- Cytokine Release Syndrome/genetics
- Cytokine Release Syndrome/immunology
- Cytokine Release Syndrome/physiopathology
- Cytokine Release Syndrome/virology
- Cytokines/genetics
- Cytokines/immunology
- Female
- Fever/genetics
- Fever/immunology
- Fever/physiopathology
- Fever/virology
- Gene Expression Profiling
- Gene Expression Regulation
- Headache/genetics
- Headache/immunology
- Headache/physiopathology
- Headache/virology
- Humans
- Influenza, Human/genetics
- Influenza, Human/immunology
- Influenza, Human/physiopathology
- Influenza, Human/virology
- Male
- Middle Aged
- Myalgia/genetics
- Myalgia/immunology
- Myalgia/physiopathology
- Myalgia/virology
- Orthomyxoviridae/pathogenicity
- Pandemics
- Pneumonia, Viral/genetics
- Pneumonia, Viral/immunology
- Pneumonia, Viral/physiopathology
- Pneumonia, Viral/virology
- Protein Array Analysis
- Proteome/genetics
- Proteome/immunology
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2
- Signal Transduction/immunology
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Affiliation(s)
- Xin Hou
- Department of Clinical Laboratory & Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Xian Wu
- Department of Clinical Laboratory & Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Minya Lu
- Department of Clinical Laboratory & Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Dan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Meng Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Te Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Jiayu Dai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Hu Duan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory & Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China.
| | - Yongzhe Li
- Department of Clinical Laboratory & Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
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16
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Jiang J, Ding Y, Wu M, Lyu X, Wang H, Chen Y, Wang H, Teng L. Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis. Front Oncol 2020; 10:1765. [PMID: 33014868 PMCID: PMC7516284 DOI: 10.3389/fonc.2020.01765] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Gastric cancer (GC) is the fifth most frequently diagnosed malignancy, and the third leading cause of tumor-related mortalities worldwide. Due to a high heterogeneity in GC, its treatment and prognosis are challenging, necessitating urgent identification of novel prognostic predictors for GC patients. Methods: We downloaded RNA sequence data, from the Cancer Genome Atlas and microarray data from Gene Expression Omnibus database, then identified common differentially-expressed genes (DEGs) between GC and normal gastric tissues across four datasets. We then used a combination of protein-protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) to identify key genes with prognostic value in GC. Thereafter, we used quantitative real time polymerase chain reaction (qRT-PCR) to validate expression of the identified key genes in the Zhejiang University (ZJU) cohort. Finally, we evaluated the relationships between gene expression and immune factors, including immune cells and biomarkers of immunotherapy. Results: Among 426 common DEGs screened, 333 and 93 were upregulated and downregulated, respectively. PPI network and WGCNA successfully identified the top 30 hub genes, among which PTPRC, TYROBP, CCR1, CYBB, LCP2, and C1QB were common. Furthermore, TYROBP and C1QB were negatively associated with prognosis of GC patients, implying that they were key GC predictors. Interestingly, TYROBP and C1QB were positively correlated with predictive biomarkers for GC immunotherapy, including PD-L1 expression, CD8+ T cells infiltration, and EBV status. Conclusions: TYROBP and C1QB were identified as two novel key genes with prognostic value in GC by network analysis.
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Affiliation(s)
- Junjie Jiang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengjie Wu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiadong Lyu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haifeng Wang
- Department of Hematology & Oncology, The People's Hospital of Beilun District, Beilun Branch Hospital of the First Affiliated Hospital of Medical School of Zhejiang University, Ningbo, China
| | - Yanyan Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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17
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Cortés Llorca L, Li R, Yon F, Schäfer M, Halitschke R, Robert CAM, Kim SG, Baldwin IT. ZEITLUPE facilitates the rhythmic movements of Nicotiana attenuata flowers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:308-322. [PMID: 32130751 DOI: 10.1111/tpj.14732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/31/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Circadian organ movements are ubiquitous in plants. These rhythmic outputs are thought to be regulated by the circadian clock and auxin signalling, but the underlying mechanisms have not been clarified. Flowers of Nicotiana attenuata change their orientation during the daytime through a 140° arc to balance the need for pollinators and the protection of their reproductive organs. This rhythmic trait is under the control of the circadian clock and results from bending and re-straightening movements of the pedicel, stems that connect flowers to the inflorescence. Using an explant system that allowed pedicel growth and curvature responses to be characterized with high spatial and temporal resolution, we demonstrated that this movement is organ autonomous and mediated by auxin. Changes in the growth curvature of the pedicel are accompanied by an auxin gradient and dorsiventral asymmetry in auxin-dependent transcriptional responses; application of auxin transport inhibitors influenced the normal movements of this organ. Silencing the expression of the circadian clock component ZEITLUPE (ZTL) arrested changes in the growth curvature of the pedicel and altered auxin signalling and responses. IAA19-like, an Aux/IAA transcriptional repressor that is circadian regulated and differentially expressed between opposite tissues of the pedicel, and therefore possibly involved in the regulation of changes in organ curvature, physically interacted with ZTL. Together, these results are consistent with a direct link between the circadian clock and the auxin signalling pathway in the regulation of this rhythmic floral movement.
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Affiliation(s)
- Lucas Cortés Llorca
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
| | - Ran Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
| | - Felipe Yon
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
| | - Martin Schäfer
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
| | - Christelle A M Robert
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
| | - Sang-Gyu Kim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 007745, Germany
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18
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Kim J, Ahn JK, Cheong YE, Lee SJ, Cha HS, Kim KH. Systematic re-evaluation of the long-used standard protocol of urease-dependent metabolome sample preparation. PLoS One 2020; 15:e0230072. [PMID: 32182259 PMCID: PMC7077817 DOI: 10.1371/journal.pone.0230072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/20/2020] [Indexed: 11/24/2022] Open
Abstract
In the urinary metabolomics for finding biomarkers in urine, owing to high concentrations of urea, for chromatography-based metabolomic analysis, urea needed to be degraded by urease. This urease pretreatment has been the key step of sample preparation for standard urinary metabolomics until today even for mass spectrometry-based analysis. The urease pretreatment involving incubation of urine with urease contradicts the concept of metabolome sampling, which should immediately arrest metabolic reactions to prevent alterations of a metabolite profile. Nonetheless, the impact of urease pretreatment has not been clearly elucidated yet. We found that activities of urease and endogenous urinary enzymes and metabolite contaminants from the urease preparations introduce artefacts into metabolite profiles, thus leading to misinterpretation.
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Affiliation(s)
- Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Joong Kyong Ahn
- Division of Rheumatology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yu Eun Cheong
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Sung-Joon Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Hoon-Suk Cha
- Division of Rheumatology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- * E-mail: (KHK); (HSC)
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
- * E-mail: (KHK); (HSC)
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19
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Lewis V, Laberge F, Heyland A. Temporal Profile of Brain Gene Expression After Prey Catching Conditioning in an Anuran Amphibian. Front Neurosci 2020; 13:1407. [PMID: 31992968 PMCID: PMC6971186 DOI: 10.3389/fnins.2019.01407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
A key goal in modern neurobiology is to understand the mechanisms underlying learning and memory. To that end, it is essential to identify the patterns of gene expression and the temporal sequence of molecular events associated with learning and memory processes. It is also important to ascertain if and how these molecular events vary between organisms. In vertebrates, learning and memory processes are characterized by distinct phases of molecular activity involving gene transcription, structural change, and long-term maintenance of such structural change in the nervous system. Utilizing next generation sequencing techniques, we profiled the temporal expression patterns of genes in the brain of the fire-bellied toad Bombina orientalis after prey catching conditioning. The fire-bellied toad is a basal tetrapod whose neural architecture and molecular pathways may help us understand the ancestral state of learning and memory mechanisms in tetrapods. Differential gene expression following conditioning revealed activity in molecular pathways related to immediate early genes (IEG), cytoskeletal modification, axon guidance activity, and apoptotic processes. Conditioning induced early IEG activity coinciding with transcriptional activity and neuron structural modification, followed by axon guidance and cell adhesion activity, and late neuronal pruning. While some of these gene expression patterns are similar to those found in mammals submitted to conditioning, some interesting divergent expression profiles were seen, and differential expression of some well-known learning-related mammalian genes is missing altogether. These results highlight the importance of using a comparative approach in the study of the mechanisms of leaning and memory and provide molecular resources for a novel vertebrate model in the relatively poorly studied Amphibia.
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Affiliation(s)
- Vern Lewis
- Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | | - Andreas Heyland
- Integrative Biology, University of Guelph, Guelph, ON, Canada
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20
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Hayakawa K, Nishitani K, Tanaka S. Kynurenine, 3-OH-kynurenine, and anthranilate are nutrient metabolites that alter H3K4 trimethylation and H2AS40 O-GlcNAcylation at hypothalamus-related loci. Sci Rep 2019; 9:19768. [PMID: 31875008 PMCID: PMC6930210 DOI: 10.1038/s41598-019-56341-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022] Open
Abstract
Epigenetic mechanisms can establish and maintain mitotically stable patterns of gene expression while retaining the DNA sequence. These mechanisms can be affected by environmental factors such as nutrients. The importance of intracellular dosages of nutrient metabolites such as acetyl coenzyme A and S-adenosylmethionine, which are utilized as donors for post-translational modifications, is well-known in epigenetic regulation; however, the significance of indirect metabolites in epigenetic regulation is not clear. In this study, we screened for metabolites that function as epigenetic modulators. Because the expression of genes related to hypothalamic function is reportedly affected by nutritional conditions, we used a neural cell culture system and evaluated hypothalamic-linked loci. We supplemented the culture medium with 129 metabolites separately during induction of human-iPS-derived neural cells and used high-throughput ChIP-qPCR to determine the epigenetic status at 37 hypothalamus-linked loci. We found three metabolites (kynurenine, 3-OH-kynurenine, and anthranilate) from tryptophan pathways that increased H3K4 trimethylation and H2AS40 O-GlcNAcylation, resulting in upregulated gene expression at most loci, except those encoding pan-neural markers. Dietary supplementation of these three metabolites and the resulting epigenetic modification were important for stability in gene expression. In conclusion, our findings provide a better understanding of how nutrients play a role in epigenetic mechanisms.
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Affiliation(s)
- Koji Hayakawa
- Department of Toxicology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan. .,Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences /Veterinary Medical Sciences, The University of Tokyo, Tokyo, Japan.
| | - Kenta Nishitani
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences /Veterinary Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Satoshi Tanaka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences /Veterinary Medical Sciences, The University of Tokyo, Tokyo, Japan
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21
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Boter M, Calleja-Cabrera J, Carrera-Castaño G, Wagner G, Hatzig SV, Snowdon RJ, Legoahec L, Bianchetti G, Bouchereau A, Nesi N, Pernas M, Oñate-Sánchez L. An Integrative Approach to Analyze Seed Germination in Brassica napus. FRONTIERS IN PLANT SCIENCE 2019; 10:1342. [PMID: 31708951 PMCID: PMC6824160 DOI: 10.3389/fpls.2019.01342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/26/2019] [Indexed: 05/23/2023]
Abstract
Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.
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Affiliation(s)
- Marta Boter
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Julián Calleja-Cabrera
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Gerardo Carrera-Castaño
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Geoffrey Wagner
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sarah Vanessa Hatzig
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Laurie Legoahec
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Grégoire Bianchetti
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Alain Bouchereau
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Nathalie Nesi
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Mónica Pernas
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
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22
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Jiao X, Ye J, Wang X, Yin X, Zhang G, Cheng X. KIAA1199, a Target of MicoRNA-486-5p, Promotes Papillary Thyroid Cancer Invasion by Influencing Epithelial-Mesenchymal Transition (EMT). Med Sci Monit 2019; 25:6788-6796. [PMID: 31501407 PMCID: PMC6752488 DOI: 10.12659/msm.918682] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background KIAA1199 has been reported to be associated with malignant progression and poor clinical outcomes in various human malignancies. However, its clinical role and molecular function remain unknown in papillary thyroid cancer (PTC). Material/Methods The Cancer Genome Atlas (TCGA) was used to investigate the expression profiles of KIAA1199 and miR-486-5p in PTC. Immunohistochemistry was used to validate the protein expression of KIAA1199 in PTC. The Weighted Gene Co-expression Network Analysis (WGCNA) and Gene Set Enrichment Analysis (GSEA) were used to explore the potential pathway underling KIAA1199 in PTC. In vitro and in vivo experiments were performed to investigate the biological role of KIAA1199 in PTC progression. Luciferase reporter assays and Western blot analysis were performed to determine whether KIAA1199 is a downstream target of miR-486-5p. Results We found that KIAA1199 was aberrantly elevated in PTC tissues compared with normal tissues, and upregulation of KIAA1199 was positively correlated with more advanced clinical variables. Additionally, bioinformatic analysis indicated that KIAA1199 was involved in cell migration and invasion. KIAA1199 silencing inhibited the invasive ability of PTC cells by affecting epithelial-mesenchymal transition (EMT) in vitro and in vivo. Furthermore, miR-486-5p was identified as an upstream microRNA that directly targets the 3′-UTR region of KIAA1199. Conclusions The miR-486-5p/KIAA1199/EMT axis might play a critical role in PTC invasion and metastasis and offers a potential therapeutic strategy for PTC.
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Affiliation(s)
- Xuehua Jiao
- Department of Endocrinology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland).,Department of Endocrinology, The First People's Hospital of Wujiang District, Suzhou, Jiangsu, China (mainland)
| | - Jiandong Ye
- Department of General Surgery, The First People's Hospital of Wujiang District, Suzhou, Jiangsu, China (mainland)
| | - Xiujie Wang
- Department of Endocrinology, The First People's Hospital of Wujiang District, Suzhou, Jiangsu, China (mainland)
| | - Xueyan Yin
- Department of Endocrinology, The First People's Hospital of Wujiang District, Suzhou, Jiangsu, China (mainland)
| | - Guodong Zhang
- Department of Endocrinology, Suzhou Yongding Hospital, Suzhou, Jiangsu, China (mainland)
| | - Xingbo Cheng
- Department of Endocrinology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
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23
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Caporali S, Amaro A, Levati L, Alvino E, Lacal PM, Mastroeni S, Ruffini F, Bonmassar L, Antonini Cappellini GC, Felli N, Carè A, Pfeffer U, D'Atri S. miR-126-3p down-regulation contributes to dabrafenib acquired resistance in melanoma by up-regulating ADAM9 and VEGF-A. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:272. [PMID: 31227006 PMCID: PMC6588909 DOI: 10.1186/s13046-019-1238-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/21/2019] [Indexed: 02/06/2023]
Abstract
Background Development of resistance to inhibitors of BRAF (BRAFi) and MEK (MEKi) remains a great challenge for targeted therapy in patients with BRAF-mutant melanoma. Here, we explored the role of miRNAs in melanoma acquired resistance to BRAFi. Methods miRNA expression in two BRAF-mutant melanoma cell lines and their dabrafenib-resistant sublines was determined using Affymetrix GeneChip® miRNA 3.1 microarrays and/or qRT-PCR. The effects of miR-126-3p re-expression on proliferation, apoptosis, cell cycle, ERK1/2 and AKT phosphorylation, dabrafenib sensitivity, invasiveness and VEGF-A secretion were evaluated in the dabrafenib-resistant sublines using MTT assays, flow cytometry, immunoblotting, invasion assays in Boyden chambers and ELISA. ADAM9, PIK3R2, MMP7 and CXCR4 expression in the sensitive and dabrafenib-resistant cells was determined by immunoblotting. Small RNA interference was performed to investigate the consequence of VEGFA or ADAM9 silencing on proliferation, invasiveness or dabrafenib sensitivity of the resistant sublines. Long-term proliferation assays were carried out in dabrafenib-sensitive cells to assess the effects of enforced miR-126-3p expression or ADAM9 silencing on resistance development. VEGF-A serum levels in melanoma patients treated with BRAFi or BRAFi+MEKi were evaluated at baseline (T0), after two months of treatment (T2) and at progression (TP) by ELISA. Results miR-126-3p was significantly down-regulated in the dabrafenib-resistant sublines as compared with their parental counterparts. miR-126-3p replacement in the drug-resistant cells inhibited proliferation, cell cycle progression, phosphorylation of ERK1/2 and/or AKT, invasiveness, VEGF-A and ADAM9 expression, and increased dabrafenib sensitivity. VEGFA or ADAM9 silencing impaired proliferation and invasiveness of the drug-resistant sublines. ADAM9 knock-down in the resistant cells increased dabrafenib sensitivity, whereas miR-126-3p enforced expression or ADAM9 silencing in the drug-sensitive cells delayed the development of resistance. At T0 and T2, statistically significant differences were observed in VEGF-A serum levels between patients who responded to therapy and patients who did not. In responder patients, a significant increase of VEGF-A levels was observed at TP versus T2. Conclusions Strategies restoring miR-126-3p expression or targeting VEGF-A or ADAM9 could restrain growth and metastasis of dabrafenib-resistant melanomas and increase their drug sensitivity. Circulating VEGF-A is a promising biomarker for predicting patients’ response to BRAFi or BRAFi+MEKi and for monitoring the onset of resistance. Electronic supplementary material The online version of this article (10.1186/s13046-019-1238-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simona Caporali
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Via dei Monti di Creta 104, 00167, Rome, Italy
| | - Adriana Amaro
- Molecular Pathology, IRCCS-Ospedale Policlinico San Martino, Genoa, Italy
| | - Lauretta Levati
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Via dei Monti di Creta 104, 00167, Rome, Italy
| | - Ester Alvino
- Institute of Translational Pharmacology, National Council of Research, Rome, Italy
| | - Pedro Miguel Lacal
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Via dei Monti di Creta 104, 00167, Rome, Italy
| | | | - Federica Ruffini
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Via dei Monti di Creta 104, 00167, Rome, Italy
| | - Laura Bonmassar
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Via dei Monti di Creta 104, 00167, Rome, Italy
| | | | - Nadia Felli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Carè
- Center of Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Ulrich Pfeffer
- Molecular Pathology, IRCCS-Ospedale Policlinico San Martino, Genoa, Italy
| | - Stefania D'Atri
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Via dei Monti di Creta 104, 00167, Rome, Italy.
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24
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Kim J, Choi KB, Park JH, Kim KH. Metabolite profile changes and increased antioxidative and antiinflammatory activities of mixed vegetables after fermentation by Lactobacillus plantarum. PLoS One 2019; 14:e0217180. [PMID: 31116776 PMCID: PMC6530839 DOI: 10.1371/journal.pone.0217180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/06/2019] [Indexed: 02/05/2023] Open
Abstract
Fermented vegetables have emerged as prebiotics with various health benefits. However, the possible mechanisms behind their health benefits are unclear. To relate the metabolite profile changes in fermented mixed vegetables with associated health benefits of fermented vegetables, we analyzed the metabolite profiles of mixed vegetables, before and after fermentation by Lactobacillus plantarum, using gas chromatography/time-of-flight-mass spectrometry (GC/TOF-MS). To analyze health benefits of fermented vegetables, antioxidative and antiinflammatory activities were measured using RAW 264.7 cells. Among 78 metabolites identified by GC/TOF-MS in this study, those significantly increased after fermentation include antioxidative and/or antiinflammatory agents such as lactate, 3-phennyllactate, indole-3-lactate, β-hydroxybutyrate, γ-aminobutyrate, and glycerol. These metabolites may have been either newly synthesized or depolymerized from high molecular weight polymers from vegetables during fermentation. This is the first metabolomics study to relate metabolite profile changes with increased health benefits of fermented vegetables.
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Affiliation(s)
- Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, South Korea
| | - Kum-Boo Choi
- Pulmuone Institute of Technology, Pulmuone, Seoul, South Korea
| | - Ju Hun Park
- Pulmuone Institute of Technology, Pulmuone, Seoul, South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, South Korea
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25
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Srivastava M, Bencurova E, Gupta SK, Weiss E, Löffler J, Dandekar T. Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle. Front Cell Infect Microbiol 2019; 9:168. [PMID: 31192161 PMCID: PMC6540932 DOI: 10.3389/fcimb.2019.00168] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DCs) are antigen presenting cells which serve as a passage between the innate and the acquired immunity. Aspergillosis is a major lethal condition in immunocompromised patients caused by the adaptable saprophytic fungus Aspergillus fumigatus. The healthy human immune system is capable to ward off A. fumigatus infections however immune-deficient patients are highly vulnerable to invasive aspergillosis. A. fumigatus can persist during infection due to its ability to survive the immune response of human DCs. Therefore, the study of the metabolism specific to the context of infection may allow us to gain insight into the adaptation strategies of both the pathogen and the immune cells. We established a metabolic model of A. fumigatus central metabolism during infection of DCs and calculated the metabolic pathway (elementary modes; EMs). Transcriptome data were used to identify pathways activated when A. fumigatus is challenged with DCs. In particular, amino acid metabolic pathways, alternative carbon metabolic pathways and stress regulating enzymes were found to be active. Metabolic flux modeling identified further active enzymes such as alcohol dehydrogenase, inositol oxygenase and GTP cyclohydrolase participating in different stress responses in A. fumigatus. These were further validated by qRT-PCR from RNA extracted under these different conditions. For DCs, we outlined the activation of metabolic pathways in response to the confrontation with A. fumigatus. We found the fatty acid metabolism plays a crucial role, along with other metabolic changes. The gene expression data and their analysis illuminate additional regulatory pathways activated in the DCs apart from interleukin regulation. In particular, Toll-like receptor signaling, NOD-like receptor signaling and RIG-I-like receptor signaling were active pathways. Moreover, we identified subnetworks and several novel key regulators such as UBC, EGFR, and CUL3 of DCs to be activated in response to A. fumigatus. In conclusion, we analyze the metabolic and regulatory responses of A. fumigatus and DCs when confronted with each other.
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Affiliation(s)
- Mugdha Srivastava
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Shishir K Gupta
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Esther Weiss
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,EMBL Heidelberg, Structural and Computational Biology, Heidelberg, Germany
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26
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Sonoda H, Lee BR, Park KH, Nihalani D, Yoon JH, Ikeda M, Kwon SH. miRNA profiling of urinary exosomes to assess the progression of acute kidney injury. Sci Rep 2019; 9:4692. [PMID: 30886169 PMCID: PMC6423131 DOI: 10.1038/s41598-019-40747-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/20/2019] [Indexed: 12/28/2022] Open
Abstract
Because exosomes have gained attention as a source of biomarkers, we investigated if miRNAs in exosomes (exo-miRs) can report the disease progression of organ injury. Using rat renal ischemia-reperfusion injury (IRI) as a model of acute kidney injury (AKI), we determined temporally-released exo-miRs in urine during IRI and found that these exo-miRs could reliably mirror the progression of AKI. From the longitudinal measurements of miRNA expression in kidney and urine, we found that release of exo- miRs was a regulated sorting process. In the injury state, miR-16, miR-24, and miR-200c were increased in the urine. Interestingly, expression of target mRNAs of these exo-miRs was significantly altered in renal medulla. Next, in the early recovery state, exo-miRs (miR-9a, miR-141, miR-200a, miR-200c, miR-429), which share Zeb1/2 as a common target mRNA, were upregulated together, indicating that they reflect TGF-β-associated renal fibrosis. Finally, release of exo-miRs (miR-125a, miR-351) was regulated by TGF-β1 and was able to differentiate the sham and IRI even after the injured kidneys were recovered. Altogether, these data indicate that exo-miRs released in renal IRI are associated with TGF-β signaling. Temporal release of exo-miRs which share targets might be a regulatory mechanism to control the progression of AKI.
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Affiliation(s)
- Hiroko Sonoda
- Department of Veterinary Pharmacology, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Byung Rho Lee
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Ki-Hoon Park
- Department of Medicine, Nephrology Division, Medical University of South Carolina, Charleston, SC, USA
| | - Deepak Nihalani
- Department of Medicine, Nephrology Division, Medical University of South Carolina, Charleston, SC, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular biology, Medical University of South Carolina, Charleston, SC, USA
| | - Masahiro Ikeda
- Department of Veterinary Pharmacology, University of Miyazaki, Miyazaki, 889-2192, Japan.
| | - Sang-Ho Kwon
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA.
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27
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Rambow F, Rogiers A, Marin-Bejar O, Aibar S, Femel J, Dewaele M, Karras P, Brown D, Chang YH, Debiec-Rychter M, Adriaens C, Radaelli E, Wolter P, Bechter O, Dummer R, Levesque M, Piris A, Frederick DT, Boland G, Flaherty KT, van den Oord J, Voet T, Aerts S, Lund AW, Marine JC. Toward Minimal Residual Disease-Directed Therapy in Melanoma. Cell 2018; 174:843-855.e19. [PMID: 30017245 DOI: 10.1016/j.cell.2018.06.025] [Citation(s) in RCA: 397] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/13/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023]
Abstract
Many patients with advanced cancers achieve dramatic responses to a panoply of therapeutics yet retain minimal residual disease (MRD), which ultimately results in relapse. To gain insights into the biology of MRD, we applied single-cell RNA sequencing to malignant cells isolated from BRAF mutant patient-derived xenograft melanoma cohorts exposed to concurrent RAF/MEK-inhibition. We identified distinct drug-tolerant transcriptional states, varying combinations of which co-occurred within MRDs from PDXs and biopsies of patients on treatment. One of these exhibited a neural crest stem cell (NCSC) transcriptional program largely driven by the nuclear receptor RXRG. An RXR antagonist mitigated accumulation of NCSCs in MRD and delayed the development of resistance. These data identify NCSCs as key drivers of resistance and illustrate the therapeutic potential of MRD-directed therapy. They also highlight how gene regulatory network architecture reprogramming may be therapeutically exploited to limit cellular heterogeneity, a key driver of disease progression and therapy resistance.
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Affiliation(s)
- Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Aljosja Rogiers
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Oskar Marin-Bejar
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, KU Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Julia Femel
- Department of Cell, Developmental, and Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Michael Dewaele
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Daniel Brown
- Laboratory of reproductive genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, USA
| | - Maria Debiec-Rychter
- Laboratory for Genetics of Malignant Disorders, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Adriaens
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Enrico Radaelli
- Comparative Pathology Core, University of Pennsylvania, Department of Pathobiology, Philadelphia, PA, USA
| | - Pascal Wolter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Oliver Bechter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Reinhard Dummer
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Mitchell Levesque
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Adriano Piris
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Dennie T Frederick
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve Boland
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Keith T Flaherty
- Department of Medical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Joost van den Oord
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Thierry Voet
- Laboratory of reproductive genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, KU Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Amanda W Lund
- Department of Cell, Developmental, and Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
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Aherfi S, Andreani J, Baptiste E, Oumessoum A, Dornas FP, Andrade ACDSP, Chabriere E, Abrahao J, Levasseur A, Raoult D, La Scola B, Colson P. A Large Open Pangenome and a Small Core Genome for Giant Pandoraviruses. Front Microbiol 2018; 9:1486. [PMID: 30042742 PMCID: PMC6048876 DOI: 10.3389/fmicb.2018.01486] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/14/2018] [Indexed: 01/09/2023] Open
Abstract
Giant viruses of amoebae are distinct from classical viruses by the giant size of their virions and genomes. Pandoraviruses are the record holders in size of genomes and number of predicted genes. Three strains, P. salinus, P. dulcis, and P. inopinatum, have been described to date. We isolated three new ones, namely P. massiliensis, P. braziliensis, and P. pampulha, from environmental samples collected in Brazil. We describe here their genomes, the transcriptome and proteome of P. massiliensis, and the pangenome of the group encompassing the six pandoravirus isolates. Genome sequencing was performed with an Illumina MiSeq instrument. Genome annotation was performed using GeneMarkS and Prodigal softwares and comparative genomic analyses. The core genome and pangenome were determined using notably ProteinOrtho and CD-HIT programs. Transcriptomics was performed for P. massiliensis with the Illumina MiSeq instrument; proteomics was also performed for this virus using 1D/2D gel electrophoresis and mass spectrometry on a Synapt G2Si Q-TOF traveling wave mobility spectrometer. The genomes of the three new pandoraviruses are comprised between 1.6 and 1.8 Mbp. The genomes of P. massiliensis, P. pampulha, and P. braziliensis were predicted to harbor 1,414, 2,368, and 2,696 genes, respectively. These genes comprise up to 67% of ORFans. Phylogenomic analyses showed that P. massiliensis and P. braziliensis were more closely related to each other than to the other pandoraviruses. The core genome of pandoraviruses comprises 352 clusters of genes, and the ratio core genome/pangenome is less than 0.05. The extinction curve shows clearly that the pangenome is still open. A quarter of the gene content of P. massiliensis was detected by transcriptomics. In addition, a product for a total of 162 open reading frames were found by proteomic analysis of P. massiliensis virions, including notably the products of 28 ORFans, 99 hypothetical proteins, and 90 core genes. Further analyses should allow to gain a better knowledge and understanding of the evolution and origin of these giant pandoraviruses, and of their relationships with viruses and cellular microorganisms.
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Affiliation(s)
- Sarah Aherfi
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Julien Andreani
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Emeline Baptiste
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Amina Oumessoum
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Fábio P Dornas
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Claudia Dos S P Andrade
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eric Chabriere
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Jonatas Abrahao
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anthony Levasseur
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Bernard La Scola
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Philippe Colson
- Microbes Evolution Phylogenie et Infections (MEϕI), Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
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29
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Baltazar LM, Zamith-Miranda D, Burnet MC, Choi H, Nimrichter L, Nakayasu ES, Nosanchuk JD. Concentration-dependent protein loading of extracellular vesicles released by Histoplasma capsulatum after antibody treatment and its modulatory action upon macrophages. Sci Rep 2018; 8:8065. [PMID: 29795301 PMCID: PMC5966397 DOI: 10.1038/s41598-018-25665-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/23/2018] [Indexed: 12/03/2022] Open
Abstract
Diverse pathogenic fungi secrete extracellular vesicles (EV) that contain macromolecules, including virulence factors that can modulate the host immune response. We recently demonstrated that the binding of monoclonal antibodies (mAb) modulates how Histoplasma capsulatum load and releases its extracellular vesicles (EV). In the present paper, we addressed a concentration-dependent impact on the fungus' EV loading and release with different mAb, as well as the pathophysiological role of these EV during the host-pathogen interaction. We found that the mAbs differentially regulate EV content in concentration-dependent and independent manners. Enzymatic assays demonstrated that laccase activity in EV from H. capsulatum opsonized with 6B7 was reduced, but urease activity was not altered. The uptake of H. capsulatum by macrophages pre-treated with EV, presented an antibody concentration-dependent phenotype. The intracellular killing of yeast cells was potently inhibited in macrophages pre-treated with EV from 7B6 (non-protective) mAb-opsonized H. capsulatum and this inhibition was associated with a decrease in the reactive-oxygen species generated by these macrophages. In summary, our findings show that opsonization quantitatively and qualitatively modifies H. capsulatum EV load and secretion leading to distinct effects on the host's immune effector mechanisms, supporting the hypothesis that EV sorting and secretion are dynamic mechanisms for a fine-tuned response by fungal cells.
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Affiliation(s)
- Ludmila Matos Baltazar
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Joshua D Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA.
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30
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Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. J Proteome Res 2018; 17:2226-2236. [PMID: 29734811 DOI: 10.1021/acs.jproteome.8b00217] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol. We describe a universally applicable strategy that requires minimal individual sample processing and permits the seamless addition of a phosphopeptide enrichment step ("mini-phos") with little deviation from the deep proteome analysis. To showcase our workflow, we profile the proteome of wild-type Saccharomyces cerevisiae yeast grown with either glucose or pyruvate as the carbon source. Here, we have established a streamlined TMT protocol that enables deep proteome and medium-scale phosphoproteome analysis.
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Affiliation(s)
- José Navarrete-Perea
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Qing Yu
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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31
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Nucleosomes of polyploid trophoblast giant cells mostly consist of histone variants and form a loose chromatin structure. Sci Rep 2018; 8:5811. [PMID: 29643413 PMCID: PMC5895725 DOI: 10.1038/s41598-018-23832-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/20/2018] [Indexed: 12/31/2022] Open
Abstract
Trophoblast giant cells (TGCs) are one of the cell types that form the placenta and play multiple essential roles in maintaining pregnancy in rodents. TGCs have large, polyploid nuclei resulting from endoreduplication. While previous studies have shown distinct gene expression profiles of TGCs, their chromatin structure remains largely unknown. An appropriate combination of canonical and non-canonical histones, also known as histone variants, allows each cell to exert its cell type-specific functions. Here, we aimed to reveal the dynamics of histone usage and chromatin structure during the differentiation of trophoblast stem cells (TSCs) into TGCs. Although the expression of most genes encoding canonical histones was downregulated, the expression of a few genes encoding histone variants such as H2AX, H2AZ, and H3.3 was maintained at a relatively high level in TGCs. Both the micrococcal nuclease digestion assay and nucleosome stability assay using a microfluidic device indicated that chromatin became increasingly loose as TSCs differentiated. Combinatorial experiments involving H3.3-knockdown and -overexpression demonstrated that variant H3.3 resulted in the formation of loose nucleosomes in TGCs. In conclusion, our study revealed that TGCs possessed loose nucleosomes owing to alterations in their histone composition during differentiation.
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32
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Wang H, Guo R, Ki JS. 6.0 K microarray reveals differential transcriptomic responses in the dinoflagellate Prorocentrum minimum exposed to polychlorinated biphenyl (PCB). CHEMOSPHERE 2018; 195:398-409. [PMID: 29274579 DOI: 10.1016/j.chemosphere.2017.12.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/23/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Abstract
Endocrine disrupting chemicals (EDCs) have toxic effects on algae; however, their molecular genomic responses have not been sufficiently elucidated. Here, we evaluated genome-scaled responses of the dinoflagellate alga Prorocentrum minimum exposed to an EDC, polychlorinated biphenyl (PCB), using a 6.0 K microarray. Based on two-fold change cut-off, we identified that 609 genes (∼10.2%) responded to the PCB treatment. KEGG pathway analysis showed that differentially expressed genes (DEGs) were related to ribosomes, biosynthesis of amino acids, spliceosomes, and cellular processes. Many DEGs were involved in cell cycle progression, apoptosis, signal transduction, ion binding, and cellular transportation. In contrast, only a few genes related to photosynthesis and oxidative stress were expressed in response to PCB exposure. This was supported by that fact that there were no obvious changes in the photosynthetic efficiency and reactive oxygen species (ROS) production. These results suggest that PCB might not cause chloroplast and oxidative damage, but could lead to cell cycle arrest and apoptosis. In addition, various signal transduction and transport pathways might be disrupted in the cells, which could further contribute to cell death. These results expand the genomic understanding of the effects of EDCs on this dinoflagellate protist.
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Affiliation(s)
- Hui Wang
- Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea
| | - Ruoyu Guo
- Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea.
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Chandran AKN, Bhatnagar N, Yoo YH, Moon S, Park SA, Hong WJ, Kim BG, An G, Jung KH. Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles. PLANT MOLECULAR BIOLOGY 2018; 96:17-34. [PMID: 29086189 DOI: 10.1007/s11103-017-0675-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was used to validate the expression of genes that were clustered according to their leaf or root preference. Taking a molecular and genetics approach, we examined meta-expression data and found that 127 genes were differentially expressed between japonica and indica rice cultivars. This is potentially significant for future agronomic applications. We also used a T-DNA insertional mutant and performed a co-expression network analysis of Sword shape dwarf1 (SSD1), a gene that regulates cell division. This network was refined via RT-PCR analysis. Our results suggested that SSD1 represses the expression of four genes related to the processes of DNA replication or cell division and provides insight into possible molecular mechanisms. Together, these strategies present a valuable tool for in-depth characterization of currently unannotated genes.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Nikita Bhatnagar
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sun-Ah Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea.
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Zhang Y, Hu Y, Fang JY, Xu J. Gain-of-function miRNA signature by mutant p53 associates with poor cancer outcome. Oncotarget 2017; 7:11056-66. [PMID: 26840456 PMCID: PMC4905457 DOI: 10.18632/oncotarget.7090] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/15/2016] [Indexed: 01/05/2023] Open
Abstract
Missense mutation of p53 not only impairs its tumor suppression function, but also causes oncogenic gain of function (GOF). The molecular underpinning of mutant p53 (mutp53) GOF is not fully understood, especially for the potential roles of non-coding genes. Here we identify the microRNA expression profile (microRNAome) of mutp53 on Arg282 by controlled microarray experiments, and clarify the prognostic significance of mutp53-regulated miRNAs in cancers. A predominant repression effect on miRNA expression was found for mutant p53, with 183 significantly downregulated and only 12 upregulated miRNAs. Mutp53 and wild-type (wtp53) commonly upregulate let-7i, and other two miRNAs were upregulated by wtp53 but repressed by mutp53 (miR-610 and miR-3065–3p). Based the mutp53-regulated miRNA signature, a non-negative matrix factorization (NMF) model classified gastric cancer (GC) cases into subgroups with significantly different Disease-free survival (Kaplan-Meier test, P = 0.013). In contrast, the NMF model based on all miRNAs did not associate with cancer outcome. The mutp53 miRNA signature associated with the outcomes of breast cancer (P = 0.024) and hepatocellular cancer (P = 0.012). The miRPath analysis revealed that mutp53-suppressed miRNAs associate with Hippo, TGF-β and stem cell signaling pathways. Taken together, our results highlight a miRNA-mediated GOF mechanism of mutant p53 on Arg282, and suggest the prognostic potential of mutp53-associated miRNA signature.
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Affiliation(s)
- Yao Zhang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai, China
| | - Ye Hu
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai, China.,Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai, China
| | - Jie Xu
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai, China
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Bdeir R, Muchero W, Yordanov Y, Tuskan GA, Busov V, Gailing O. Quantitative trait locus mapping of Populus bark features and stem diameter. BMC PLANT BIOLOGY 2017; 17:224. [PMID: 29179673 PMCID: PMC5704590 DOI: 10.1186/s12870-017-1166-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/10/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Bark plays important roles in photosynthate transport and storage, along with physical and chemical protection. Bark texture varies extensively among species, from smooth to fissured to deeply furrowed, but its genetic control is unknown. This study sought to determine the main genomic regions associated with natural variation in bark features and stem diameter. Quantitative trait loci (QTL) were mapped using an interspecific pseudo-backcross pedigree (Populus trichocarpa x P. deltoides and P. deltoides) for bark texture, bark thickness and diameter collected across three years, two sites and three biological replicates per site. RESULTS QTL specific to bark texture were highly reproducible in shared intervals across sites, years and replicates. Significant positive correlations and co-localization between trait QTL suggest pleiotropic regulators or closely linked genes. A list of candidate genes with related putative function, location close to QTL maxima and with the highest expression level in the phloem, xylem and cambium was identified. CONCLUSION Candidate genes for bark texture included an ortholog of Arabidopsis ANAC104 (PopNAC128), which plays a role in lignified fiber cell and ray development, as well as Pinin and Fasciclin (PopFLA) genes with a role in cell adhesion, cell shape and migration. The results presented in this study provide a basis for future genomic characterization of genes found within the QTL for bark texture, bark thickness and diameter in order to better understand stem and bark development in Populus and other woody perennial plants. The QTL mapping approach identified a list of prime candidate genes for further validation using functional genomics or forward genetics approaches.
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Affiliation(s)
- Roba Bdeir
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Yordan Yordanov
- Departement of Biology, Eastern Illinois University, 600 Lincoln Ave, Charleston, IL 61920 USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Victor Busov
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Oliver Gailing
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
- Present address: Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
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Köhler C, Nittner D, Rambow F, Radaelli E, Stanchi F, Vandamme N, Baggiolini A, Sommer L, Berx G, van den Oord JJ, Gerhardt H, Blanpain C, Marine JC. Mouse Cutaneous Melanoma Induced by Mutant BRaf Arises from Expansion and Dedifferentiation of Mature Pigmented Melanocytes. Cell Stem Cell 2017; 21:679-693.e6. [PMID: 29033351 DOI: 10.1016/j.stem.2017.08.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 06/28/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022]
Abstract
To identify the cells at the origin of melanoma, we combined single-cell lineage-tracing and transcriptomics approaches with time-lapse imaging. A mouse model that recapitulates key histopathological features of human melanomagenesis was created by inducing a BRafV600E-driven melanomagenic program in tail interfollicular melanocytes. Most targeted mature, melanin-producing melanocytes expanded clonally within the epidermis before losing their differentiated features through transcriptional reprogramming and eventually invading the dermis. Tumors did not form within interscales, which contain both mature and dormant amelanotic melanocytes. The hair follicle bulge, which contains melanocyte stem cells, was also refractory to melanomagenesis. These studies identify varying tumor susceptibilities within the melanocytic lineage, highlighting pigment-producing cells as the melanoma cell of origin, and indicate that regional variation in tumor predisposition is dictated by microenvironmental cues rather than intrinsic differences in cellular origin. Critically, this work provides in vivo evidence that differentiated somatic cells can be reprogrammed into cancer initiating cells.
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Affiliation(s)
- Corinna Köhler
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, 3000 Leuven, Belgium
| | - David Nittner
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, 3000 Leuven, Belgium
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, 3000 Leuven, Belgium
| | - Enrico Radaelli
- Mouse Histopathology Core Facility, VIB Center for Brain Disease, VIB, 3000 Leuven, Belgium; Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-6051, USA
| | - Fabio Stanchi
- Vascular Patterning Laboratory, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Niels Vandamme
- Molecular and Cellular Oncology Laboratory, Cancer Research Institute Ghent (CRIG), 9052 Ghent University, Ghent, Belgium
| | - Arianna Baggiolini
- Stem Cell Biology, Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Lukas Sommer
- Stem Cell Biology, Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Cancer Research Institute Ghent (CRIG), 9052 Ghent University, Ghent, Belgium
| | - Joost J van den Oord
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KULeuven and UZ Leuven, 3000 Leuven, Belgium
| | - Holger Gerhardt
- Vascular Patterning Laboratory, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Cedric Blanpain
- Laboratory of Stem Cells and Cancer, Welbio, Université Libre de Bruxelles, 1070 Bruxelles, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, 3000 Leuven, Belgium.
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Hayakawa K, Hirosawa M, Tani R, Yoneda C, Tanaka S, Shiota K. H2A O-GlcNAcylation at serine 40 functions genomic protection in association with acetylated H2AZ or γH2AX. Epigenetics Chromatin 2017; 10:51. [PMID: 29084613 PMCID: PMC5663087 DOI: 10.1186/s13072-017-0157-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 12/11/2022] Open
Abstract
Background We have previously reported a novel O-GlcNAc modification at serine 40 (S40) of H2A (H2AS40Gc). S40-type H2A isoforms susceptible to O-GlcNAcylation are evolutionarily new and restricted to the viviparous animals; however, the biological function of H2AS40Gc is largely unknown. H2A isoforms are consisted of S40 and alanine 40 (A40) type and this residue on H2A is located in the L1 of the globular domain, which is also known as a variable portion that distinguishes between the canonical and non-canonical H2A variants. In this study, by considering the similarity between the S40-type H2A and histone H2A variants, we explored the function of H2AS40Gc in mouse embryonic stem cells (mESCs). Results We found several similarities between the S40-type H2A isoforms and histone H2A variants such H2AZ and H2AX. mRNA of S40-type H2A isoforms (H2A1 N and H2A3) had a poly(A) tail and was produced throughout the cell cycle in contrast to that of A40-type. Importantly, H2AS40Gc level increased owing to chemical-induced DNA damage, similar to phosphorylated H2AX (γH2AX) and acetylated H2AZ (AcH2AZ). H2AS40Gc was accumulated at the restricted area (± 1.5 kb) of DNA damage sites induced by CRISPR/CAS9 system in contrast to accumulation of γH2AX, which was widely scattered. Overexpression of the wild-type (WT) H2A3, but not the S40 to A40 mutation (S40A-mutant), protected the mESC genome against chemical-induced DNA damage. Furthermore, 3 h after the DNA damage treatment, the genome was almost recovered in WT mESCs, whereas the damage advanced further in the S40A-mutant mESCs, suggesting functions of H2AS40Gc in the DNA repair mechanism. Furthermore, the S40A mutant prevented the accumulation of the DNA repair apparatus such as DNA-PKcs and Rad51 at the damage site. Co-immunoprecipitation experiment in WT and S40A-mutant mESCs revealed that H2AS40Gc physiologically bound to AcH2AZ at the initial phase upon DNA damage, followed by binding with γH2AX during the DNA damage repair process. Conclusions These data suggest that H2AS40Gc functions to maintain genome integrity through the DNA repair mechanism in association with AcH2AZ and γH2AX. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0157-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Koji Hayakawa
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Mitsuko Hirosawa
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Ruiko Tani
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Chikako Yoneda
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Satoshi Tanaka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Kunio Shiota
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan. .,Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan.
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Niu X, Guan Y, Chen S, Li H. Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon. BMC Genomics 2017; 18:619. [PMID: 28810832 PMCID: PMC5558667 DOI: 10.1186/s12864-017-4044-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/09/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions. CONCLUSION One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.
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Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yuxiang Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Xinjiang Agricultural Vocational Technical College, Changji, China
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The role of microRNAs in the therapeutic action of D-cycloserine in a post-traumatic stress disorder animal model. Psychiatr Genet 2017; 27:139-151. [DOI: 10.1097/ypg.0000000000000176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gormley M, Ona K, Kapidzic M, Garrido-Gomez T, Zdravkovic T, Fisher SJ. Preeclampsia: novel insights from global RNA profiling of trophoblast subpopulations. Am J Obstet Gynecol 2017; 217:200.e1-200.e17. [PMID: 28347715 DOI: 10.1016/j.ajog.2017.03.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND The maternal signs of preeclampsia, which include the new onset of high blood pressure, can occur because of faulty placentation. We theorized that transcriptomic analyses of trophoblast subpopulations in situ would lend new insights into the role of these cells in preeclampsia pathogenesis. OBJECTIVE Our goal was to enrich syncytiotrophoblasts, invasive cytotrophoblasts, or endovascular cytotrophoblasts from the placentas of severe preeclampsia cases. Total RNA was subjected to global transcriptional profiling to identify RNAs that were misexpressed compared with controls. STUDY DESIGN This was a cross-sectional analysis of placentas from women who had been diagnosed with severe preeclampsia. Gestational age-matched controls were placentas from women who had a preterm birth with no signs of infection. Laser microdissection enabled enrichment of syncytiotrophoblasts, invasive cytotrophoblasts, or endovascular cytotrophoblasts. After RNA isolation, a microarray approach was used for global transcriptional profiling. Immunolocalization identified changes in messenger RNA expression that carried over to the protein level. Differential expression of non-protein-coding RNAs was confirmed by in situ hybridization. A 2-way analysis of variance of non-coding RNA expression identified particular classes that distinguished trophoblasts in cases vs controls. Cajal body foci were visualized by coilin immunolocalization. RESULTS Comparison of the trophoblast subtype data within each group (severe preeclampsia or noninfected preterm birth) identified many highly differentially expressed genes. They included molecules that are known to be expressed by each subpopulation, which is evidence that the method worked. Genes that were expressed differentially between the 2 groups, in a cell-type-specific manner, encoded a combination of molecules that previous studies associated with severe preeclampsia and those that were not known to be dysregulated in this pregnancy complication. Gene ontology analysis of the syncytiotrophoblast data highlighted the dysregulation of immune functions, morphogenesis, transport, and responses to vascular endothelial growth factor and progesterone. The invasive cytotrophoblast data provided evidence of alterations in cellular movement, which is consistent with the shallow invasion often associated with severe preeclampsia. Other dysregulated pathways included immune, lipid, oxygen, and transforming growth factor-beta responses. The data for endovascular cytotrophoblasts showed disordered metabolism, signaling, and vascular development. Additionally, the transcriptional data revealed the differential expression in severe preeclampsia of 2 classes of non-coding RNAs: long non-coding RNAs and small nucleolar RNAs. The long non-coding RNA, urothelial cancer associated 1, was the most highly up-regulated in this class. In situ hybridization confirmed severe preeclampsia-associated expression in syncytiotrophoblasts. The small nucleolar RNAs, which chemically modify RNA structure, also correlated with severe preeclampsia. Thus, we enumerated Cajal body foci, sites of small nucleolar RNA activity, in primary cytotrophoblasts that were isolated from control and severe preeclampsia placentas. In severe preeclampsia, cytotrophoblasts had approximately double the number of these foci as the control samples. CONCLUSION A laser microdissection approach enabled the identification of novel messenger RNAs and non-coding RNAs that were misexpressed by various trophoblast subpopulations in severe preeclampsia. The results suggested new avenues of investigation, in particular, the roles of PRG2, Kell blood group determinants, and urothelial cancer associated 1 in syncytiotrophoblast diseases. Additionally, many of the newly identified dysregulated molecules might have clinical utility as biomarkers of severe preeclampsia.
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Affiliation(s)
- Matthew Gormley
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology, and Reproductive Sciences; The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research; and the Department of Anatomy, University of California San Francisco, San Francisco, CA
| | - Katherine Ona
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology, and Reproductive Sciences; The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research; and the Department of Anatomy, University of California San Francisco, San Francisco, CA
| | - Mirhan Kapidzic
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology, and Reproductive Sciences; The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research; and the Department of Anatomy, University of California San Francisco, San Francisco, CA
| | - Tamara Garrido-Gomez
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology, and Reproductive Sciences; The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research; and the Department of Anatomy, University of California San Francisco, San Francisco, CA
| | - Tamara Zdravkovic
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology, and Reproductive Sciences; The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research; and the Department of Anatomy, University of California San Francisco, San Francisco, CA
| | - Susan J Fisher
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology, and Reproductive Sciences; The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research; and the Department of Anatomy, University of California San Francisco, San Francisco, CA.
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Yordanov YS, Ma C, Yordanova E, Meilan R, Strauss SH, Busov VB. BIG LEAF is a regulator of organ size and adventitious root formation in poplar. PLoS One 2017; 12:e0180527. [PMID: 28686626 PMCID: PMC5501567 DOI: 10.1371/journal.pone.0180527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/17/2017] [Indexed: 01/08/2023] Open
Abstract
Here we report the discovery through activation tagging and subsequent characterization of the BIG LEAF (BL) gene from poplar. In poplar, BL regulates leaf size via positively affecting cell proliferation. Up and downregulation of the gene led to increased and decreased leaf size, respectively, and these phenotypes corresponded to increased and decreased cell numbers. BL function encompasses the early stages of leaf development as native BL expression was specific to the shoot apical meristem and leaf primordia and was absent from the later stages of leaf development and other organs. Consistently, BL downregulation reduced leaf size at the earliest stages of leaf development. Ectopic expression in mature leaves resulted in continued growth most probably via sustained cell proliferation and thus the increased leaf size. In contrast to the positive effect on leaf growth, ectopic BL expression in stems interfered with and significantly reduced stem thickening, suggesting that BL is a highly specific activator of growth. In addition, stem cuttings from BL overexpressing plants developed roots, whereas the wild type was difficult to root, demonstrating that BL is a positive regulator of adventitious rooting. Large transcriptomic changes in plants that overexpressed BL indicated that BL may have a broad integrative role, encompassing many genes linked to organ growth. We conclude that BL plays a fundamental role in control of leaf size and thus may be a useful tool for modifying plant biomass productivity and adventitious rooting.
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Affiliation(s)
- Yordan S. Yordanov
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois, United States of America
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, United States of America
| | - Elena Yordanova
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois, United States of America
| | - Richard Meilan
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, United States of America
| | - Victor B. Busov
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
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Ccorahua-Santo R, Eca A, Abanto M, Guerra G, Ramírez P. Physiological and comparative genomic analysis of Acidithiobacillus ferrivorans PQ33 provides psychrotolerant fitness evidence for oxidation at low temperature. Res Microbiol 2017; 168:482-492. [DOI: 10.1016/j.resmic.2017.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/24/2022]
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Khomtchouk BB, Hennessy JR, Wahlestedt C. shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics. PLoS One 2017; 12:e0176334. [PMID: 28493881 PMCID: PMC5426587 DOI: 10.1371/journal.pone.0176334] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/10/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps. RESULTS We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Also, shinyheatmap features a built-in high performance web plug-in, fastheatmap, for rapidly plotting interactive heatmaps of datasets as large as 105-107 rows within seconds, effectively shattering previous performance benchmarks of heatmap rendering speed. CONCLUSIONS shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap. Users can access fastheatmap directly from within the shinyheatmap web interface, and all source code has been made publicly available on Github: https://github.com/Bohdan-Khomtchouk/fastheatmap.
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Affiliation(s)
- Bohdan B. Khomtchouk
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave., Miami, FL, 33136, United States of America
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th St., Miami, FL, 33136, United States of America
| | - James R. Hennessy
- Department of Mathematics, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33146, United States of America
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave., Miami, FL, 33136, United States of America
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th St., Miami, FL, 33136, United States of America
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Borriello F, Iannone R, Di Somma S, Vastolo V, Petrosino G, Visconte F, Raia M, Scalia G, Loffredo S, Varricchi G, Galdiero MR, Granata F, Del Vecchio L, Portella G, Marone G. Lipopolysaccharide-Elicited TSLPR Expression Enriches a Functionally Discrete Subset of Human CD14+CD1c+Monocytes. THE JOURNAL OF IMMUNOLOGY 2017; 198:3426-3435. [DOI: 10.4049/jimmunol.1601497] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/24/2017] [Indexed: 12/26/2022]
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Bhatnagar N, Min MK, Choi EH, Kim N, Moon SJ, Yoon I, Kwon T, Jung KH, Kim BG. The protein phosphatase 2C clade A protein OsPP2C51 positively regulates seed germination by directly inactivating OsbZIP10. PLANT MOLECULAR BIOLOGY 2017; 93:389-401. [PMID: 28000033 DOI: 10.1007/s11103-016-0568-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 11/26/2016] [Indexed: 05/20/2023]
Abstract
Protein phosphatase 2C clade A members are major signaling components in the ABA-dependent signaling cascade that regulates seed germination. To elucidate the role of PP2CA genes in germination of rice seed, we selected OsPP2C51, which shows highly specific expression in the embryo compared with other protein phosphatases based on microarray data. GUS histochemical assay confirmed that OsPP2C51 is expressed in the seed embryo and that this expression pattern is unique compared with those of other OsPP2CA genes. Data obtained from germination assays and alpha-amylase assays of OsPP2C51 knockout and overexpression lines suggest that OsPP2C51 positively regulates seed germination in rice. The expression of alpha-amylase synthesizing genes was high in OsPP2C51 overexpressing plants, suggesting that elevated levels of OsPP2C51 might enhance gene expression related to higher rates of seed germination. Analysis of protein interactions between ABA signaling components showed that OsPP2C51 interacts with OsPYL/RCAR5 in an ABA-dependent manner. Furthermore, interactions were observed between OsPP2C51 and SAPK2, and between OsPP2C51 and OsbZIP10 and we found out that OsPP2C51 can dephosphorylates OsbZIP10. These findings suggest the existence of a new branch in ABA signaling pathway consisting of OsPYL/RCAR-OsPP2C-bZIP apart from the previously reported OsPYL/RCAR-OsPP2C-SAPK-bZIP. Overall, our result suggests that OsPP2C51 is a positive regulator of seed germination by directly suppressing active phosphorylated OsbZIP10.
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Affiliation(s)
- Nikita Bhatnagar
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 466-701, South Korea
| | - Myung-Ki Min
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Eun-Hye Choi
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Namhyo Kim
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Seok-Jun Moon
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Insun Yoon
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Taekryoun Kwon
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 466-701, South Korea
| | - Beom-Gi Kim
- Gene Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea.
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Xiang T, Yang G, Liu X, Zhou Y, Fu Z, Lu F, Gu J, Taniguchi N, Tan Z, Chen X, Xie Y, Guan F, Zhang XL. Alteration of N-glycan expression profile and glycan pattern of glycoproteins in human hepatoma cells after HCV infection. Biochim Biophys Acta Gen Subj 2017; 1861:1036-1045. [PMID: 28229927 DOI: 10.1016/j.bbagen.2017.02.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/09/2017] [Accepted: 02/11/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection causes chronic liver diseases, liver fibrosis and even hepatocellular carcinoma (HCC). However little is known about any information of N-glycan pattern in human liver cell after HCV infection. METHODS The altered profiles of N-glycans in HCV-infected Huh7.5.1 cell were analyzed by using mass spectrometry. Then, lectin microarray, lectin pull-down assay, reverse transcription-quantitative real time PCR (RT-qPCR) and western-blotting were used to identify the altered N-glycosylated proteins and glycosyltransferases. RESULTS Compared to uninfected cells, significantly elevated levels of fucosylated, sialylated and complex N-glycans were found in HCV infected cells. Furthermore, Lens culinaris agglutinin (LCA)-binding glycoconjugates were increased most. Then, the LCA-agarose was used to precipitate the specific glycosylated proteins and identify that fucosylated modified annexin A2 (ANXA2) and heat shock protein 90 beta family member 1 (HSP90B1) was greatly increased in HCV-infected cells. However, the total ANXA2 and HSP90B1 protein levels remained unchanged. Additionally, we screened the mRNA expressions of 47 types of different glycosyltransferases and found that α1,6-fucosyltransferase 8 (FUT8) was the most up-regulated and contributed to strengthen the LCA binding capability to fucosylated modified ANXA2 and HSP90B1 after HCV infection. CONCLUSIONS HCV infection caused the altered N-glycans profiles, increased expressions of FUT8, fucosylated ANXA2 and HSP90B1 as well as enhanced LCA binding to Huh7.5.1. GENERAL SIGNIFICANCE Our results may lay the foundation for clarifying the role of N-glycans and facilitate the development of novel diagnostic biomarkers and therapeutic targets based on the increased FUT8, fucosylated ANXA2 and HSP90B1 after HCV infection.
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Affiliation(s)
- Tian Xiang
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Ganglong Yang
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyu Liu
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Yidan Zhou
- University of Illinois at Urbana-Champaign, School of Molecular and Cellular Biology, Department of Microbiology, IL 61801, USA
| | - Zhongxiao Fu
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Fangfang Lu
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Jianguo Gu
- Division of Regulatory Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aobaku, Sendai, Miyagi 981-8558, Japan
| | - Naoyuki Taniguchi
- Systems Glycobiology Group, Global Research Cluster, RIKEN and RIKEN-Max Planck Joint Research Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Zengqi Tan
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xi Chen
- Wuhan Institute of Biotechnology, Medical Research Institute of Wuhan University, Wuhan 430071, China
| | - Yan Xie
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Feng Guan
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology. Hubei province Key Laboratory of Allergy and Immune-related diseases, Medical Research Institute, Department of Immunology of Wuhan University School of Basic Medical Sciences, Wuhan 430071, China.
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Kumar M, Gho YS, Jung KH, Kim SR. Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:1120. [PMID: 28713404 PMCID: PMC5491850 DOI: 10.3389/fpls.2017.01120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/09/2017] [Indexed: 05/14/2023]
Abstract
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.
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Affiliation(s)
- Manu Kumar
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
| | - Seong-Ryong Kim
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
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Abstract
Quantitative proteomics represents a powerful approach for the comprehensive analysis of proteins expressed under defined conditions. These properties have been used to investigate the proteome of disease states, including cancer. It has become a major subject of studies to apply proteomics for biomarker and therapeutic target identification. In the last decades, technical advances in mass spectrometry have increased the capacity of protein identification and quantification. Moreover, the analysis of posttranslational modification (PTM), especially phosphorylation, has allowed large-scale identification of biological mechanisms. Even so, increasing evidence indicates that global protein quantification is often insufficient for the explanation of biology and has shown to pose challenges in identifying new and robust biomarkers. As a consequence, to improve the accuracy of the discoveries made using proteomics in human tumors, it is necessary to combine (i) robust and reproducible methods for sample preparation allowing statistical comparison, (ii) PTM analyses in addition to global proteomics for additional levels of knowledge, and (iii) use of bioinformatics for decrypting protein list. Herein, we present technical specificities for samples preparation involving isobaric tag labeling, TiO2-based phosphopeptides enrichment and hydrazyde-based glycopeptides purification as well as the key points for the quantitative analysis and interpretation of the protein lists. The method is based on our experience with tumors analysis derived from hepatocellular carcinoma, chondrosarcoma, human embryonic intervertebral disk, and chordoma experiments.
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Khomtchouk BB, Hennessy JR, Wahlestedt C. MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. BMC Bioinformatics 2016; 17:390. [PMID: 27659774 PMCID: PMC5034416 DOI: 10.1186/s12859-016-1260-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 09/14/2016] [Indexed: 11/10/2022] Open
Abstract
Background Heatmaps are an indispensible visualization tool for examining large-scale snapshots of genomic activity across various types of next-generation sequencing datasets. However, traditional heatmap software do not typically offer multi-scale insight across multiple layers of genomic analysis (e.g., differential expression analysis, principal component analysis, gene ontology analysis, and network analysis) or multiple types of next-generation sequencing datasets (e.g., ChIP-seq and RNA-seq). As such, it is natural to want to interact with a heatmap’s contents using an extensive set of integrated analysis tools applicable to a broad array of genomic data types. Results We propose a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis. Conclusions MicroScope is hosted online as an R Shiny web application based on the D3 JavaScript library: http://microscopebioinformatics.org/. The methods are implemented in R, and are available as part of the MicroScope project at: https://github.com/Bohdan-Khomtchouk/Microscope.
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Affiliation(s)
- Bohdan B Khomtchouk
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136, FL, USA.
| | - James R Hennessy
- Department of Mathematics, University of Miami, 1365 Memorial Drive, Coral Gables, 33146, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136, FL, USA
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Huang RL, Su PH, Liao YP, Wu TI, Hsu YT, Lin WY, Wang HC, Weng YC, Ou YC, Huang THM, Lai HC. Integrated Epigenomics Analysis Reveals a DNA Methylation Panel for Endometrial Cancer Detection Using Cervical Scrapings. Clin Cancer Res 2016; 23:263-272. [DOI: 10.1158/1078-0432.ccr-16-0863] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/27/2016] [Accepted: 07/19/2016] [Indexed: 11/16/2022]
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