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Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs. Int J Mol Sci 2017; 18:ijms18020317. [PMID: 28165358 PMCID: PMC5343853 DOI: 10.3390/ijms18020317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/31/2016] [Accepted: 10/08/2016] [Indexed: 12/19/2022] Open
Abstract
This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS) and peptidoglycan (PGN)). Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO) showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs), carrier proteins/membrane transport (approximately 15%), effectors/modulators and cell communication (approximately 11%), nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5%) and intracellular transducers/signal transduction (approximately 5%). Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ) that provides a platform enriched for the study of gene expression in S. aurata with an emphasis upon immunity and the immune response.
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Salehi R, Tsoi SCM, Colazo MG, Ambrose DJ, Robert C, Dyck MK. Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform. J Vis Exp 2017:53754. [PMID: 28190024 PMCID: PMC5352306 DOI: 10.3791/53754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Early embryonic loss is a large contributor to infertility in cattle. Moreover, bovine becomes an interesting model to study human preimplantation embryo development due to their similar developmental process. Although genetic factors are known to affect early embryonic development, the discovery of such factors has been a serious challenge. Microarray technology allows quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. One of the main decisions that have to be made when planning a microarray experiment is whether to use a one- or two-color approach. Two-color design increases technical replication, minimizes variability, improves sensitivity and accuracy as well as allows having loop designs, defining the common reference samples. Although microarray is a powerful biological tool, there are potential pitfalls that can attenuate its power. Hence, in this technical paper we demonstrate an optimized protocol for RNA extraction, amplification, labeling, hybridization of the labeled amplified RNA to the array, array scanning and data analysis using the two-color analysis strategy.
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Affiliation(s)
- Reza Salehi
- Department of Agricultural, Food and Nutritional Science, University of Alberta
| | - Stephen C M Tsoi
- Department of Agricultural, Food and Nutritional Science, University of Alberta
| | | | - Divakar J Ambrose
- Department of Agricultural, Food and Nutritional Science, University of Alberta; Livestock Research Branch, Alberta Agriculture and Forestry
| | - Claude Robert
- Laboratory of Functional Genomics of Early Embryonic Development, Université Laval
| | - Michael K Dyck
- Department of Agricultural, Food and Nutritional Science, University of Alberta;
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Furuse T, Miyake K, Kohda T, Kaneda H, Hirasawa T, Yamada I, Kushida T, Kashimura M, Kobayashi K, Ishino F, Kubota T, Wakana S. Protein-restricted diet during pregnancy after insemination alters behavioral phenotypes of the progeny. GENES AND NUTRITION 2017; 12:1. [PMID: 28127411 PMCID: PMC5248510 DOI: 10.1186/s12263-016-0550-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/31/2016] [Indexed: 01/23/2023]
Abstract
Background Epidemiological studies suggest that hyponutrition during the fetal period increases the risk of mental disorders such as attention deficit hyperactivity disorder and autism-spectrum disorder, which has been experimentally supported using animal models. However, previous experimental hyponutrition or protein-restricted (PR) diets affected stages other than the fetal stage, such as formation of the egg before insemination, milk composition during lactation, and maternal nursing behavior. Results We conducted in vitro fertilization and embryo transfer in mice and allowed PR diet and folic acid-supplemented PR diet to affect only fetal environments. Comprehensive phenotyping of PR and control-diet progenies showed moderate differences in fear/anxiety-like, novelty-seeking, and prosocial behaviors, irrespective of folic-acid supplementation. Changes were also detected in gene expression and genomic methylation in the brain. Conclusions These results suggest that epigenetic factors in the embryo/fetus influence behavioral and epigenetic phenotypes of progenies. Significant epigenetic alterations in the brains of the progenies induced by the maternal-protein restriction were observed in the present study. To our knowledge, this is first study to evaluate the effect of maternal hyponutrition on behavioral phenotypes using reproductive technology. Electronic supplementary material The online version of this article (doi:10.1186/s12263-016-0550-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamio Furuse
- Japan mouse clinic, RIKEN BRC, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Kunio Miyake
- Department of Epigenetic Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan
| | - Takashi Kohda
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8510 Japan
| | - Hideki Kaneda
- Japan mouse clinic, RIKEN BRC, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Takae Hirasawa
- Department of Epigenetic Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan
| | - Ikuko Yamada
- Japan mouse clinic, RIKEN BRC, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Tomoko Kushida
- Japan mouse clinic, RIKEN BRC, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Misho Kashimura
- Japan mouse clinic, RIKEN BRC, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Kimio Kobayashi
- Japan mouse clinic, RIKEN BRC, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8510 Japan
| | - Takeo Kubota
- Department of Epigenetic Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898 Japan
| | - Shigeharu Wakana
- Japan mouse clinic, RIKEN BRC, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
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Wang Y, Zhou Z, Gao J, Wu Y, Xia Z, Zhang H, Wu J. The Mechanisms of Maize Resistance to Fusarium verticillioides by Comprehensive Analysis of RNA-seq Data. FRONTIERS IN PLANT SCIENCE 2016; 7:1654. [PMID: 27867390 PMCID: PMC5096342 DOI: 10.3389/fpls.2016.01654] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/20/2016] [Indexed: 05/21/2023]
Abstract
Fusarium verticillioides is the most commonly reported fungal species responsible for ear rot of maize which substantially reduces grain yield. It also results in a substantial accumulation of mycotoxins that give rise to toxic response when ingested by animals and humans. For inefficient control by chemical and agronomic measures, it thus becomes more desirable to select more resistant varieties. However, the molecular mechanisms underlying the infection process remain poorly understood, which hampers the application of quantitative resistance in breeding programs. Here, we reveal the disease-resistance mechanism of the maize inbred line of BT-1 which displays high resistance to ear rot using RNA high throughput sequencing. By analyzing RNA-seq data from the BT-1 kernels before and after F. verticillioides inoculation, we found that transcript levels of genes associated with key pathways are dramatically changed compared with the control treatment. Differential gene expression in ear rot resistant and susceptible maize was confirmed by RNA microarray and qRT-PCR analyses. Further investigation suggests that the small heat shock protein family, some secondary metabolites, and the signaling pathways of abscisic acid, jasmonic acid, or salicylic acids (SA) may be involved in the pathogen-associated molecular pattern-triggered immunity against F. verticillioides. These data will not only provide new insights into the molecular resistant mechanisms against fungi invading, but may also result in the identification of key molecular factors associated with ear rot resistance in maize.
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Affiliation(s)
| | | | | | | | | | - Huiyong Zhang
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural UniversityZhengzhou, China
| | - Jianyu Wu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural UniversityZhengzhou, China
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Ho NT, Busik JV, Resau JH, Paneth N, Khoo SK. Effect of storage time on gene expression data acquired from unfrozen archived newborn blood spots. Mol Genet Metab 2016; 119:207-213. [PMID: 27553879 PMCID: PMC5083152 DOI: 10.1016/j.ymgme.2016.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/13/2016] [Indexed: 01/11/2023]
Abstract
Unfrozen archived newborn blood spots (NBS) have been shown to retain sufficient messenger RNA (mRNA) for gene expression profiling. However, the effect of storage time at ambient temperature for NBS samples in relation to the quality of gene expression data is relatively unknown. Here, we evaluated mRNA expression from quantitative real-time PCR (qRT-PCR) and microarray data obtained from NBS samples stored at ambient temperature to determine the effect of storage time on the quality of gene expression. These data were generated in a previous case-control study examining NBS in 53 children with cerebral palsy (CP) and 53 matched controls. NBS sample storage period ranged from 3 to 16years at ambient temperature. We found persistently low RNA integrity numbers (RIN=2.3±0.71) and 28S/18S rRNA ratios (~0) across NBS samples for all storage periods. In both qRT-PCR and microarray data, the expression of three common housekeeping genes-beta cytoskeletal actin (ACTB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and peptidylprolyl isomerase A (PPIA)-decreased with increased storage time. Median values of each microarray probe intensity at log2 scale also decreased over time. After eight years of storage, probe intensity values were largely reduced to background intensity levels. Of 21,500 genes tested, 89% significantly decreased in signal intensity, with 13,551, 10,730, and 9925 genes detected within 5years, > 5 to <10years, and >10years of storage, respectively. We also examined the expression of two gender-specific genes (X inactivation-specific transcript, XIST and lysine-specific demethylase 5D, KDM5D) and seven gene sets representing the inflammatory, hypoxic, coagulative, and thyroidal pathways hypothesized to be related to CP risk to determine the effect of storage time on the detection of these biologically relevant genes. We found the gender-specific genes and CP-related gene sets detectable in all storage periods, but exhibited differential expression (between male vs. female or CP vs. control) only within the first six years of storage. We concluded that gene expression data quality deteriorates in unfrozen archived NBS over time and that differential gene expression profiling and analysis is recommended for those NBS samples collected and stored within six years at ambient temperature.
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Affiliation(s)
- Nhan T Ho
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Julia V Busik
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - James H Resau
- Graduate School, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Nigel Paneth
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI, USA; Department of Pediatrics & Human Development, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
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56
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Thomson JM. Impacts of environment on gene expression and epigenetic modification in grazing animals. J Anim Sci 2016. [DOI: 10.2527/jas.2016-0556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Yang MQ, Elnitski L. A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PLoS One 2016; 11:e0163353. [PMID: 27788148 PMCID: PMC5082879 DOI: 10.1371/journal.pone.0163353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 09/07/2016] [Indexed: 12/14/2022] Open
Abstract
Ovarian carcinomas can be aggressive with a high mortality rate (e.g., high-grade serous ovarian carcinomas, or HGSOCs), or indolent with much better long-term outcomes (e.g., low-malignant-potential, or LMP, serous ovarian carcinomas). By comparing LMP and HGSOC tumors, we can gain insight into the mechanisms underlying malignant progression in ovarian cancer. However, previous studies of the two subtypes have been focused on gene expression analysis. Here, we applied a systems biology approach, integrating gene expression profiles derived from two independent data sets containing both LMP and HGSOC tumors with protein-protein interaction data. Genes and related networks implicated by both data sets involved both known and novel disease mechanisms and highlighted the different roles of BRCA1 and CREBBP in the two tumor types. In addition, the incorporation of somatic mutation data revealed that amplification of PAK4 is associated with poor survival in patients with HGSOC. Thus, perturbations in protein interaction networks demonstrate differential trafficking of network information between malignant and benign ovarian cancers. The novel network-based molecular signatures identified here may be used to identify new targets for intervention and to improve the treatment of invasive ovarian cancer as well as early diagnosis.
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Affiliation(s)
- Mary Qu Yang
- MidSouth Bioinformatics Center and Joint Bioinformatics Ph.D. Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2801 S. University Avenue, Little Rock, Arkansas, 72204, United States of America
- * E-mail: (MQY); (LE)
| | - Laura Elnitski
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, 20852, United States of America
- * E-mail: (MQY); (LE)
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Abstract
The revolution of genomic technologies, including gene expression profiling, high-resolution mapping of genomic imbalances, and next-generation sequencing, allows us to establish molecular portraits of cancer cells with unprecedented accuracy. This generates hope and justifies anticipation that disease diagnosis, prognosis, and the choice of treatment will be adapted to the individual needs of patients based on molecular evidence. Preoperative treatment strategies are now recommended for a variety of human cancers. Unfortunately, the response of individual tumors to a preoperative treatment is not uniform, and ranges from complete regression to resistance. This poses a considerable clinical dilemma, as patients with a priori resistant tumors could either be spared exposure to radiation or DNA-damaging drugs, i.e., could be referred to primary surgery, or dose-intensified protocols could be pursued. Because the response of an individual tumor as well as therapy-induced side effects represent the major limiting factors of current treatment strategies, identifying molecular markers of response or for treatment toxicity has become exceedingly important. However, complex phenotypes such as tumor responsiveness to multimodal treatments probably do not depend on the expression levels of just one or a few genes and proteins. Therefore, methods that allow comprehensive interrogation of genetic pathways and networks hold great promise in delivering such tumor-specific signatures, since expression levels of thousands of genes can be monitored simultaneously. Over the past few years, microarray technology has emerged as a central tool in addressing pertinent clinical questions, the answers to which are critical for the realization of a personalized genomic medicine, in which patients will be treated based on the biology of their tumor and their genetic profile (Quackenbush, N Engl J Med 354:2463-72, 2006; Jensen et al., Curr Opin Oncol 18:374-380, 2006; Bol and Ebner, Pharmacogenomics 7:227-235, 2006; Nevins and Potti, Nat Rev Genet 8:601-609, 2007).
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Affiliation(s)
- B Michael Ghadimi
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Georg-August-University, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
| | - Peter Jo
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Georg-August-University, Robert-Koch-Str. 40, 37075, Göttingen, Germany
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Yang W, Rosenstiel PC, Schulenburg H. ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences. BMC Genomics 2016; 17:541. [PMID: 27488180 PMCID: PMC4973090 DOI: 10.1186/s12864-016-2848-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/20/2016] [Indexed: 11/18/2022] Open
Abstract
Background The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inferences of biological functions are built. Yet, for identification of these subsequently analysed genes, most studies use an additional minimal threshold of differential expression that is not captured by the applied statistical procedures. Results Here we introduce a new analysis approach, ABSSeq, which uses a negative binomal distribution to model absolute expression differences between conditions, taking into account variations across genes and samples as well as magnitude of differences. In comparison to alternative methods, ABSSeq shows higher performance on controling type I error rate and at least a similar ability to correctly identify differentially expressed genes. Conclusions ABSSeq specifically considers the overall magnitude of expression differences, which enhances the power in detecting truly differentially expressed genes by reducing false positives at both very low and high expression level. In addition, ABSSeq offers to calculate shrinkage of fold change to facilitate gene ranking and effective outlier detection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2848-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wentao Yang
- Evolutionary Ecology and Genetics, Zoological Institute, CAU Kiel, Am Botanischen Garten 9, 24118, Kiel, Germany.
| | - Philip C Rosenstiel
- Centre for Molecular Biology, Institute for Clinical Molecular Biology, CAU Kiel, Am Botanischen Garten 11, 24118, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, CAU Kiel, Am Botanischen Garten 9, 24118, Kiel, Germany.
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Sun P, Miao H, Yu X, Jia C, Liu J, Zhang J, Wang J, Wang Z, Wang A, Xu B, Jin Z. A Novel Role for Banana MaASR in the Regulation of Flowering Time in Transgenic Arabidopsis. PLoS One 2016; 11:e0160690. [PMID: 27486844 PMCID: PMC4972433 DOI: 10.1371/journal.pone.0160690] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/23/2016] [Indexed: 11/18/2022] Open
Abstract
The abscisic acid (ABA)-, stress-, and ripening-induced (ASR) protein is a plant-specific hydrophilic transcriptional factor involved in fruit ripening and the abiotic stress response. To date, there have been no studies on the role of ASR genes in delayed flowering time. Here, we found that the ASR from banana, designated as MaASR, was preferentially expressed in the banana female flowers from the eighth, fourth, and first cluster of the inflorescence. MaASR transgenic lines (L14 and L38) had a clear delayed-flowering phenotype. The number of rosette leaves, sepals, and pedicel trichomes in L14 and L38 was greater than in the wild type (WT) under long day (LD) conditions. The period of buds, mid-flowers, and full bloom of L14 and L38 appeared later than the WT. cDNA microarray and quantitative real-time PCR (qRT-PCR) analyses revealed that overexpression of MaASR delays flowering through reduced expression of several genes, including photoperiod pathway genes, vernalization pathway genes, gibberellic acid pathway genes, and floral integrator genes, under short days (SD) for 28 d (from vegetative to reproductive transition stage); however, the expression of the autonomous pathway genes was not affected. This study provides the first evidence of a role for ASR genes in delayed flowering time in plants.
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Affiliation(s)
- Peiguang Sun
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 570102, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaomeng Yu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Anbang Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 570102, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- * E-mail: (BX); (ZJ)
| | - Zhiqiang Jin
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 570102, China
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- * E-mail: (BX); (ZJ)
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Kricka LJ. Quality assurance for multiplexed assays - how can it be achieved? Scand J Clin Lab Invest Suppl 2016; 245:S100-3. [PMID: 27454808 DOI: 10.1080/00365513.2016.1210335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Multiplexed assays are now a common form of analysis in routine clinical and research laboratories. Assuring the quality of this type of complex, massively-parallel testing poses challenges not encountered in the traditional single-plex assay. A range of quality assurance measures is implemented at different stages in a multiplex assay, beginning in the manufacturing process, and the ensuing analytical and data interpretation stages. This article explores quality issues and the quality assurance measures that have been devised for multiplex assays ranging from simple two-plex assays to the types of assays that involve simultaneous testing on millions of test sites on a single analytical device.
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Affiliation(s)
- Larry J Kricka
- a Department of Pathology and Laboratory Medicine , University of Pennsylvania Medical Center , Philadelphia , PA , USA
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Nanofiber Alignment Regulates NIH3T3 Cell Orientation and Cytoskeletal Gene Expression on Electrospun PCL+Gelatin Nanofibers. PLoS One 2016; 11:e0154806. [PMID: 27196306 PMCID: PMC4873125 DOI: 10.1371/journal.pone.0154806] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/19/2016] [Indexed: 12/27/2022] Open
Abstract
To examine the influence of substrate topology on the behavior of fibroblasts, tissue engineering scaffolds were electrospun from polycaprolactone (PCL) and a blend of PCL and gelatin (PCL+Gel) to produce matrices with both random and aligned nanofibrous orientations. The addition of gelatin to the scaffold was shown to increase the hydrophilicity of the PCL matrix and to increase the proliferation of NIH3T3 cells compared to scaffolds of PCL alone. The orientation of nanofibers within the matrix did not have an effect on the proliferation of adherent cells, but cells on aligned substrates were shown to elongate and align parallel to the direction of substrate fiber alignment. A microarray of cyotoskeleton regulators was probed to examine differences in gene expression between cells grown on an aligned and randomly oriented substrates. It was found that transcriptional expression of eight genes was statistically different between the two conditions, with all of them being upregulated in the aligned condition. The proteins encoded by these genes are linked to production and polymerization of actin microfilaments, as well as focal adhesion assembly. Taken together, the data indicates NIH3T3 fibroblasts on aligned substrates align themselves parallel with their substrate and increase production of actin and focal adhesion related genes.
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Xu J, Thakkar S, Gong B, Tong W. The FDA's Experience with Emerging Genomics Technologies-Past, Present, and Future. AAPS JOURNAL 2016; 18:814-8. [PMID: 27116022 PMCID: PMC4973466 DOI: 10.1208/s12248-016-9917-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/12/2016] [Indexed: 01/30/2023]
Abstract
The rapid advancement of emerging genomics technologies and their application for assessing safety and efficacy of FDA-regulated products require a high standard of reliability and robustness supporting regulatory decision-making in the FDA. To facilitate the regulatory application, the FDA implemented a novel data submission program, Voluntary Genomics Data Submission (VGDS), and also to engage the stakeholders. As part of the endeavor, for the past 10 years, the FDA has led an international consortium of regulatory agencies, academia, pharmaceutical companies, and genomics platform providers, which was named MicroArray Quality Control Consortium (MAQC), to address issues such as reproducibility, precision, specificity/sensitivity, and data interpretation. Three projects have been completed so far assessing these genomics technologies: gene expression microarrays, whole genome genotyping arrays, and whole transcriptome sequencing (i.e., RNA-seq). The resultant studies provide the basic parameters for fit-for-purpose application of these new data streams in regulatory environments, and the solutions have been made available to the public through peer-reviewed publications. The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on next-generation sequencing. Using reference samples with built-in controls, SEQC studies have demonstrated that relative gene expression can be measured accurately and reliably across laboratories and RNA-seq platforms. Besides prediction performance comparable to microarrays in clinical settings and safety assessments, RNA-seq is shown to have better sensitivity for low expression and reveal novel transcriptomic features. Future effort of MAQC will be focused on quality control of whole genome sequencing and targeted sequencing.
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Affiliation(s)
- Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Shraddha Thakkar
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA.
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Nie Z, Kang G, Duan C, Li Y, Dai L, Zeng R. Profiling Ethylene-Responsive Genes Expressed in the Latex of the Mature Virgin Rubber Trees Using cDNA Microarray. PLoS One 2016; 11:e0152039. [PMID: 26985821 PMCID: PMC4795647 DOI: 10.1371/journal.pone.0152039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 02/22/2016] [Indexed: 12/19/2022] Open
Abstract
Ethylene is commonly used as a latex stimulant of Hevea brasiliensis by application of ethephon (chloro-2-ethylphosphonic acid); however, the molecular mechanism by which ethylene increases latex production is not clear. To better understand the effects of ethylene stimulation on the laticiferous cells of rubber trees, a latex expressed sequence tag (EST)-based complementary DNA microarray containing 2,973 unique genes (probes) was first developed and used to analyze the gene expression changes in the latex of the mature virgin rubber trees after ethephon treatment at three different time-points: 8, 24 and 48 h. Transcript levels of 163 genes were significantly altered with fold-change values ≥ 2 or ≤ –2 (q-value < 0.05) in ethephon-treated rubber trees compared with control trees. Of the 163 genes, 92 were up-regulated and 71 down-regulated. The microarray results were further confirmed using real-time quantitative reverse transcript-PCR for 20 selected genes. The 163 ethylene-responsive genes were involved in several biological processes including organic substance metabolism, cellular metabolism, primary metabolism, biosynthetic process, cellular response to stimulus and stress. The presented data suggest that the laticifer water circulation, production and scavenging of reactive oxygen species, sugar metabolism, and assembly and depolymerization of the latex actin cytoskeleton might play important roles in ethylene-induced increase of latex production. The results may provide useful insights into understanding the molecular mechanism underlying the effect of ethylene on latex metabolism of H. brasiliensis.
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Affiliation(s)
- Zhiyi Nie
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Guijuan Kang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Cuifang Duan
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Yu Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Longjun Dai
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Rizhong Zeng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
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65
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Xu X, Li H. Integrated microRNA‑gene analysis of coronary artery disease based on miRNA and gene expression profiles. Mol Med Rep 2016; 13:3063-73. [PMID: 26936111 PMCID: PMC4805068 DOI: 10.3892/mmr.2016.4936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/12/2016] [Indexed: 12/14/2022] Open
Abstract
The present study aimed to investigate the key genes and microRNAs (miRNA/miRs) associated with coronary artery disease (CAD) progression. The gene expression profile of GSE20680 and GSE12288, and the miRNA expression profile of GSE28858 were downloaded from the gene expression omnibus database. The differentially expressed genes (DEGs) in GSE20680 and GSE12288, and the differentially expressed miRNAs in GSE28858 were screened using the limma package in R software. Common DEGs between GSE20680 and GSE12288 were selected. Functions and pathways of DEGs and miRNAs were enriched using the DAVID tool from the GO and KEGG databases. The regulatory network of miRNA and selected CAD-associated DEGs was constructed. A total of 270 DEGs (167 upregulated and 103 downregulated) based on the GSE20680 dataset, and 2,268 DEGs (534 upregulated and 1,734 downregulated) based on the GSE12288 dataset, were screened. For the differentially expressed miRNAs, 214 were identified (102 upregulated and 112 downregulated) in CAD samples and were screened. Interferon regulatory factor 2 (IRF2) and cell death-inducing DFFA-like effector b (CIDEB), which are regulated by signal transducer and activator of transcription 3 and myc-associated factor X, were identified as common DEGs for CAD. miR-455-5p, miR-455-3p and miR-1257, which are involved in the major histocompatibility complex (MHC)protein assembly pathway and peptide antigen assembly with MHC class I protein complex pathway, may regulate various miRNAs and target genes, including pro-opiomelancortin (POMC), toll-like receptor 4 (TLR4), interleukin 10 (IL10), activating transcription factor 6 (ATF6) and calreticulin (CALR). The current study identified IRF2 and CIDEB as crucial genes, and miRNA-455-5p, miRNA-455-3p and miR-1257 along with their target genes POMC, TLR4 and CALR, as miRNAs involved in CAD progression. Thus, the present study may provide a basis for future research into the progression mechanism of CAD.
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Affiliation(s)
- Xiangdong Xu
- Vasculocardiology Department, Jiading Central Hospital, Shanghai 201800, P.R China
| | - Hongsong Li
- Vasculocardiology Department, Jiading Central Hospital, Shanghai 201800, P.R China
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66
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Tu S, Guo SJ, Chen CS, Liu CX, Jiang HW, Ge F, Deng JY, Zhou YM, Czajkowsky DM, Li Y, Qi BR, Ahn YH, Cole PA, Zhu H, Tao SC. YcgC represents a new protein deacetylase family in prokaryotes. eLife 2015; 4. [PMID: 26716769 PMCID: PMC4709262 DOI: 10.7554/elife.05322] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 10/28/2015] [Indexed: 01/08/2023] Open
Abstract
Reversible lysine acetylation is one of the most important protein posttranslational modifications that plays essential roles in both prokaryotes and eukaryotes. However, only a few lysine deacetylases (KDACs) have been identified in prokaryotes, perhaps in part due to their limited sequence homology. Herein, we developed a ‘clip-chip’ strategy to enable unbiased, activity-based discovery of novel KDACs in the Escherichia coli proteome. In-depth biochemical characterization confirmed that YcgC is a serine hydrolase involving Ser200 as the catalytic nucleophile for lysine deacetylation and does not use NAD+ or Zn2+ like other established KDACs. Further, in vivo characterization demonstrated that YcgC regulates transcription by catalyzing deacetylation of Lys52 and Lys62 of a transcriptional repressor RutR. Importantly, YcgC targets a distinct set of substrates from the only known E. coli KDAC CobB. Analysis of YcgC’s bacterial homologs confirmed that they also exhibit KDAC activity. YcgC thus represents a novel family of prokaryotic KDACs. DOI:http://dx.doi.org/10.7554/eLife.05322.001 After proteins have been made, they can be modified in several ways. For example, chemical tags called acetyl groups may be added to (and later removed from) the protein to regulate cell activities such as aging and metabolism. Enzymes are proteins that help catalyze the reactions that add or remove the acetyl tags on certain “substrate” proteins. In the bacteria species Escherichia coli, many enzymes that help to add acetyl groups to proteins have been discovered. However, only a single E. coli “deacetylase” enzyme that removes the acetyl group has been identified. Now, Tu, Guo, Chen et al. have devised a technique to identify new deacetylases, called the “clip-chip” approach. In this method, thousands of proteins that are potential deacetylases are arrayed on a glass slide, and substrate proteins are immobilized on another slide. The two slides are then clipped together face-to-face, allowing the potential enzymes to transfer to the substrate slide and interact with the substrates. Using this approach, Tu, Guo, Chen et al. identified a protein called YcgC as a deacetylase in bacteria. Further characterization experiments revealed that YcgC works in a different way to other known deacetylases, and that it targets different substrates to the previously known E. coli deacetylase. Tu, Guo, Chen et al. found that the equivalents of YcgC in other bacteria species are also deacetylases; these enzymes therefore represent a new deacetylase family. In the future, the clip-chip approach could be used to discover new members of other enzyme families. DOI:http://dx.doi.org/10.7554/eLife.05322.002
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Affiliation(s)
- Shun Tu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
| | - Cheng-Xi Liu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jiao-Yu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yi-Ming Zhou
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Bang-Ruo Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Young-Hoon Ahn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, United States.,The High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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67
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Wang Y, Shen W, Chan Z, Wu Y. Endogenous Cytokinin Overproduction Modulates ROS Homeostasis and Decreases Salt Stress Resistance in Arabidopsis Thaliana. FRONTIERS IN PLANT SCIENCE 2015; 6:1004. [PMID: 26635831 PMCID: PMC4652137 DOI: 10.3389/fpls.2015.01004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/30/2015] [Indexed: 05/20/2023]
Abstract
Cytokinins in plants are crucial for numerous biological processes, including seed germination, cell division and differentiation, floral initiation and adaptation to abiotic stresses. The salt stress can promote reactive oxygen species (ROS) production in plants which are highly toxic and ultimately results in oxidative stress. However, the correlation between endogenous cytokinin production and ROS homeostasis in responding to salt stress is poorly understood. In this study, we analyzed the correlation of overexpressing the cytokinin biosynthetic gene AtIPT8 (adenosine phosphate-isopentenyl transferase 8) and the response of salt stress in Arabidopsis. Overproduction of cytokinins, which was resulted by the inducible overexpression of AtIPT8, significantly inhibited the primary root growth and true leaf emergence, especially under the conditions of exogenous salt, glucose and mannitol treatments. Upon cytokinin overproduction, the salt stress resistance was declined, and resulted in less survival rates and chlorophyll content. Interestingly, ROS production was obviously increased with the salt treatment, accompanied by endogenously overproduced cytokinins. The activities of catalase (CAT) and superoxide dismutase (SOD), which are responsible for scavenging ROS, were also affected. Transcription profiling revealed that the differential expressions of ROS-producing and scavenging related genes, the photosynthesis-related genes and stress responsive genes were existed in transgenic plants of overproducing cytokinins. Our results suggested that broken in the homeostasis of cytokinins in plant cells could modulate the salt stress responses through a ROS-mediated regulation in Arabidopsis.
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Affiliation(s)
- Yanping Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Wenzhong Shen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
| | - Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Yan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
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68
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Zheng Y, Qing T, Song Y, Zhu J, Yu Y, Shi W, Pusztai L, Shi L. Standardization efforts enabling next-generation sequencing and microarray based biomarkers for precision medicine. Biomark Med 2015; 9:1265-72. [PMID: 26502353 DOI: 10.2217/bmm.15.99] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Microarrays and next-generation sequencing technologies have been increasingly employed in biomedical research. However, before they can be reliably used as clinical biomarker tests, standardization and quality control measures need to be developed to ensure their analytical validity. This review summarizes community-wide efforts such as the MicroArray and Sequencing Quality Control (MAQC/SEQC) project which have identified factors influencing the performance of these technologies. Consequently, consensus-based standards and well-documented best practices have been developed to improve the quality of scientific research, and reference materials and reference datasets have been made available for evaluating the technical proficiency in future studies. These efforts have built the foundation on which the translational application of genomics based technologies can help realize precision medicine.
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Affiliation(s)
- Yuanting Zheng
- Center for Pharmacogenomics & Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Tao Qing
- Center for Pharmacogenomics & Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Yunjie Song
- Center for Pharmacogenomics & Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Jinhang Zhu
- Center for Pharmacogenomics & Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Ying Yu
- Collaborative Innovation Center for Genetics & Development, State Key Laboratory of Genetic Engineering & MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Weiwei Shi
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Lajos Pusztai
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Leming Shi
- Center for Pharmacogenomics & Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China.,Collaborative Innovation Center for Genetics & Development, State Key Laboratory of Genetic Engineering & MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
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69
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Iresjö BM, Wang W, Nilsberth C, Andersson M, Lönnroth C, Smedh U. Food intake, tumor growth, and weight loss in EP2 receptor subtype knockout mice bearing PGE2-producing tumors. Physiol Rep 2015. [PMID: 26197930 PMCID: PMC4552524 DOI: 10.14814/phy2.12441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Previous studies in our laboratory have demonstrated that prostaglandin (PG) E2 is involved in anorexia/cachexia development in MCG 101 tumor-bearing mice. In the present study, we investigate the role of PGE receptor subtype EP2 in the development of anorexia after MCG 101 implantation in wild-type (EP2+/+) or EP2-receptor knockout (EP2−/−) mice. Our results showed that host absence of EP2 receptors attenuated tumor growth and development of anorexia in tumor-bearing EP2 knockout mice compared to tumor-bearing wild-type animals. Microarray profiling of the hypothalamus revealed a relative twofold change in expression of around 35 genes including mRNA transcripts coding for Phospholipase A2 and Prostaglandin D2 synthase (Ptgds) in EP2 receptor knockout mice compared to wild-type mice. Prostaglandin D2 synthase levels were increased significantly in EP2 receptor knockouts, suggesting that improved food intake may depend on altered balance of prostaglandin production in hypothalamus since PGE2 and PGD2 display opposing effects in feeding control.
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Affiliation(s)
- Britt-Marie Iresjö
- Surgical Metabolic Research Laboratory, Department of Surgery, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Wenhua Wang
- Surgical Metabolic Research Laboratory, Department of Surgery, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Camilla Nilsberth
- Department of Geriatric Medicine and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Marianne Andersson
- Surgical Metabolic Research Laboratory, Department of Surgery, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christina Lönnroth
- Surgical Metabolic Research Laboratory, Department of Surgery, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ulrika Smedh
- Surgical Metabolic Research Laboratory, Department of Surgery, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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70
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Identification of Alzheimer's disease-associated long noncoding RNAs. Neurobiol Aging 2015; 36:2925-2931. [PMID: 26318290 DOI: 10.1016/j.neurobiolaging.2015.07.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 06/24/2015] [Accepted: 07/08/2015] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is the most common dementia among the elderly that involves complex neurodegenerative alterations. Multiple cellular processes including regulation of amyloid-β peptide, tau, inflammation, and cell death have been suggested to associate with AD, but it remains largely unknown if long noncoding RNAs (lncRNAs) may be playing a role in AD pathogenesis. Here, we identify AD-associated lncRNAs by reannotation of microarray data based on postmortem tissue samples of AD patients and matched elderly controls. We found 24 upregulated and 84 downregulated lncRNAs in AD patients compared with controls, most being intergenic. An analysis of lncRNAs in various tissues indicated that most downregulated lncRNAs in AD are highly expressed in the brain but not in other tissues. Gene set enrichment analysis identified a downregulated lncRNA n341006 in association with protein ubiquitination pathway, and a significantly upregulated lncRNA n336934 linked to cholesterol homeostasis. Interestingly, lncRNA expression signatures could predict tissue types with equal accuracy as protein-coding genes, but the number of lncRNAs required for optimal prediction was less than protein-coding genes. Taken together, our study provides a resource for AD-associated lncRNAs for the development of lncRNA biomarkers and the identification of functional lncRNAs involved in AD pathogenesis.
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71
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Bentley PA, Wall EH, Dahl GE, McFadden TB. Responses of the mammary transcriptome of dairy cows to altered photoperiod during late gestation. Physiol Genomics 2015; 47:488-99. [PMID: 26175502 DOI: 10.1152/physiolgenomics.00112.2014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 07/13/2015] [Indexed: 11/22/2022] Open
Abstract
Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day nonlactating period prior to parturition produce more milk in their subsequent lactation compared with cows exposed to long day photoperiod (LD, 16L:8D). Although this response is well established in dairy cows, the underlying mechanisms are not understood. We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation. Pregnant, multiparous cows were maintained on an SD or LD photoperiod for 60 days prior to parturition. Mammary biopsies were obtained on days -24 and -9 relative to parturition and Affymetrix GeneChip Bovine Genome Arrays were used to quantify gene expression. Sixty-four genes were differentially expressed (P ≤ 0.05 and fold-change ≥ |1.5|) between SD and LD treatments. Many of these genes were associated with cell growth and proliferation, or immune function. Ingenuity Pathway Analysis predicted upstream regulators to include TNF, TGF-β1, interferon-γ, and several interleukins. In addition, expression of 125 genes was significantly different between day -24 and day -9; those genes were associated with milk component metabolism and immune function. The interaction of photoperiod and time affected 32 genes associated with insulin-like growth factor I signaling. Genes differentially expressed in response to photoperiod were associated with mammary development and immune function consistent with the enhancement of milk yield in the ensuing lactation. Our results provide insight into the mechanisms by which photoperiod affects the mammary gland and subsequently lactation.
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Affiliation(s)
- P A Bentley
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - E H Wall
- Department of Animal Science, University of Vermont, Burlington, Vermont
| | - G E Dahl
- Department of Animal Sciences, University of Florida, Gainesville, Florida; and
| | - T B McFadden
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada; Department of Animal Science, University of Vermont, Burlington, Vermont; Division of Animal Sciences, University of Missouri, Columbia, Missouri
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72
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Teoh JP, Park KM, Broskova Z, Jimenez FR, Bayoumi AS, Archer K, Su H, Johnson J, Weintraub NL, Tang Y, Kim IM. Identification of gene signatures regulated by carvedilol in mouse heart. Physiol Genomics 2015; 47:376-85. [PMID: 26152686 DOI: 10.1152/physiolgenomics.00028.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/06/2015] [Indexed: 01/14/2023] Open
Abstract
Chronic treatment with the β-blocker carvedilol has been shown to reduce established maladaptive left ventricle (LV) hypertrophy and to improve LV function in experimental heart failure. However, the detailed mechanisms by which carvedilol improves LV failure are incompletely understood. We previously showed that carvedilol is a β-arrestin-biased β1-adrenergic receptor ligand, which activates cellular pathways in the heart independent of G protein-mediated second messenger signaling. More recently, we have demonstrated by microRNA (miR) microarray analysis that carvedilol upregulates a subset of mature and pre-mature miRs, but not their primary miR transcripts in mouse hearts. Here, we next sought to identify the effects of carvedilol on LV gene expression on a genome-wide basis. Adult mice were treated with carvedilol or vehicle for 1 wk. RNA was isolated from LV tissue and hybridized for microarray analysis. Gene expression profiling analysis revealed a small group of genes differentially expressed after carvedilol treatment. Further analysis categorized these genes into pathways involved in tight junction, malaria, viral myocarditis, glycosaminoglycan biosynthesis, and arrhythmogenic right ventricular cardiomyopathy. Genes encoding proteins in the tight junction, malaria, and viral myocarditis pathways were upregulated in the LV by carvedilol, while genes encoding proteins in the glycosaminoglycan biosynthesis and arrhythmogenic right ventricular cardiomyopathy pathways were downregulated by carvedilol. These gene expression changes may reflect the molecular mechanisms that underlie the functional benefits of carvedilol therapy.
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Affiliation(s)
- Jian-Peng Teoh
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Kyoung-Mi Park
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Zuzana Broskova
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Felix R Jimenez
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Ahmed S Bayoumi
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Krystal Archer
- Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia; and
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia; Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - John Johnson
- Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Neal L Weintraub
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia; Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia; and
| | - Yaoliang Tang
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia; Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia; and
| | - Il-Man Kim
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
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73
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Li HH, Hyduke DR, Chen R, Heard P, Yauk CL, Aubrecht J, Fornace AJ. Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:505-19. [PMID: 25733355 PMCID: PMC4506269 DOI: 10.1002/em.21941] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/19/2015] [Indexed: 05/11/2023]
Abstract
The development of in vitro molecular biomarkers to accurately predict toxicological effects has become a priority to advance testing strategies for human health risk assessment. The application of in vitro transcriptomic biomarkers promises increased throughput as well as a reduction in animal use. However, the existing protocols for predictive transcriptional signatures do not establish appropriate guidelines for dose selection or account for the fact that toxic agents may have pleiotropic effects. Therefore, comparison of transcriptome profiles across agents and studies has been difficult. Here we present a dataset of transcriptional profiles for TK6 cells exposed to a battery of well-characterized genotoxic and nongenotoxic chemicals. The experimental conditions applied a new dose optimization protocol that was based on evaluating expression changes in several well-characterized stress-response genes using quantitative real-time PCR in preliminary dose-finding studies. The subsequent microarray-based transcriptomic analyses at the optimized dose revealed responses to the test chemicals that were typically complex, often exhibiting substantial overlap in the transcriptional responses between a variety of the agents making analysis challenging. Using the nearest shrunken centroids method we identified a panel of 65 genes that could accurately classify toxicants as genotoxic or nongenotoxic. To validate the 65-gene panel as a genomic biomarker of genotoxicity, the gene expression profiles of an additional three well-characterized model agents were analyzed and a case study demonstrating the practical application of this genomic biomarker-based approach in risk assessment was performed to demonstrate its utility in genotoxicity risk assessment.
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Affiliation(s)
- Heng-Hong Li
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
| | - Daniel R. Hyduke
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
- Biological Engineering Department, Utah State University, Logan, UT 84321
| | - Renxiang Chen
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
| | - Pamela Heard
- Pfizer Global Research and Development, Drug Safety Research and Development, Eastern Point Road, Groton, CT 06340
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Jiri Aubrecht
- Pfizer Global Research and Development, Drug Safety Research and Development, Eastern Point Road, Groton, CT 06340
| | - Albert J. Fornace
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
- To whom correspondence should be addressed at: Lombardi Comprehensive Cancer Center, 3970 Reservoir Rd. NW, Room E504, Washington, DC 20057. Fax: (202) 687-3140.,
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74
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Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes. Sci Rep 2015; 5:11763. [PMID: 26123364 PMCID: PMC4485256 DOI: 10.1038/srep11763] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/03/2015] [Indexed: 12/26/2022] Open
Abstract
The gut microbiota is commonly referred to as a hidden organ due to its pivotal effects on host physiology, metabolism, nutrition and immunity. The gut microbes may be shaped by environmental and host genetic factors, and previous studies have focused on the roles of protein-coding genes. Here we show a link between long non-coding RNA (lncRNA) expression and gut microbes. By repurposing exon microarrays and comparing the lncRNA expression profiles between germ-free, conventional and different gnotobiotic mice, we revealed subgroups of lncRNAs that were specifically enriched in each condition. A nearest shrunken centroid methodology was applied to obtain lncRNA-based signatures to identify mice in different conditions. The lncRNA-based prediction model successfully identified different gnotobiotic mice from conventional and germ-free mice, and also discriminated mice harboring transplanted microbes from fecal samples of mice or zebra fishes. To achieve optimal prediction accuracy, fewer lncRNAs were required in the prediction model than protein-coding genes. Taken together, our study demonstrated the effecacy of lncRNA expression profiles in discriminating the types of microbes in the gut. These results also provide a resource of gut microbe-associated lncRNAs for the development of lncRNA biomarkers and the identification of functional lncRNAs in host-microbes interactions.
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75
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Yang J, Fu Z, Hong Y, Wu H, Jin Y, Zhu C, Li H, Lu K, Shi Y, Yuan C, Cheng G, Feng X, Liu J, Lin J. The Differential Expression of Immune Genes between Water Buffalo and Yellow Cattle Determines Species-Specific Susceptibility to Schistosoma japonicum Infection. PLoS One 2015; 10:e0130344. [PMID: 26125181 PMCID: PMC4488319 DOI: 10.1371/journal.pone.0130344] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/19/2015] [Indexed: 01/10/2023] Open
Abstract
Water buffalo are less susceptible to Schistosoma japonicum infection than yellow cattle. The factors that affect such differences in susceptibility remain unknown. A Bos taurus genome-wide gene chip was used to analyze gene expression profiles in the peripheral blood of water buffalo and yellow cattle pre- and post-infection with S. japonicum. This study showed that most of the identified differentially expressed genes (DEGs) between water buffalo and yellow cattle pre- and post-infection were involved in immune-related processes, and the expression level of immune genes was lower in water buffalo. The unique DEGs (390) in yellow cattle were mainly associated with inflammation pathways, while the unique DEGs (2,114) in water buffalo were mainly associated with immune-related factors. The 83 common DEGs may be the essential response genes during S. japonicum infection, the highest two gene ontology (GO) functions were associated with the regulation of fibrinolysis. The pathway enrichment analysis showed that the DEGs constituted similar immune-related pathways pre- and post-infection between the two hosts. This first analysis of the transcriptional profiles of natural hosts has enabled us to gain new insights into the mechanisms that govern their susceptibility or resistance to S. japonicum infections.
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Affiliation(s)
- Jianmei Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Zhiqiang Fu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Yang Hong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Haiwei Wu
- Department of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, Providence, Rhode Island, United States of America
| | - Yamei Jin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Chuangang Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Hao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Ke Lu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Yaojun Shi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Chunxiu Yuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Guofeng Cheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Xingang Feng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Jinming Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
| | - Jiaojiao Lin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, People’s Republic of China
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Zhang L, Boeren S, van Hooijdonk ACM, Vervoort JM, Hettinga KA. A proteomic perspective on the changes in milk proteins due to high somatic cell count. J Dairy Sci 2015; 98:5339-51. [PMID: 26094216 DOI: 10.3168/jds.2014-9279] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/27/2015] [Indexed: 12/21/2022]
Abstract
Although cows with subclinical mastitis have no difference in the appearance of their milk, milk composition and milk quality are altered because of the inflammation. To know the changes in milk quality with different somatic cell count (SCC) levels, 5 pooled bovine milk samples with SCC from 10(5) to 10(6) cells/mL were analyzed qualitatively and quantitatively using both one-dimension sodium dodecyl sulfate PAGE and filter-aided sample preparation coupled with dimethyl labeling, both followed by liquid chromatography tandem mass spectrometry. Minor differences were found on the qualitative level in the proteome from milk with different SCC levels, whereas the concentration of milk proteins showed remarkable changes. Not only immune-related proteins (cathelicidins, IGK protein, CD59 molecule, complement regulatory protein, lactadherin), but also proteins with other biological functions (e.g., lipid metabolism: platelet glycoprotein 4, butyrophilin subfamily 1 member A1, perilipin-2) were significantly different in milk from cows with high SCC level compared with low SCC level. The increased concentration of protease inhibitors in the milk with higher SCC levels may suggest a protective role in the mammary gland against protease activity. Prostaglandin-H2 D-isomerase showed a linear relation with SCC, which was confirmed with an ELISA. However, the correlation coefficient was lower in individual cows compared with bulk milk. These results indicate that prostaglandin-H2 D-isomerase may be used as an indicator to evaluate bulk milk quality and thereby reduce the economic loss in the dairy industry. The results from this study reflect the biological phenomena occurring during subclinical mastitis and in addition provide a potential indicator for the detection of bulk milk with high SCC.
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Affiliation(s)
- L Zhang
- Dairy Science and Technology Group, Wageningen University, 6700EV, Wageningen, the Netherlands
| | - S Boeren
- Laboratory of Biochemistry, Wageningen University, 6700EV, Wageningen, the Netherlands
| | - A C M van Hooijdonk
- Dairy Science and Technology Group, Wageningen University, 6700EV, Wageningen, the Netherlands
| | - J M Vervoort
- Laboratory of Biochemistry, Wageningen University, 6700EV, Wageningen, the Netherlands
| | - K A Hettinga
- Dairy Science and Technology Group, Wageningen University, 6700EV, Wageningen, the Netherlands.
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Yunusi K, Zhang J, Zhong L, Mosha G, Nuermaimaiti A, Abudula M, Upur H. Uygur medicine Xipayi Kui Jie'an affects gene expression profiles in intestinal tissue lesions in a rat model of ulcerative colitis. Altern Ther Health Med 2015; 15:152. [PMID: 25997744 PMCID: PMC4440515 DOI: 10.1186/s12906-015-0672-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/13/2015] [Indexed: 12/19/2022]
Abstract
Background The aim of this study was to investigate the mechanisms underlying the therapeutic effect of Uygur medicine KJA on UC in a rat model. Methods UC was induced in Wistar rats by application of 2, 4-dinitrochlorobenzene and acetic acid and were then treated with three different doses of KJA, and normal saline as control. After treatment for 20 days, the gene expression profile of colonic tissue was analyzed by microarray and verified by quantitative real-time RT-PCR. Results Animals treated with the three different doses of KJA were compared with normal saline controls, wherein microarray analysis identified 1991, 2163, and 1677 differentially expressed genes respectively, of which 444 genes were raised and 670 genes were decrease spliced together in the three doses tested. The KEGG pathway analyses found commonly raised genes related to several different biological functions. Interesting genes included TRL2, IL-1β, TGF-β1, and NF-κB were confirmed by quantitative PCR. Conclusions The therapeutic effect of KJA on UC is likely explained by specific effects on the expression of genes, which are the effector molecules known to be involved in the development of UC. Further studies on differentially expressed genes will help explain the mechanism of action of Uygur medicine KJA.
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Ge D, Han L, Huang S, Peng N, Wang P, Jiang Z, Zhao J, Su L, Zhang S, Zhang Y, Kung H, Zhao B, Miao J. Identification of a novel MTOR activator and discovery of a competing endogenous RNA regulating autophagy in vascular endothelial cells. Autophagy 2015; 10:957-71. [PMID: 24879147 DOI: 10.4161/auto.28363] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
MTOR, a central regulator of autophagy, is involved in cancer and cardiovascular and neurological diseases. Modulating the MTOR signaling balance could be of great significance for numerous diseases. No chemical activators of MTOR have been found, and the urgent challenge is to find novel MTOR downstream components. In previous studies, we found a chemical small molecule, 3-benzyl-5-((2-nitrophenoxy) methyl)-dihydrofuran-2(3H)-one (3BDO), that inhibited autophagy in human umbilical vein endothelial cells (HUVECs) and neuronal cells. Here, we found that 3BDO activated MTOR by targeting FKBP1A (FK506-binding protein 1A, 12 kDa). We next used 3BDO to detect novel factors downstream of the MTOR signaling pathway. Activation of MTOR by 3BDO increased the phosphorylation of TIA1 (TIA1 cytotoxic granule-associated RNA binding protein/T-cell-restricted intracellular antigen-1). Finally, we used gene microarray, RNA interference, RNA-ChIP assay, bioinformatics, luciferase reporter assay, and other assays and found that 3BDO greatly decreased the level of a long noncoding RNA (lncRNA) derived from the 3' untranslated region (3'UTR) of TGFB2, known as FLJ11812. TIA1 was responsible for processing FLJ11812. Further experiments results showed that FLJ11812 could bind with MIR4459 targeting ATG13 (autophagy-related 13), and ATG13 protein level was decreased along with 3BDO-decreased FLJ11812 level. Here, we provide a new activator of MTOR, and our findings highlight the role of the lncRNA in autophagy.
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Affiliation(s)
- Di Ge
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Lei Han
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - ShuYa Huang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Nan Peng
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - PengChong Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Zheng Jiang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Jing Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Le Su
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - ShangLi Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research; Chinese Ministry of Education and Chinese Ministry of Health; Shandong University Qilu Hospital; Jinan, China
| | - HsiangFu Kung
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China; Institute of Pathology and Southwest Cancer Center; Third Military Medical University; Chongqing, China
| | - BaoXiang Zhao
- Institute of Organic Chemistry; School of Chemistry and Chemical Engineering; Shandong University; Jinan, China
| | - JunYing Miao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University; Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research; Chinese Ministry of Education and Chinese Ministry of Health; Shandong University Qilu Hospital; Jinan, China
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Li S, Pan XX, Berry JO, Wang Y, Ma S, Tan S, Xiao W, Zhao WZ, Sheng XY, Yin LP. OsSEC24, a functional SEC24-like protein in rice, improves tolerance to iron deficiency and high pH by enhancing H(+) secretion mediated by PM-H(+)-ATPase. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:61-71. [PMID: 25711814 DOI: 10.1016/j.plantsci.2015.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/29/2014] [Accepted: 01/01/2015] [Indexed: 05/16/2023]
Abstract
Iron is abundant in the soil, but its low solubility in neutral or alkaline soils limits its uptake. Plants can rely on rhizosphere acidification to increase iron solubility. OsSEC27p was previously found to be a highly up-regulated gene in iron-deficient rice roots. Here, pH-dependent complementation assays using yeast mutants sec24Δ/SEC24 and sec27Δ/SEC27 showed that OsSEC27 could functionally complement SEC24 but not SEC27 in yeast; thus, it was renamed as OsSEC24. We found that OsSEC24-transgenic tobacco plants increased the length and number of roots under iron deficiency at pH 8.0. To explore how OsSEC24 confers tolerance to iron deficiency, we utilized transgenic tobacco, rice and rice protoplasts. H(+) flux measurements using Non-invasive Micro-test Technology (NMT) indicated that the transgenic OsSEC24 tobacco and rice enhanced H(+) efflux under iron deficiency. Conversely, the application of plasma membrane PM-H(+)-ATPase inhibitor vanadate elucidated that H(+) secretion increased by OsSEC24 was mediated by PM-H(+)-ATPase. OsPMA2 was used as a representative of iron deficiency-responsive PM-H(+)-ATPases in rice root via RT-PCR analysis. In transgenic rice protoplasts OsPMA2 was packaged into OsSEC24 vesicles after export from the ER through confocal-microscopy observation. Together, OsSEC24 vesicles, along with PM-H(+)-ATPases stimulate roots formation under iron deficiency by enhancing rhizosphere acidification.
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Affiliation(s)
- Shuang Li
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - Xiao-Xi Pan
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - James O Berry
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
| | - Yi Wang
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - Shuang Ma
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - Song Tan
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - Wei-Zhong Zhao
- Institute of Mathematics and Interdisciplinary Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - Xian-Yong Sheng
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China
| | - Li-Ping Yin
- College of Life Sciences, Capital Normal University, No. 105 Xisanhuan North Street, Beijing 100048, China.
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80
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Deferme L, Briedé JJ, Claessen SMH, Cavill R, Kleinjans JCS. Cell line-specific oxidative stress in cellular toxicity: A toxicogenomics-based comparison between liver and colon cell models. Toxicol In Vitro 2015; 29:845-55. [PMID: 25800948 DOI: 10.1016/j.tiv.2015.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 02/20/2015] [Accepted: 03/03/2015] [Indexed: 12/12/2022]
Abstract
Imbalance between high reactive oxygen species formation and antioxidant capacity in the colon and liver has been linked to increased cancer risk. However, knowledge about possible cell line-specific oxidative stress-mechanisms is limited. To explore this further, gene expression data from a human liver and colon cell line (HepG2/Caco-2), both exposed to menadione and H2O2 at six time points (0.5-1-2-4-8 and 24h) were compared in association with cell cycle distribution. In total, 3164 unique- and 1827 common genes were identified between HepG2 and Caco-2 cells. Despite the higher number of unique genes, most oxidative stress-related genes such as CAT, OGG1, NRF2, NF-κB, GCLC, HMOX1 and GSR were differentially expressed in both cell lines. However, cell-specific regulation of genes such as KEAP1 and GCLM, or of the EMT pathway, which are of pathophysiological importance, indicates that oxidative stress induces different transcriptional effects and outcomes in the two selected cell lines. In addition, expression levels and/or -direction of common genes were often different in HepG2 and Caco-2 cells, and this led to very diverse downstream effects as confirmed by correlating pathways to cell cycle changes. Altogether, this work contributes to obtaining a better molecular understanding of cell line-specific toxicity upon exposure to oxidative stress-inducing compounds.
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Affiliation(s)
- L Deferme
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands.
| | - J J Briedé
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - S M H Claessen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - R Cavill
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - J C S Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
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Wang S, Sun Y, Gan W, Liu Y, Xiang G, Wang D, Wang L, Cheng J, Liu P. An automated microfluidic system for single-stranded DNA preparation and magnetic bead-based microarray analysis. BIOMICROFLUIDICS 2015; 9:024102. [PMID: 25825617 PMCID: PMC4352165 DOI: 10.1063/1.4914024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/18/2015] [Indexed: 05/25/2023]
Abstract
We present an integrated microfluidic device capable of performing single-stranded DNA (ssDNA) preparation and magnetic bead-based microarray analysis with a white-light detection for detecting mutations that account for hereditary hearing loss. The entire operation process, which includes loading of streptavidin-coated magnetic beads (MBs) and biotin-labeled polymerase chain reaction products, active dispersion of the MBs with DNA for binding, alkaline denaturation of DNA, dynamic hybridization of the bead-labeled ssDNA to a tag array, and white-light detection, can all be automatically accomplished in a single chamber of the microchip, which was operated on a self-contained instrument with all the necessary components for thermal control, fluidic control, and detection. Two novel mixing valves with embedded polydimethylsiloxane membranes, which can alternately generate a 3-μl pulse flow at a peak rate of around 160 mm/s, were integrated into the chip for thoroughly dispersing magnetic beads in 2 min. The binding efficiency of biotinylated oligonucleotides to beads was measured to be 80.6% of that obtained in a tube with the conventional method. To critically test the performance of this automated microsystem, we employed a commercial microarray-based detection kit for detecting nine mutation loci that account for hereditary hearing loss. The limit of detection of the microsystem was determined as 2.5 ng of input K562 standard genomic DNA using this kit. In addition, four blood samples obtained from persons with mutations were all correctly typed by our system in less than 45 min per run. The fully automated, "amplicon-in-answer-out" operation, together with the white-light detection, makes our system an excellent platform for low-cost, rapid genotyping in clinical diagnosis.
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Yi X, Gu H, Gao Q, Liu ZL, Bao J. Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:153. [PMID: 26396591 PMCID: PMC4578398 DOI: 10.1186/s13068-015-0333-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/03/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Phenolic aldehydes generated from lignocellulose pretreatment exhibited severe toxic inhibitions on microbial growth and fermentation. Numerous tolerance studies against furfural, 5-hydroxymethyl-2-furaldehyde (HMF), acetate, and ethanol were reported, but studies on inhibition of phenolic aldehyde inhibitors are rare. For ethanologenic strains, Zymomonas mobilis ZM4 is high in ethanol productivity and genetic manipulation feasibility, but sensitive to phenolic aldehyde inhibitors. Molecular mechanisms of tolerance for Z. mobilis toward phenolic aldehydes are not known. RESULTS We took the first insight into genomic response of Z. mobilis ZM4 to the phenolic aldehyde inhibitors derived from lignocellulose pretreatment. The results suggest that the toxicity to cells is caused by the functional group of phenolic aldehyde, similar to furfural and HMF, rather than aromatic groups or phenolic hydroxyl groups. Transcriptome response against 4-hydroxybenzaldehyde, syringaldehyde, and vanillin, representing phenolic groups H, S, and G, respectively, was investigated. The atlas of the important genes responsible for significantly enhanced and repressed genes at the genomic level was illustrated. 272 genes with twofold greater expressions than non-treated controls and 36 gene clusters in response to challenges of these phenolic aldehydes were identified. Several reductases encoded by ZMO1116, ZMO1696, and ZMO1885 were found to play the key roles in reducing phenolic aldehydes into the corresponding phenolic alcohols. Reduction of phenolic aldehydes by overexpression of ZMO1116, ZMO1696, and ZMO1885 in Z. mobilis ZM4 resulted in the increased inhibitor conversion and ethanol productivity, especially for 4-hydroxybenzaldehyde and vanillin. Several transporter genes such as ZMO0282, ZMO0283, ZMO0798, ZMO0799, and ZMO0800 was also displayed significantly increased expressions against the phenolic aldehydes. CONCLUSIONS The genes encoding reductases are with potentials on phenolic aldehydes-tolerant genes contributing to the reduction of phenolic aldehydes into the corresponding phenolic alcohols forms for Z. mobilis ZM4. Overexpression of the key genes improved the conversion ratio and ethanol productivity of 4-hydroxybenzaldehyde and vanillin with high toxicity. New knowledge obtained from this research aids understanding the mechanisms of bacterial tolerance and the development of the next-generation biocatalysts for advanced biofuels production.
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Affiliation(s)
- Xia Yi
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Hanqi Gu
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Qiuqiang Gao
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Z. Lewis Liu
- />US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 North University Street, Peoria, IL 61604 USA
| | - Jie Bao
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
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Bi H, Zhou J, Wu D, Gao W, Li L, Yu L, Liu F, Huang M, Adcock IM, Barnes PJ, Yao X. Microarray analysis of long non-coding RNAs in COPD lung tissue. Inflamm Res 2014; 64:119-26. [DOI: 10.1007/s00011-014-0790-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 10/24/2022] Open
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84
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Zang S, Guo R, Xing R, Zhang L, Li W, Zhao M, Fang J, Hu F, Kang B, Ren Y, Zhuang Y, Liu S, Wang R, Li X, Yu Y, Cheng J, Lu Y. Identification of differentially-expressed genes in intestinal gastric cancer by microarray analysis. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:276-83. [PMID: 25500430 PMCID: PMC4411479 DOI: 10.1016/j.gpb.2014.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/18/2014] [Accepted: 09/30/2014] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is one of the most frequent malignant tumors. In order to systematically characterize the cellular and molecular mechanisms of intestinal GC development, in this study, we used 22K oligonucleotide microarrays and bioinformatics analysis to evaluate the gene expression profiles of GC in 45 tissue samples, including 20 intestinal GC tissue samples, 20 normal appearing tissues (NATs) adjacent to tumors and 5 noncancerous gastric mucosa tissue samples. These profiles allowed us to explore the transcriptional characteristics of GC and determine the change patterns in gene expression that may be of clinical significance. 1519 and 1255 differentially-expressed genes (DEGs) were identified in intestinal GC tissues and NATs, respectively, as determined by Bayesian analysis (P<0.001). These genes were associated with diverse functions such as mucosa secretion, metabolism, proliferation, signaling and development, which occur at different stages of GC development.
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Affiliation(s)
- Shizhu Zang
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ruifang Guo
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Rui Xing
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Liang Zhang
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Wenmei Li
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Min Zhao
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jingyuan Fang
- Department of Gastroenterology, Renji Hospital of Shanghai Second Medical University, Shanghai 200001, China
| | - Fulian Hu
- Department of Gastroenterology, Peking University First Hospital, Beijing 100034, China
| | - Bin Kang
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yonghong Ren
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Yonglong Zhuang
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Siqi Liu
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Xianghong Li
- Department of Pathology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yingyan Yu
- Shanghai Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Youyong Lu
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China.
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Wang RL, Bencic DC, Garcia-Reyero N, Perkins EJ, Villeneuve DL, Ankley GT, Biales AD. Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PLoS One 2014; 9:e114178. [PMID: 25493933 PMCID: PMC4262388 DOI: 10.1371/journal.pone.0114178] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/04/2014] [Indexed: 01/18/2023] Open
Abstract
Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, better characterization and understanding are needed for natural variation in gene expression among fish individuals from lab cultures. Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples. As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to differentially impact subsets of fish transcriptomes in a nonsystematic way. Temporally more closely spaced batches tended to share a greater transcriptomic similarity among one another. The overall level of within-batch variation was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects. The observed differences in the within-batch variability of gene expression, at the levels of both individual genes and pathways, were probably both technical and biological. This suggests that biological interpretation and prioritization of genes and pathways targeted by experimental conditions should take into account both their intrinsic variability and the size of induced transcriptional changes. There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish. The high degree of conservation offers promising opportunities in not only studying fish molecular responses to environmental stressors by a comparative biology approach, but also effective sharing of a large amount of existing public transcriptomics data for developing toxicogenomics applications.
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Affiliation(s)
- Rong-Lin Wang
- Ecological Exposure Research Division, National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, Ohio, United States of America
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota, United States of America
- * E-mail:
| | - David C. Bencic
- Ecological Exposure Research Division, National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, Ohio, United States of America
| | - Natàlia Garcia-Reyero
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi, United States of America
| | - Edward J. Perkins
- Environmental Laboratory, US Army Engineer Research and Development Center, US Army Corps of Engineers, Vicksburg, Mississippi, United States of America
| | - Daniel L. Villeneuve
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota, United States of America
| | - Gerald T. Ankley
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota, United States of America
| | - Adam D. Biales
- Ecological Exposure Research Division, National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, Ohio, United States of America
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86
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Akiyama H, Ueda Y, Nobumasa H, Ooshima H, Ishizawa Y, Kitahiro K, Miyagawa I, Watanabe K, Nakamura T, Tanaka R, Yamamoto N, Nakae H, Kawase M, Gemma N, Sekiguchi Y, Fujibuchi W, Matoba R. A set of external reference controls/probes that enable quality assurance between different microarray platforms. Anal Biochem 2014; 472:75-83. [PMID: 25481737 DOI: 10.1016/j.ab.2014.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/16/2014] [Accepted: 11/19/2014] [Indexed: 11/29/2022]
Abstract
RNA external standards, although important to ensure equivalence across many microarray platforms, have yet to be fully implemented in the research community. In this article, a set of unique RNA external standards (or RNA standards) and probe pairs that were added to total RNA in the samples before amplification and labeling are described. Concentration-response curves of RNA external standards were used across multiple commercial DNA microarray platforms and/or quantitative real-time polymerase chain reaction (RT-PCR) and next-generation sequencing to identify problematic assays and potential sources of variation in the analytical process. A variety of standards can be added in a range of concentrations spanning high and low abundances, thereby enabling the evaluation of assay performance across the expected range of concentrations found in a clinical sample. Using this approach, we show that we are able to confirm the dynamic range and the limit of detection for each DNA microarray platform, RT-PCR protocol, and next-generation sequencer. In addition, the combination of a series of standards and their probes was investigated on each platform, demonstrating that multiplatform calibration and validation is possible.
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Affiliation(s)
- Hideo Akiyama
- New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa 248-8555, Japan.
| | - Yoji Ueda
- New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa 248-8555, Japan
| | - Hitoshi Nobumasa
- New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa 248-8555, Japan
| | - Hiroyuki Ooshima
- Yokohama Research Laboratories, Mitsubishi Rayon Co. Ltd., Yokohama, Kanagawa 230-0053, Japan
| | - Yohei Ishizawa
- DNA Chip Research Inc., Yokohama, Kanagawa 230-0045, Japan
| | - Koji Kitahiro
- Technical Research Laboratory, Kurabo Industries Ltd., Neyagawa, Osaka 572-0823, Japan
| | - Isao Miyagawa
- Technical Research Laboratory, Kurabo Industries Ltd., Neyagawa, Osaka 572-0823, Japan
| | | | - Takazumi Nakamura
- S-BIO Business Division, Sumitomo Bakelite Co. Ltd., Amagasaki, Hyogo 661-8588, Japan
| | - Ritsuka Tanaka
- Department of Bio Research, Kamakura Techno-Science, Inc., Kamakura, Kanagawa 248-0036, Japan
| | - Nobuko Yamamoto
- Japan Multiplex bio-Analysis Consortium (JMAC), Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hiroki Nakae
- Japan Multiplex bio-Analysis Consortium (JMAC), Chiyoda-ku, Tokyo 102-0083, Japan
| | - Mitsuo Kawase
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Nobuhiro Gemma
- Ricoh Institute of Technology, Ricoh Company, Ltd., Yokohama, Kanagawa 224-0035, Japan
| | - Yuji Sekiguchi
- Bio-Measurement Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Ibaraki 305-8566, Japan
| | - Wataru Fujibuchi
- Computational Biology Research Center, Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Ryo Matoba
- DNA Chip Research Inc., Yokohama, Kanagawa 230-0045, Japan.
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87
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Liu X, Tian J, Zhou X, Chen R, Wang L, Zhang C, Zhao J, Fan Y. Identification and characterization of promoters specifically and strongly expressed in maize embryos. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1286-1296. [PMID: 25052028 DOI: 10.1111/pbi.12227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/21/2014] [Accepted: 06/12/2014] [Indexed: 06/03/2023]
Abstract
The use of maize seeds as bioreactors has several advantages for the production of recombinant proteins in plant biotechnology, but available embryo-specific and strong promoters are limited. Here, we describe a genome-scale microarray-based approach to identify embryo-specifically and strongly expressed genes and their promoters in maize. We identified 28 embryo-preferred and abundantly expressed genes based on our microarray data. These embryo-preferred genes were further analysed using the UniGene database and by quantitative reverse transcriptase-PCR leading to the identification of seven genes (Zm.2098, Zm.13387, Zm.66589, Zm.85502, Zm.68129, Zm.3896 and Zm.2941) as embryo-specific genes with higher expression levels relative to maize globulin-1. The putative promoters of five embryo-specific genes (Zm.13387, Zm.66589, Zm.85502, Zm.3896 and Zm.2941) were isolated and all exhibited strong promoter activities when transiently expressed in maize embryos of 20 DAP. The embryo specificity and expression levels of the promoters of four genes (Zm.13387, Zm.85502, Zm.3896 and Zm.2941) were further examined in transgenic maize plants, revealing that they are strong promoters in embryos of all four developmental stages tested compared with reference globulin-1 promoter. Moreover, Zm.2941 and Zm.3896 promoters are stringently embryo-specific promoters, while Zm.85502 promoter is basically embryo specific yet wounding inducible in non-seed tissues, and Zm.13387 promoter is developmentally expressed in both embryo and aleurone with wounding-induced activity in non-seed tissues. Our study provides novel embryo-specific and strong promoters that are suitable for production of high-level recombinant proteins in maize embryos.
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Affiliation(s)
- Xiaoqing Liu
- Faculty of Maize Functional Genomics, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, China
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88
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Zhang L, Hu W, Wang Y, Feng R, Zhang Y, Liu J, Jia C, Miao H, Zhang J, Xu B, Jin Z. The MaASR gene as a crucial component in multiple drought stress response pathways in Arabidopsis. Funct Integr Genomics 2014; 15:247-60. [DOI: 10.1007/s10142-014-0415-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/06/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
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89
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Modulation of gene expression by 3-iodothyronamine: genetic evidence for a lipolytic pattern. PLoS One 2014; 9:e106923. [PMID: 25379707 PMCID: PMC4224367 DOI: 10.1371/journal.pone.0106923] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/04/2014] [Indexed: 01/11/2023] Open
Abstract
3-Iodothyronamine (T1AM) is an endogenous biogenic amine, structurally related to thyroid hormone, which is regarded as a novel chemical messenger. The molecular mechanisms underlying T1AM effects are not known, but it is possible to envisage changes in gene expression, since delayed and long-lasting phenotypic effects have been reported, particularly with regard to the modulation of lipid metabolism and body weight. To test this hypothesis we analysed gene expression profiles in adipose tissue and liver of eight rats chronically treated with T1AM (10 mg/Kg twice a day for five days) as compared with eight untreated rats. In vivo T1AM administration produced significant transcriptional effects, since 378 genes were differentially expressed in adipose tissue, and 114 in liver. The reported changes in gene expression are expected to stimulate lipolysis and beta-oxidation, while inhibiting adipogenesis. T1AM also influenced the expression of several genes linked to lipoprotein metabolism suggesting that it may play an important role in the regulation of cholesterol homeostasis. No effect on the expression of genes linked to toxicity was observed. The assay of tissue T1AM showed that in treated animals its endogenous concentration increased by about one order of magnitude, without significant changes in tissue thyroid hormone concentration. Therefore, the effects that we observed might have physiological or pathophysiological importance. Our results provide the basis for the reported effectiveness of T1AM as a lipolytic agent and gain importance in view of a possible clinical use of T1AM in obesity and/or dyslipidaemia.
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90
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Chen Y, Zhang S, Wang X, Guo W, Wang L, Zhang D, Yuan L, Zhang Z, Xu Y, Liu S. Disordered signaling governing ferroportin transcription favors breast cancer growth. Cell Signal 2014; 27:168-76. [PMID: 25451081 DOI: 10.1016/j.cellsig.2014.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/23/2014] [Accepted: 11/03/2014] [Indexed: 12/17/2022]
Abstract
Iron is a necessary chemical element needed by all organisms. Iron metabolism is finely tuned in mammals, and the hepcidin-ferroportin (FPN) axis is the central signaling in governing systemic iron homeostasis. Deregulation of this signaling would lead to iron disorders and likely other diseases including cancers. Reduced FPN was previously found to correlate with poor prognosis in breast cancer patients. Nonetheless, the biological effects of abnormal FPN expression in tumor cells remain largely unexplored, and the mechanisms underlying misregulated expression of FPN in cancers keep elusive. In the current study, we scrutinized the effects of abnormal FPN on tumor growth and the molecular mechanisms of diminished tumor FPN. Downregulation of FPN significantly promoted breast cancer growth, whereas FPN upregulation impeded tumor growth. We demonstrated that the transcription factors Nrf2 (nuclear factor erythroid 2-like 2) and MZF-1 (myeloid zinc finger-1) synergistically transactivated FPN expression in breast cancer cells. Moreover, CpG island methylation at the FPN promoter was the reason of attenuated FPN expression. Downregulation of Nrf2 and MZF-1 and hypermethylation of the FPN promoter were concurrently associated with decreased FPN concentration in breast tumors. Taken together, our study highlighted the contribution of disordered iron metabolism to breast cancer growth, and also signified an oncogenic effect of misregulated ferroportin in breast cancers. This work represents a promising starting point to the possibility of restraining breast cancer through targeting FPN or its upstream regulatory factors.
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Affiliation(s)
- Yue Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Urology, the Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Shuping Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xiaoyan Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenli Guo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Daoqiang Zhang
- Weifang Medical College, Wendeng Central Hospital, Weihai 264400, China
| | - Lin Yuan
- Weifang Medical College, Wendeng Central Hospital, Weihai 264400, China
| | - Zhihong Zhang
- Department of Urology, the Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Yong Xu
- Department of Urology, the Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China.
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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91
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Rai MF, Patra D, Sandell LJ, Brophy RH. Relationship of gene expression in the injured human meniscus to body mass index: a biologic connection between obesity and osteoarthritis. Arthritis Rheumatol 2014; 66:2152-64. [PMID: 24692131 DOI: 10.1002/art.38643] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 03/20/2014] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Higher body mass index (BMI) increases the risk of meniscus injury and knee osteoarthritis (OA). However, it is unknown if and how obesity affects meniscus biology. We analyzed transcriptome-wide gene expression profiles of injured human menisci to test the hypothesis that meniscal gene expression signatures relate to patient BMI. METHODS Meniscus samples were obtained from patients undergoing arthroscopic partial meniscectomy. Transcriptome-wide analysis of gene expression followed by validation of selected transcripts by QuantiGene Plex assay was performed. Correlations of gene expression with BMI and relative fold changes (≥1.5-fold) in 3 BMI categories (lean [BMI 18.5-24.9 kg/m(2) ], overweight [BMI 25.0-29.9 kg/m(2) ], and obese [BMI >30.0 kg/m(2) ]) were analyzed, and integrated functional classifications were probed computationally. RESULTS The obese versus overweight comparison resulted in the largest set of differences (565 transcripts) followed by obese versus lean (280 transcripts) and overweight versus lean (125 transcripts). Biologic reproducibility was confirmed by cluster analysis of expressed transcripts. Differentially regulated transcripts represented important functional classifications. Transcripts associated with oxygen transport, calcium ion binding, and cell homeostasis were elevated with BMI, while those related to extracellular matrix deposition, cell migration, and glucosamine metabolic processes were repressed. While these functional classifications may play key roles in cartilage/meniscus homeostasis, failure of extracellular matrix deposition and increase in calcium ion binding likely contribute to OA development following meniscal injury. CONCLUSION Our results indicate greater differences in gene expression between obese and overweight groups than between overweight and lean groups. This may indicate that there is a weight threshold at which injured meniscus responds severely to increased BMI. BMI-related changes in gene expression present a plausible explanation for the role of meniscal injury in OA development among obese patients.
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Affiliation(s)
- Muhammad Farooq Rai
- Washington University School of Medicine at Barnes-Jewish Hospital, St. Louis, Missouri
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92
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Sánchez Hernández A, José Juan O, Vidal Martínez J, Blanco R, Maciá S, Esquerdo Galiana G, Aparisi Aparisi F, Garde Noguera J, Catot S, Losa Gaspá F, García-Piñon F. Quantification of circulating endothelial cells as a predictor of response to chemotherapy with platinum and pemetrexed in patients with advanced non-squamous non-small cell lung carcinoma. Clin Transl Oncol 2014; 17:281-8. [PMID: 25236392 DOI: 10.1007/s12094-014-1223-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/01/2014] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Circulating endothelial cells (CEC) play an important role in tumor neovascularization and may have prognostic value in cancer patients. This study was designed to investigate the role of CEC as a marker for predicting platinum plus pemetrexed first-line chemotherapy efficacy in advanced non-squamous non-small cell lung cancer (NSCLC). METHODS A prospective study was performed whose main objective was to study whether the numbers of CEC at baseline and prior to the second and third cycle of chemotherapy were response predictors. Sixty-nine patients received cisplatin plus pemetrexed, and peripheral blood samples were performed at baseline and after second and third cycle. Separation and CEC count were performed using inmunomagnetic separation (CellSearch). RESULTS The CEC count in 4 mL of peripheral blood was obtained prior to the first, second, and third cycle of treatment. Baseline levels and evolution of CEC were correlated with response to treatment according to RECIST criteria after three cycles of treatment. Sixty-nine patients were included: 43 (64.2 %) received cisplatin/pemetrexed and 24 (35.8 %) carboplatin/pemetrexed. Range of baseline CEC: 8-965 (mean of 153 cel/4 mL). The results after 3 cycles were: 25 partial responses (36.2 %), 17 cases of stabilization of disease (24.6 %), 16 of progressive disease (23.2 %) and 11 non-evaluables (16 %). No significant relationship between the baseline CEC count and response was found (p value = 0.831). Increase >50 % between the first and second cycle was correlated significantly with progression disease (p = 0.008). Patients who had a baseline CEC count greater than the mean (>153 cells/4 mL) showed longer progression-free survival and global survival without statistical significance. CONCLUSIONS In this homogeneous group of patients with NSCLC, there is no correlation between response to treatment and CEC baseline levels. The increase in CEC numbers after the first cycle could be a negative predictive factor.
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Affiliation(s)
- Alfredo Sánchez Hernández
- Servicio de Oncología Médica, Consorcio Hospitalario Provincial de Castellón, Avda Dr Clará 19, 12003, Castellón, Spain,
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93
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Cong L, Liao Y, Lu X, Xia Z, Li H, Yang R. Early transcriptional response of human monocyte-like THP-1 cells in response to Trichosporon asahii infection. Mycopathologia 2014; 179:11-20. [PMID: 25179349 DOI: 10.1007/s11046-014-9784-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 06/28/2014] [Indexed: 11/30/2022]
Abstract
Trichosporon asahii is the major cause of invasive trichosporonosis, but little is known about the host immune response to this pathogen. In this study, the early transcriptional response of human monocyte-like THP-1 cells to T. asahii infection was evaluated using cDNA microarray and 1,315 differentially expressed genes were identified. The up-regulated genes were mostly involved in both innate and adaptive immune responses, as well as apoptosis and anti-apoptosis processes. Genes encoding the pro-inflammatory cytokines TNF-α, IL-1β, IL18 and IL-23α, along with the both C-C motif and C-X-C motif chemokines were strongly up-regulated, suggesting that THP-1 cells can mount a powerful inflammatory response to T. asahii infection. Genes encoding pattern recognition receptors were found up-regulated, such as dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin, cluster of differentiation 36 and the long pentraxin 3. Genes encoding members of the dual-spasticity phosphates family were up-regulated, and these genes were considered as a negative feedback mechanism to prevent excessive inflammatory response. The down-regulated genes in T. asahii-infected THP-1 cells were predominantly associated with cell cycle, mitosis, cell division and DNA repair. Thus, our study defines the early transcriptional response of monocyte-like THP-1 cells to T. asahii infection and provides a foundation for further investigations into the pathogenesis of T. asahii infection.
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Affiliation(s)
- Lin Cong
- Department of Dermatology, General Hospital of Beijing Military Command, 5 Nanmencang, Dongcheng District, Beijing, 100700, China
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94
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Panova M, Johansson T, Canbäck B, Bentzer J, Rosenblad MA, Johannesson K, Tunlid A, André C. Species and gene divergence in Littorina snails detected by array comparative genomic hybridization. BMC Genomics 2014; 15:687. [PMID: 25135785 PMCID: PMC4148934 DOI: 10.1186/1471-2164-15-687] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/11/2014] [Indexed: 12/11/2022] Open
Abstract
Background Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis. Results We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis. Conclusions The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Panova
- Department of Biological and Environmental Sciences - Tjärnö, Gothenburg University, Gothenburg, Sweden.
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95
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Ball N, Rasoulpour RJ, Zablotny C, Ellis-Hutchings R, Andrus A, Carney EW. Distinguishing between maternally-mediated and directly embryotoxic modes-of-action for postimplantation loss induced in rats by 2-amino-2-methylpropanol. Reprod Toxicol 2014; 49:55-64. [PMID: 25088246 DOI: 10.1016/j.reprotox.2014.07.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 07/11/2014] [Accepted: 07/22/2014] [Indexed: 11/26/2022]
Abstract
In rats, 2-amino-2-methylpropanol (AMP) caused an increase in postimplantation loss in an oral reproductive/developmental toxicity screening assay but not in a dermal developmental toxicity assay. Studies were performed to characterize the mode of action and determine whether the postimplantation loss was a result of direct embryotoxicity or a maternally mediated effect. The studies identified that the postimplantation loss occurs shortly after implantation, has a steep dose response with a clear threshold, requires exposure to AMP for a period of approximately 2-3 weeks prior to gestation and does not involve direct embryo toxicity. The uterine histopathology and gene array analysis of decidual swellings suggested AMP acts via a maternally mediated mechanism affecting the ability of the uterus to support an implanted embryo. Since the postimplantation loss occurs only at maternally toxic doses, the implications for human risk assessment are discussed.
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Affiliation(s)
- Nicholas Ball
- Toxicology and Environmental Research & Consulting, Dow Europe GmbH, Horgen CH-8810, Switzerland
| | - Reza J Rasoulpour
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI 48674, USA.
| | - Carol Zablotny
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI 48674, USA
| | - Robert Ellis-Hutchings
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI 48674, USA
| | - Amanda Andrus
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI 48674, USA
| | - Edward W Carney
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI 48674, USA
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96
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Li Z, Guan YQ, Liu JM. The role of STAT-6 as a key transcription regulator in HeLa cell death induced by IFN-γ/TNF-α co-immobilized on nanoparticles. Biomaterials 2014; 35:5016-27. [DOI: 10.1016/j.biomaterials.2014.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 03/03/2014] [Indexed: 02/08/2023]
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Abstract
In Arabidopsis research, microarrays have typically been employed for the measurement of gene expression under different conditions. Microarray analysis is often used to analyze the effects of the expression of wild-type genes (control) versus mutants, the effects of varying environmental conditions, and the effects of hormones. In addition, microarray analysis is used to analyze differences in gene expression between growth stages and tissues. Other array applications include comparative genomic hybridization, chromatin immunoprecipitation, mutation detection, and genotyping. This chapter focuses on gene expression profiling, which is typically performed by the competitive hybridization of two samples, each labeled with a fluorescent dye such as cyanine 3-CTP or cyanine 5-CTP. We describe the steps, from RNA purification to data analysis, that are involved in obtaining data from DNA microarrays.
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Peng J, Hao B, Liu L, Wang S, Ma B, Yang Y, Xie F, Li Y. RNA-Seq and microarrays analyses reveal global differential transcriptomes of Mesorhizobium huakuii 7653R between bacteroids and free-living cells. PLoS One 2014; 9:e93626. [PMID: 24695521 PMCID: PMC3973600 DOI: 10.1371/journal.pone.0093626] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/04/2014] [Indexed: 11/18/2022] Open
Abstract
Mesorhizobium huakuii 7653R occurs either in nitrogen-fixing symbiosis with its host plant, Astragalus sinicus, or free-living in the soil. The M. huakuii 7653R genome has recently been sequenced. To better understand the complex biochemical and developmental changes that occur in 7653R during bacteroid development, RNA-Seq and Microarrays were used to investigate the differential transcriptomes of 7653R bacteroids and free-living cells. The two approaches identified several thousand differentially expressed genes. The most prominent up-regulation occurred in the symbiosis plasmids, meanwhile gene expression is concentrated to a set of genes (clusters) in bacteroids to fulfill corresponding functional requirements. The results suggested that the main energy metabolism is active while fatty acid metabolism is inactive in bacteroid and that most of genes relevant to cell cycle are down-regulated accordingly. For a global analysis, we reconstructed a protein-protein interaction (PPI) network for 7653R and integrated gene expression data into the network using Cytoscape. A highly inter-connected subnetwork, with function enrichment for nitrogen fixation, was found, and a set of hubs and previously uncharacterized genes participating in nitrogen fixation were identified. The results described here provide a broader biological landscape and novel insights that elucidate rhizobial bacteroid differentiation, nitrogen fixation and related novel gene functions.
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Affiliation(s)
- Jieli Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Baohai Hao
- Center for Bioinformatics, School of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Liu Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Shanming Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Binguang Ma
- Center for Bioinformatics, School of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yi Yang
- Center for Bioinformatics, School of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Fuli Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
- * E-mail:
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Ge D, Kong X, Liu W, Zhao J, Su L, Zhang S, Zhang Y, Zhao B, Miao J. Phosphorylation and nuclear translocation of integrin β4 induced by a chemical small molecule contribute to apoptosis in vascular endothelial cells. Apoptosis 2014; 18:1120-31. [PMID: 23677256 DOI: 10.1007/s10495-013-0860-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Integrin β4 and its Y-1494 phosphorylation play an important role in cell signaling. We found a small molecule, ethyl1-(3-(4-chlorophenoxy)-2-hydroxypropyl)-3-(4-chlorophenyl)-1H-pyrazole-5-carboxylate (ECPC), that could elevate the levels of KIT ligand (KITLG), interleukin 8 (IL-8), prostaglandin-endoperoxide synthase 2 (PTGS2) and activating transcription factor 3 (ATF3) and promote apoptosis in vascular endothelial cells (VECs) through integrin β4. We investigated the underlying mechanism of integrin β4 participating in this process. ECPC treatment increased the phosphorylation of Y-1494 in the integrin β4 cytoplasmic domain via a well-known receptor tyrosine kinase, fibroblast growth factor receptor 1 (FGFR1), and integrin β4 translocated from the cytoplasm to nucleus. With suppression of Y-1494 phosphorylation by FGF-2 or siRNA of FGFR1, ECPC failed to promote integrin β4 nuclear translocation and could not increase the expression of KITLG, IL-8, PTGS2 or ATF3. Y-1494 phosphorylation and nuclear translocation of integrin β4 may be important during ECPC-induced apoptosis in VECs.
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Affiliation(s)
- Di Ge
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan, 250100, China
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In vitro and in vivo activities of pterostilbene against Candida albicans biofilms. Antimicrob Agents Chemother 2014; 58:2344-55. [PMID: 24514088 DOI: 10.1128/aac.01583-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pterostilbene (PTE) is a stilbene-derived phytoalexin that originates from several natural plant sources. In this study, we evaluated the activity of PTE against Candida albicans biofilms and explored the underlying mechanisms. In 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) reduction assays, biofilm biomass measurement, confocal laser scanning microscopy, and scanning electron microscopy, we found that ≤16 μg/ml PTE had a significant effect against C. albicans biofilms in vitro, while it had no fungicidal effect on planktonic C. albicans cells, which suggested a unique antibiofilm effect of PTE. Then we found that PTE could inhibit biofilm formation and destroy the maintenance of mature biofilms. At 4 μg/ml, PTE decreased cellular surface hydrophobicity (CSH) and suppressed hyphal formation. Gene expression microarrays and real-time reverse transcription-PCR showed that exposure of C. albicans to 16 μg/ml PTE altered the expression of genes that function in morphological transition, ergosterol biosynthesis, oxidoreductase activity, and cell surface and protein unfolding processes (heat shock proteins). Filamentation-related genes, especially those regulated by the Ras/cyclic AMP (cAMP) pathway, including ECE1, ALS3, HWP1, HGC1, and RAS1 itself, were downregulated upon PTE treatment, indicating that the antibiofilm effect of PTE was related to the Ras/cAMP pathway. Then, we found that the addition of exogenous cAMP reverted the PTE-induced filamentous growth defect. Finally, with a rat central venous catheter infection model, we confirmed the in vivo activity of PTE against C. albicans biofilms. Collectively, PTE had strong activities against C. albicans biofilms both in vitro and in vivo, and these activities were associated with the Ras/cAMP pathway.
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