1301
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Wang R, Sheps JA, Liu L, Han J, Chen PSK, Lamontagne J, Wilson PD, Welch I, Borchers CH, Ling V. Hydrophilic bile acids prevent liver damage caused by lack of biliary phospholipid in Mdr2-/- mice. J Lipid Res 2019; 60:85-97. [PMID: 30416103 PMCID: PMC6314265 DOI: 10.1194/jlr.m088070] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/04/2018] [Indexed: 12/15/2022] Open
Abstract
Bile acid imbalance causes progressive familial intrahepatic cholestasis type 2 (PFIC2) or type 3 (PFIC3), severe liver diseases associated with genetic defects in the biliary bile acid transporter bile salt export pump (BSEP; ABCB11) or phosphatidylcholine transporter multidrug resistance protein 3 (MDR3; ABCB4), respectively. Mdr2-/- mice (a PFIC3 model) develop progressive cholangitis, ductular proliferation, periportal fibrosis, and hepatocellular carcinoma (HCC) because the nonmicelle-bound bile acids in the bile of these mice are toxic. We asked whether the highly hydrophilic bile acids generated by Bsep-/- mice could protect Mdr2-/- mice from progressive liver damage. We generated double-KO (DKO: Bsep-/- and Mdr2-/- ) mice. Their bile acid composition resembles that of Bsep-/- mice, with increased hydrophilic muricholic acids, tetrahydroxylated bile acids (THBAs), and reduced hydrophobic cholic acid. These mice lack the liver pathology of their Mdr2-/- littermates. The livers of DKO mice have gene expression profiles very similar to Bsep-/- mice, with 4,410 of 6,134 gene expression changes associated with the Mdr2-/- mutation being suppressed. Feeding with THBAs partially alleviates liver damage in the Mdr2-/- mice. Hydrophilic changes to biliary bile acid composition, including introduction of THBA, can prevent the progressive liver pathology associated with the Mdr2-/- (PFIC3) mutation.
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Affiliation(s)
- Renxue Wang
- BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | | | - Lin Liu
- BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jun Han
- University of Victoria-Genome BC Proteomics Centre University of Victoria, Victoria, British Columbia, Canada
| | - Patrick S K Chen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jason Lamontagne
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter D Wilson
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ian Welch
- Department of Pathology University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Comparative Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre University of Victoria, Victoria, British Columbia, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Victor Ling
- BC Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology University of British Columbia, Vancouver, British Columbia, Canada
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1302
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Singh J, Singh V, Vineeth TV, Kumar P, Kumar N, Sharma PC. Differential response of Indian mustard ( Brassica juncea L., Czern and Coss) under salinity: photosynthetic traits and gene expression. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:71-83. [PMID: 30804631 PMCID: PMC6352536 DOI: 10.1007/s12298-018-0631-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/15/2018] [Accepted: 12/05/2018] [Indexed: 05/28/2023]
Abstract
To explore the effect of salt stress on photosynthetic traits and gene expression in Indian mustard, four genotypes CS 54 (national check for salinity), CS 52-SPS-1-2012 (salt tolerant mutant), CS 614-4-1-4-100-13 (salt sensitive mutant) and Pusa bold (high yielding variety) were evaluated under irrigation water salinity (ECiw 12, and 15 dS m-1). Results suggest genotype CS 52-SPS-1-2012 followed by CS 54 performed better under imposed salt stress due to differential regulation of Na+ accumulation in the roots and main stem, restriction of Na+ influx from root to shoot, maintaining higher net photosynthetic traits under saline stress compared to CS 614-4-1-4-100-13 and Pusa bold. Further, overexpression of antiporters (SOS1, SOS2, SOS3, ENH1 and NHX1) and antioxidant (APX1, APX4, DHAR1 and MDHAR) genes in salt tolerant genotypes CS 52-SPS-1-2012 and CS 54 demonstrated their significant role in imparting salt tolerance in Indian mustard.
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Affiliation(s)
- Jogendra Singh
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - Vijayata Singh
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - T. V. Vineeth
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - Parveen Kumar
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - Neeraj Kumar
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - Parbodh C. Sharma
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
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1303
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Zhu QG, Xu Y, Yang Y, Guan CF, Zhang QY, Huang JW, Grierson D, Chen KS, Gong BC, Yin XR. The persimmon ( Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. HORTICULTURE RESEARCH 2019; 6:138. [PMID: 31871686 PMCID: PMC6917749 DOI: 10.1038/s41438-019-0227-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 11/27/2019] [Indexed: 05/14/2023]
Abstract
Persimmon (Diospyros kaki) is an oriental perennial woody fruit tree whose popular fruit is produced and consumed worldwide. The persimmon fruit is unique because of the hyperaccumulation of proanthocyanidins during fruit development, causing the mature fruit of most cultivars to have an astringent taste. In this study, we obtained a chromosome-scale genome assembly for 'Youshi' (Diospyros oleifera, 2n = 2x = 30), the diploid species of persimmon, by integrating Illumina sequencing, single-molecule real-time sequencing, and high-throughput chromosome conformation capture techniques. The assembled D. oleifera genome consisted of 849.53 Mb, 94.14% (799.71 Mb) of which was assigned to 15 pseudochromosomes, and is the first assembled genome for any member of the Ebenaceae. Comparative genomic analysis revealed that the D. oleifera genome underwent an ancient γ whole-genome duplication event. We studied the potential genetic basis for astringency development (proanthocyanidin biosynthesis) and removal (proanthocyanidin insolublization). Proanthocyanidin biosynthesis genes were mainly distributed on chromosome 1, and the clustering of these genes is responsible for the genetic stability of astringency heredity. Genome-based RNA-seq identified deastringency genes, and promoter analysis showed that most of their promoters contained large numbers of low oxygen-responsive motifs, which is consistent with the efficient industrial application of high CO2 treatment to remove astringency. Using the D. oleifera genome as the reference, SLAF-seq indicated that 'Youshi' is one of the ancestors of the cultivated persimmon (2n = 6x = 90). Our study provides significant insights into the genetic basis of persimmon evolution and the development and removal astringency, and it will facilitate the improvement of the breeding of persimmon fruit.
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Affiliation(s)
- Qing-gang Zhu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
| | - Yang Xu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 PR China
| | - Yong Yang
- College of Horticulture, Northwest A&F University, Yangling, PR China
| | - Chang-fei Guan
- College of Horticulture, Northwest A&F University, Yangling, PR China
| | - Qiu-yun Zhang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
| | - Jing-wen Huang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
| | - Don Grierson
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
- Plant & Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Kun-song Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
| | - Bang-chu Gong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 PR China
| | - Xue-ren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058 PR China
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1304
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Zayed Y, Qi X, Peng C. Identification of Novel MicroRNAs and Characterization of MicroRNA Expression Profiles in Zebrafish Ovarian Follicular Cells. Front Endocrinol (Lausanne) 2019; 10:518. [PMID: 31417497 PMCID: PMC6684945 DOI: 10.3389/fendo.2019.00518] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/15/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression primarily at the post-transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus, pituitary, and ovary. Gonadotropin-releasing hormone (GnRH) stimulates the secretion of luteinizing hormone (LH), which in turn, induces the secretion of maturation-inducing hormone (MIH) from the ovary. It is documented that small early vitellogenic (or stage IIIa) follicles are unable to undergo oocyte maturation whereas oocytes in mid- to late vitellogenic (stage IIIb) follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles, we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next-generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore, bioinformatics analysis revealed the presence of 214 known, 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up-regulated, and 13 miRNAs were significantly down-regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs, dre-miR-22a-3p, dre-miR-16a, dre-miR-181a-3p, and dre-miR-29a, was validated by real-time PCR. Finally, gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function, including oocyte maturation. Taken together, this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation.
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Affiliation(s)
- Yara Zayed
- Department of Biology, York University, Toronto, ON, Canada
| | - Xin Qi
- Department of Biology, York University, Toronto, ON, Canada
| | - Chun Peng
- Department of Biology, York University, Toronto, ON, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, ON, Canada
- *Correspondence: Chun Peng
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1305
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Vinci G, Cozzolino V, Mazzei P, Monda H, Spaccini R, Piccolo A. An alternative to mineral phosphorus fertilizers: The combined effects of Trichoderma harzianum and compost on Zea mays, as revealed by 1H NMR and GC-MS metabolomics. PLoS One 2018; 13:e0209664. [PMID: 30589863 PMCID: PMC6307717 DOI: 10.1371/journal.pone.0209664] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/10/2018] [Indexed: 02/01/2023] Open
Abstract
The ability of Trichoderma harzianum (strain OMG-08) as plant growth promoting fungus (PGPF), was tested on Zea mays plants grown in soil pots added with different inorganic (triple superphosphate and rock phosphate) and organic (cow and horse manure composts) P fertilizers. The effect of treatments was evaluated by following the variations of plants dry biomass and nutrient content, as well as the metabolic changes in plant leaves by both GC-MS and NMR spectroscopy. A synergic effect was observed in treatments with both composts and fungus inoculation, in which not only plant growth and P uptake were enhanced, but also the expression of different metabolites related to an improved photosynthetic activity. Conversely, the combination of Trichoderma with inorganic fertilizers was less effective and even showed a reduction of plants shoot biomass and N content. The corresponding plant metabolome revealed metabolic compounds typical of biotic or abiotic stresses, which may be attributed to a reduced capacity of inorganic fertilizers to provide a sufficient P availability during plant growth. Our findings also indicate that the molecular composition of compost differentiated the Trichoderma activity in sustaining plant growth. The positive effects of the combined Trichoderma and compost treatment suggest that it may become an alternative to the phosphorus mineral fertilization.
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Affiliation(s)
- Giovanni Vinci
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agroalimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Portici (NA), Italy
- * E-mail: (GV); (AP)
| | - Vincenza Cozzolino
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agroalimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Portici (NA), Italy
| | - Pierluigi Mazzei
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agroalimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Portici (NA), Italy
| | - Hiarhi Monda
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agroalimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Portici (NA), Italy
| | - Riccardo Spaccini
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agroalimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Portici (NA), Italy
| | - Alessandro Piccolo
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agroalimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Portici (NA), Italy
- * E-mail: (GV); (AP)
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1306
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Genome-wide analysis of the Tetrahymena thermophila glutathione S-transferase gene superfamily. Genomics 2018; 111:534-548. [PMID: 30572113 DOI: 10.1016/j.ygeno.2018.11.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/21/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022]
Abstract
The ciliate Tetrahymena thermophila has a rapid response to detoxify xenobiotics, which presents opportunity to study the diversification of Glutathione S-Transferase superfamily. In-silico identification of putative GST genes were resulted with 70 GST genes; 49 TtGSTmu, 7 TtGSTomega, 5 TtGSTtheta, 2 TtGSTzeta, 4 TtMAPEG and 3 TtEF1G. TtGST superfamily has short intron carrying or intronless genes. The most expressed mRNAs of TtGST are limited to 4 members at all life stages. TtGST genes are widely distributed to all five micronuclear chromosomes with the highest diversified members from different classes in chromosome 4. The clustering and the orientation of some TtGSTs in the T. thermophila genome give clues about the recent gene duplication. Analysis of GSH affinity-purified GST proteins with Western blot and activity assay showed GST activity carrying purified TtGST populations. In conclusion, the enhanced genome capacity of TtGST superfamily may have evolved through improved GST enzymatic activity.
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1307
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Edlund A, Yang Y, Yooseph S, He X, Shi W, McLean JS. Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation. MICROBIOME 2018; 6:217. [PMID: 30522530 PMCID: PMC6284299 DOI: 10.1186/s40168-018-0591-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 11/06/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation. RESULTS Time course analysis of the biofilm maturation was performed by parallel sampling every 2-3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum. CONCLUSION It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.
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Affiliation(s)
- Anna Edlund
- Genomic Medicine Group, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92137, USA.
| | - Youngik Yang
- National Marine Biodiversity Institute of Korea, 75, Jansang-ro 101beon-gil, Janghang-eup, Seocheon-gun, Chungcheongnam-do, 33662, Korea
| | - Shibu Yooseph
- Department of Computer Science, University of Central Florida, 4328 Scorpius Street, Orlando, FL, 32816, USA
| | - Xuesong He
- The Forsyth Institute, Cambridge, MA, 02142, USA
| | - Wenyuan Shi
- The Forsyth Institute, Cambridge, MA, 02142, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, 98195, USA.
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1308
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Kovacik A, Tirpak F, Tomka M, Miskeje M, Tvrda E, Arvay J, Andreji J, Slanina T, Gabor M, Hleba L, Fik M, Jambor T, Cisarova M, Massanyi P. Trace elements content in semen and their interactions with sperm quality and RedOx status in freshwater fish Cyprinus carpio: A correlation study. J Trace Elem Med Biol 2018; 50:399-407. [PMID: 30262311 DOI: 10.1016/j.jtemb.2018.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 11/24/2022]
Abstract
Objective of the present study was to investigate interactions between trace elements content and RedOx status, as well as sperm quality parameters (motility features, DNA fragmentation) in fish spermatozoa in natural conditions. Reproductively mature male freshwater fish (n = 16) of Cyprinus carpio breed were used in the study. Trace elements content was determined in fish milt samples by inductively-coupled plasma optical emission spectrometry (ICP-OES) and by cold-vapor atomic absorption spectroscopy (CV-AAS). Sperm quality evaluation was realized by computer-assisted sperm analysis (CASA) quantifying several parameters: concentration, total motility, progressive motility, distance average path, distance curved line, distance straight line, velocity average path, velocity curved line, velocity straight line, straightness, linearity, amplitude of lateral head displacement and beat cross frequency. The general scheme of descending concentrations of trace metals in semen samples was following: Zn > Fe > Cu > As > Sr > Ni > Mn > Se > Pb > Cr > Cd > Hg. Total motility of spermatozoa was relatively high (91.45%), however progressive motility was not even half of this value (39.47%). Sperm DNA fragmentation values were relatively low (4.00-6.29%). The percentage of immotile spermatozoa showed a significant correlation with all RedOx status parameters and also with DNA fragmentation. Positive statistically significant correlations were observed between trace elements (Mn, Se, Sr, and Zn) and some qualitative spermatozoa parameters (velocity and distance parameters). Cu and Hg content shows similar negative associations with progressive motility. Hg also interacted with production of malondialdehyde. Overall, the present study suggests application of multi-component mixtures of environmentally related trace elements concentrations when assessing the potential reproductive risk.
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Affiliation(s)
- Anton Kovacik
- Department of Animal Physiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Filip Tirpak
- Department of Animal Physiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Marian Tomka
- Department of Biochemistry and Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Michal Miskeje
- AgroBioTech Research Centre, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic.
| | - Eva Tvrda
- Department of Animal Physiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Julius Arvay
- Department of Chemistry, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Jaroslav Andreji
- Department of Poultry Science and Small Animal Husbandry, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Tomas Slanina
- Department of Animal Physiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Michal Gabor
- Department of Animal Genetics and Breeding Biology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Lukas Hleba
- Department of Microbiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Martin Fik
- Department of Poultry Science and Small Animal Husbandry, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Tomas Jambor
- Department of Animal Physiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
| | - Miroslava Cisarova
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Nám. J. Herdu 2, Trnava, 917 01, Slovak Republic.
| | - Peter Massanyi
- Department of Animal Physiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic.
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1309
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Prasad KVSK, Xing D, Reddy ASN. Vascular Plant One-Zinc-Finger (VOZ) Transcription Factors Are Positive Regulators of Salt Tolerance in Arabidopsis. Int J Mol Sci 2018; 19:ijms19123731. [PMID: 30477148 PMCID: PMC6321167 DOI: 10.3390/ijms19123731] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
Abstract
Soil salinity, a significant problem in agriculture, severely limits the productivity of crop plants. Plants respond to and cope with salt stress by reprogramming gene expression via multiple signaling pathways that converge on transcription factors. To develop strategies to generate salt-tolerant crops, it is necessary to identify transcription factors that modulate salt stress responses in plants. In this study, we investigated the role of VOZ (VASCULAR PLANT ONE-ZINC FINGER PROTEIN) transcription factors (VOZs) in salt stress response. Transcriptome analysis in WT (wild-type), voz1-1, voz2-1 double mutant and a VOZ2 complemented line revealed that many stress-responsive genes are regulated by VOZs. Enrichment analysis for gene ontology terms in misregulated genes in voz double mutant confirmed previously identified roles of VOZs and suggested a new role for them in salt stress. To confirm VOZs role in salt stress, we analyzed seed germination and seedling growth of WT, voz1, voz2-1, voz2-2 single mutants, voz1-1voz2-1 double mutant and a complemented line under different concentrations of NaCl. Only the double mutant exhibited hypersensitivity to salt stress as compared to WT, single mutants, and a complemented line. Expression analysis showed that hypersensitivity of the double mutant was accompanied by reduced expression of salt-inducible genes. These results suggest that VOZ transcription factors act as positive regulators of several salt-responsive genes and that the two VOZs are functionally redundant in salt stress.
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Affiliation(s)
- Kasavajhala V S K Prasad
- Department of Biology and Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
| | - Denghui Xing
- Department of Biology and Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
- Genomics Core Lab, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
| | - Anireddy S N Reddy
- Department of Biology and Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
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1310
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Aygun N, Altungoz O. MYCN is amplified during S phase, and c‑myb is involved in controlling MYCN expression and amplification in MYCN‑amplified neuroblastoma cell lines. Mol Med Rep 2018; 19:345-361. [PMID: 30483774 PMCID: PMC6297758 DOI: 10.3892/mmr.2018.9686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 10/03/2018] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma derived from primitive sympathetic neural precursors is a common type of solid tumor in infants. MYCN proto-oncogene bHLH transcription factor (MYCN) amplification and 1p36 deletion are important factors associated with the poor prognosis of neuroblastoma. Expression levels of MYCN and c-MYB proto-oncogene transcription factor (c-myb) decline during the differentiation of neuroblastoma cells; E2F transcription factor 1 (E2F1) activates the MYCN promoter. However, the underlying mechanism of MYCN overexpression and amplification requires further investigation. In the present study, potential c-Myb target genes, and the effect of c-myb RNA interference (RNAi) on MYCN expression and amplification were investigated in MYCN-amplified neuroblastoma cell lines. The mRNA expression levels and MYCN gene copy number in five neuroblastoma cell lines were determined by quantitative polymerase chain reaction. In addition, variations in potential target gene expression and MYCN gene copy number between pre- and post-c-myb RNAi treatment groups in MYCN-amplified Kelly, IMR32, SIMA and MHH-NB-11 cell lines, normalized to those of non-MYCN-amplified SH-SY5Y, were examined. To determine the associations between gene expression levels and chromosomal aberrations, MYCN amplification and 1p36 alterations in interphases/metaphases were analyzed using fluorescence in situ hybridization. Statistical analyses revealed correlations between 1p36 alterations and the expression of c-myb, MYB proto-oncogene like 2 (B-myb) and cyclin dependent kinase inhibitor 1A (p21). Additionally, the results of the present study also demonstrated that c-myb may be associated with E2F1 and L3MBTL1 histone methyl-lysine binding protein (L3MBTL1) expression, and that E2F1 may contribute to MYCN, B-myb, p21 and chromatin licensing and DNA replication factor 1 (hCdt1) expression, but to the repression of geminin (GMNN). On c-myb RNAi treatment, L3MBTL1 expression was silenced, while GMNN was upregulated, indicating G2/M arrest. In addition, MYCN gene copy number increased following treatment with c-myb RNAi. Notably, the present study also reported a 43.545% sequence identity between upstream of MYCN and Drosophila melanogaster amplification control element 3, suggesting that expression and/or amplification mechanisms of developmentally-regulated genes may be evolutionarily conserved. In conclusion, c-myb may be associated with regulating MYCN expression and amplification. c-myb, B-myb and p21 may also serve a role against chromosome 1p aberrations. Together, it was concluded that MYCN gene is amplified during S phase, potentially via a replication-based mechanism.
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Affiliation(s)
- Nevim Aygun
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Oguz Altungoz
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
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1311
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Bartoletti-Stella A, Corrado P, Mometto N, Baiardi S, Durrenberger PF, Arzberger T, Reynolds R, Kretzschmar H, Capellari S, Parchi P. Analysis of RNA Expression Profiles Identifies Dysregulated Vesicle Trafficking Pathways in Creutzfeldt-Jakob Disease. Mol Neurobiol 2018; 56:5009-5024. [PMID: 30446946 DOI: 10.1007/s12035-018-1421-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/01/2018] [Indexed: 12/21/2022]
Abstract
Functional genomics applied to the study of RNA expression profiles identified several abnormal molecular processes in experimental prion disease. However, only a few similar studies have been carried out to date in a naturally occurring human prion disease. To better characterize the transcriptional cascades associated with sporadic Creutzfeldt-Jakob disease (sCJD), the most common human prion disease, we investigated the global gene expression profile in samples from the frontal cortex of 10 patients with sCJD and 10 non-neurological controls by microarray analysis. The comparison identified 333 highly differentially expressed genes (hDEGs) in sCJD. Functional enrichment Gene Ontology analysis revealed that hDEGs were mainly associated with synaptic transmission, including GABA (q value = 0.049) and glutamate (q value = 0.005) signaling, and the immune/inflammatory response. Furthermore, the analysis of cellular components performed on hDEGs showed a compromised regulation of vesicle-mediated transport with mainly up-regulated genes related to the endosome (q value = 0.01), lysosome (q value = 0.04), and extracellular exosome (q value < 0.01). A targeted analysis of the retromer core component VPS35 (vacuolar protein sorting-associated protein 35) showed a down-regulation of gene expression (p value= 0.006) and reduced brain protein levels (p value= 0.002). Taken together, these results confirm and expand previous microarray expression profile data in sCJD. Most significantly, they also demonstrate the involvement of the endosomal-lysosomal system. Since the latter is a common pathogenic pathway linking together diseases, such as Alzheimer's and Parkinson's, it might be the focus of future studies aimed to identify new therapeutic targets in neurodegenerative diseases.
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Affiliation(s)
- Anna Bartoletti-Stella
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Ospedale Bellaria, 40139, Bologna, Italy
| | - Patrizia Corrado
- Department of Biomedical and NeuroMotor Sciences, DIBINEM, University of Bologna, 40123, Bologna, Italy
| | - Nicola Mometto
- Department of Biomedical and NeuroMotor Sciences, DIBINEM, University of Bologna, 40123, Bologna, Italy
| | - Simone Baiardi
- Department of Biomedical and NeuroMotor Sciences, DIBINEM, University of Bologna, 40123, Bologna, Italy
| | - Pascal F Durrenberger
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, Rayne Building, London, UK
| | - Thomas Arzberger
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-University Munich, Munich, Germany.,Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | | | - Hans Kretzschmar
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sabina Capellari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Ospedale Bellaria, 40139, Bologna, Italy. .,Department of Biomedical and NeuroMotor Sciences, DIBINEM, University of Bologna, 40123, Bologna, Italy.
| | - Piero Parchi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Ospedale Bellaria, 40139, Bologna, Italy. .,Department of Experimental, Diagnostic and Specialty Medicine, DIMES, University of Bologna, 40138, Bologna, Italy.
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1312
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Breton TS, Kenter LW, Greenlaw K, Montgomery J, Goetz GW, Berlinsky DL, Luckenbach JA. Initiation of sex change and gonadal gene expression in black sea bass (Centropristis striata) exposed to exemestane, an aromatase inhibitor. Comp Biochem Physiol A Mol Integr Physiol 2018; 228:51-61. [PMID: 30414915 DOI: 10.1016/j.cbpa.2018.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/25/2022]
Abstract
Many teleost fishes exhibit sequential hermaphroditism, where male or female gonads develop first and later undergo sex change. Model sex change species are characterized by social hierarchies and coloration changes, which enable experimental manipulations to better understand these processes. However, other species such as the protogynous black sea bass (Centropristis striata) do not exhibit these characteristics and instead receive research attention due to their importance in fisheries or aquaculture. Black sea bass social structure is unknown, which makes sex change sampling difficult, and few molecular resources are available. The purpose of the present study was to induce sex change using exemestane, an aromatase inhibitor, and assess gonadal gene expression using sex markers (amh, zpc2) and genes involved in steroidogenesis (cyp19a1a, cyp11b), estrogen signaling (esr1, esr2b), and apoptosis or atresia (aen, casp9, fabp11, parg, pdcd4, rif1). Overall, dietary exemestane treatment was effective, and most exposed females exhibited early histological signs of sex change and significantly higher rates of ovarian atresia relative to control females. Genes associated with atresia did not reflect this, however, as expression patterns in sex changing gonads were overall similar to those of ovaries, likely due to a whole ovary dilution effect of the RNA. Still, small but insignificant expression decreases during early sex change were detected for ovary-related genes (aen, casp9, fabp11, zpc2) and anti-apoptotic factors (parg, rif1). Exemestane treatment did not impact spermatogenesis or testicular gene expression, but testes were generally characterized by elevated steroidogenic enzyme and estrogen receptor mRNAs. Further research will be needed to understand these processes in black sea bass, using isolated ovarian follicles and multiple stages of sex change.
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Affiliation(s)
- Timothy S Breton
- Division of Natural Sciences, University of Maine at Farmington, 173 High Street, Farmington, ME 04938, USA.
| | - Linas W Kenter
- Department of Biological Sciences, University of New Hampshire, 38 College Road, Durham, NH 03824, USA
| | - Katherine Greenlaw
- Division of Natural Sciences, University of Maine at Farmington, 173 High Street, Farmington, ME 04938, USA
| | - Jacob Montgomery
- Division of Natural Sciences, University of Maine at Farmington, 173 High Street, Farmington, ME 04938, USA
| | - Giles W Goetz
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA
| | - David L Berlinsky
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, 46 College Road, Durham, NH 03824, USA
| | - J Adam Luckenbach
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA; Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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1313
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Singh A, Chowdhury D, Gupta A, Meena RC, Chakrabarti A. TORC1-signalling is down-regulated in Saccharomyces cerevisiae hsp30Δ cells by SNF1-dependent mechanisms. Yeast 2018; 35:653-667. [PMID: 30335186 DOI: 10.1002/yea.3360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 01/23/2023] Open
Abstract
Hsp30 is a plasma membrane localized heat shock protein in Saccharomyces cerevisiae whose expression is induced by numerous environmental stressors. Elucidation of its mechanism of action has remained elusive primarily because hsp30Δ cells do not show a strong phenotype. To identify cellular functions associated with Hsp30, we thus compared the transcriptome of BY4741hsp30Δ with that of its wild type counterpart. Our studies indicate down-regulation of the target of rapamycin complex 1 (TORC1)-dependent gene-expression programme in hsp30Δ cells. We further show that TORC1-signalling through its effectors (Sch9 and Tap42) was down-regulated in the deletion strain. Specifically, (a) phosphorylation levels of Sch9 were lower and nuclear exclusion of Rim15 (Sch9-downstream function) was overridden in hsp30Δ cells, (b) membrane association of Tor1 and Tap42 was lower in hsp30Δ cells, and (c) Tap42-downstream functions were abrogated in the deletion strain. Furthermore, transcription factors Rtg1, Rtg3, Gat1, and Gln3 were localized in the nucleus of the hsp30Δ as observed upon inactivation of TORC1. Studies aimed at determining how TORC1-signalling is down-regulated in hsp30Δ cells indicated that total reducing sugar levels were lower and ADP:ATP ratio was higher in hsp30Δ cells -conditions known to activate the Snf1 kinase and consequently to the inactivation of TORC1. We thus determined if TORC1-signalling could be restored in hsp30Δ cells upon the deletion of SNF1. Sch9 phosphorylation levels (TORC1-signalling) was restored to wild type levels in hsp30Δsnf1Δ cells. TORC1-signalling is thus down-regulated in hsp30Δ cells by SNF1-dependent mechanisms. A probable role for Hsp30 is discussed.
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Affiliation(s)
- Ajeet Singh
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Daipayan Chowdhury
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Avinash Gupta
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Ramesh Chand Meena
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
| | - Amitabha Chakrabarti
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Delhi, India
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1314
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Edrisi Maryan K, Samizadeh Lahiji H, Farrokhi N, Hasani Komeleh H. Analysis of Brassica napus dehydrins and their Co-Expression regulatory networks in relation to cold stress. Gene Expr Patterns 2018; 31:7-17. [PMID: 30408599 DOI: 10.1016/j.gep.2018.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 10/27/2022]
Abstract
Dehydrins (DHNs) are plant specific cold and drought stress-responsive proteins that belong to late embryogenesis abundant (LEA) protein families. B. napus DHNs (BnDHNs) were computationally analyzed to establish gene regulatory- and protein-protein interaction networks. Promoter analyses suggested functionality of phytohormones in BnDHNs gene network. The relative expressions of some BnDHNs were analyzed using qRT-PCR in seedling leaves of both cold-tolerant (Zarfam) and -sensitive (Sari Gul) canola treated/untreated by cold. Our expression data were indicative of the importance of BnDHNs in cold tolerance in Zarfam. BnDHNs were classified into three classes according to the expression pattern. Moreover, expression of three BnDHN types, SKn (BnLEA10 and BnLEA18), YnKn (BnLEA90) and YnSKn (BnLEA104) were significantly high in the tolerant cultivar at 12 h of cold treatment. Our findings put forward the possibility of considering these genes as screening biomarker to determine cold-tolerant breeding lines; something that needs to be further corroborated. Furthermore, these genes may have some implications in developing such tolerant lines via transgenesis.
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Affiliation(s)
- Khazar Edrisi Maryan
- Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran
| | | | - Naser Farrokhi
- Department of Cell and Molecular Biology, Faculty of Biological Sciences and Biotechnology, Shahid Beheshti University. G.C., Evin, Tehran, Iran.
| | - Hassan Hasani Komeleh
- Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran
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1315
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Kurome M, Baehr A, Simmet K, Jemiller EM, Egerer S, Dahlhoff M, Zakhartchenko V, Nagashima H, Klymiuk N, Kessler B, Wolf E. Targeting αGal epitopes for multi-species embryo immunosurgery. Reprod Fertil Dev 2018; 31:820-826. [PMID: 30384878 DOI: 10.1071/rd18120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/20/2018] [Indexed: 11/23/2022] Open
Abstract
Immunosurgical isolation of the inner cell mass (ICM) from blastocysts is based on complement-mediated lysis of antibody-coated trophectoderm (TE) cells. Conventionally, anti-species antisera, containing antibodies against multiple undefined TE-cell epitopes, have been used as the antibody source. We previously generated α-1,3-galactosyltransferase deficient (GTKO) pigs to prevent hyperacute rejection of pig-to-primate xenotransplants. Since GTKO pigs lack galactosyl-α-1,3-galactose (αGal) but are exposed to this antigen (e.g. αGal on gut bacteria), they produce anti-αGal antibodies. In this study, we examined whether serum from GTKO pigs could be used as a novel antibody source for multi-species embryo immunosurgery. Mouse, rabbit, pig and cattle blastocysts were used for the experiment. Expression of αGal epitopes on the surface of TE cells was detected in blastocysts of all species tested. GTKO pig serum contained sufficient anti-αGal antibodies to induce complement-mediated lysis of TE cells in blastocysts from all species investigated. Intact ICMs could be successfully recovered and the majority showed the desired level of purity. Our study demonstrates that GTKO pig serum is a reliable and effective source of antibodies targeting the αGal epitopes of TE cells for multi-species embryo immunosurgery.
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Affiliation(s)
- Mayuko Kurome
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Andrea Baehr
- Klinikum Rechts der Isar, Innere Medizin I, TU Munich, Ismaninger strasse 22, 81675 Munich, Germany
| | - Kilian Simmet
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Eva-Maria Jemiller
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Stefanie Egerer
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Maik Dahlhoff
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Hiroshi Nagashima
- Meiji University International Institute for Bio-Resource Research, 1-1-1 Higashimita, Tama, Kawasaki, Kanagawa 214-8571, Japan
| | - Nikolai Klymiuk
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Barbara Kessler
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Centre for Innovative Medical Models (CiMM), LMU Munich, Hacker strasse 27, 85764 Oberschleissheim, Germany
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1316
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McGuire JT, Cozzarelli IM, Bekins BA, Link H, Martinović-Weigelt D. Toxicity Assessment of Groundwater Contaminated by Petroleum Hydrocarbons at a Well-Characterized, Aged, Crude Oil Release Site. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12172-12178. [PMID: 30272965 DOI: 10.1021/acs.est.8b03657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Management of petroleum-impacted waters by monitored natural attenuation requires an understanding of the toxicology of both the original compounds released and the transformation products formed during natural breakdown. Here, we report data from a groundwater plume consisting of a mixture of crude oil compounds and transformation products in an effort to bridge the gap between groundwater quality information and potential biological effects of human exposures. Groundwater samples were characterized for redox processes, concentrations of nonvolatile dissolved organic carbon (NVDOC) and total petroleum hydrocarbons in the diesel range, as well as for activation of human nuclear receptors (hNR) and toxicologically relevant transcriptional pathways. Results show upregulation of several biological pathways, including peroxisome proliferator-activated receptor gamma and alpha, estrogen receptor alpha, and pregnane X receptor (PXR) with higher levels of hNR activity observed in more contaminated samples. Our study of affected groundwater contaminated by a crude-oil release 39 years ago shows these types of waters may have the potential to cause adverse impacts on development, endocrine, and liver functioning in exposed populations. Additionally, positive trends in activation of some of the molecular targets (e.g., PXR) with increasing NVDOC concentrations (including polar transformation products) demonstrate the importance of improving our understanding of the toxicity associated with the unknown transformation products present in hydrocarbon-impacted waters. Our results begin to provide insight into the potential toxicity of petroleum-impacted waters, which is particularly timely given the ubiquitous nature of waters impacted by petroleum contamination not only recently but also in the past and the need to protect drinking-water quality.
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Affiliation(s)
- Jennifer T McGuire
- Department of Biology , University of St. Thomas , St. Paul , Minnesota 55105 , United States
| | | | - Barbara A Bekins
- U.S. Geological Survey , Menlo Park , California 94025 , United States
| | - Hannah Link
- Department of Biology , University of St. Thomas , St. Paul , Minnesota 55105 , United States
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1317
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López-González MJ, Escobedo S, Rodríguez A, Neves AR, Janzen T, Martínez B. Adaptive Evolution of Industrial Lactococcus lactis Under Cell Envelope Stress Provides Phenotypic Diversity. Front Microbiol 2018; 9:2654. [PMID: 30455679 PMCID: PMC6230721 DOI: 10.3389/fmicb.2018.02654] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/17/2018] [Indexed: 12/14/2022] Open
Abstract
Lactococcus lactis is widely used as a starter in the manufacture of cheese and fermented milk. Its main role is the production of lactic acid, but also contributes to the sensory attributes of cheese. Unfortunately, the diversity of suitable strains to be commercialized as dairy starters is limited. In this work, we have applied adaptive evolution under cell envelope stress (AE-CES) as means to provide evolved L. lactis strains with distinct physiological and metabolic traits. A total of seven strains, three of industrial origin and four wild nisin Z-producing L. lactis, were exposed to subinhibitory concentrations of Lcn972, a bacteriocin that triggers the cell envelope stress response in L. lactis. Stable Lcn972 resistant (Lcn972R) mutants were obtained from all of them and two mutants per strain were further characterized. Minimal inhibitory Lcn972 concentrations increased from 4- to 32-fold compared to their parental strains and the Lcn972R mutants retained similar growth parameters in broth. All the mutants acidified milk to a pH below 5.3 with the exception of one that lost the lactose plasmid during adaptation and was unable to grow in milk, and two others with slower acidification rates in milk. While in general phage susceptibility was unaltered, six mutants derived from three nisin Z producers became more sensitive to phage attack. Loss of a putative plasmid-encoded anti-phage mechanism appeared to be the reason for phage susceptibility. Otherwise, nisin production in milk was not compromised. Different inter- and intra-strain-dependent phenotypes were observed encompassing changes in cell surface hydrophobicity and in their autolytic profile with Lcn972R mutants being, generally, less autolytic. Resistance to other antimicrobials revealed cross-protection mainly to cell wall-active antimicrobials such as lysozyme, bacitracin, and vancomycin. Finally, distinct and shared non-synonymous mutations were detected in the draft genome of the Lcn972R mutants. Depending on the parental strain, mutations were found in genes involved in stress response, detoxification modules, cell envelope biogenesis and/or nucleotide metabolism. As a whole, the results emphasize the different strategies by which each strain becomes resistant to Lcn972 and supports the feasibility of AE-CES as a novel platform to introduce diversity within industrial L. lactis dairy starters.
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Affiliation(s)
- María Jesús López-González
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
| | - Susana Escobedo
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
| | - Ana Rodríguez
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
| | | | | | - Beatriz Martínez
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
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1318
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Nespolo RF, Gaitan-Espitia JD, Quintero-Galvis JF, Fernandez FV, Silva AX, Molina C, Storey KB, Bozinovic F. A functional transcriptomic analysis in the relict marsupial Dromiciops gliroides
reveals adaptive regulation of protective functions during hibernation. Mol Ecol 2018; 27:4489-4500. [DOI: 10.1111/mec.14876] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Roberto F. Nespolo
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
- Departamento de Ecología; Center of Applied Ecology and Sustainability (CAPES); Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
- Millennium Institute for Integrative Biology (iBio); Santiago Chile
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences; The University of Hong Kong; Hong Kong SAR China
- CSIRO Oceans & Atmosphere; Hobart Tasmania Australia
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Fernanda V. Fernandez
- Instituto de Fisiología; Facultad de Medicina; Universidad Austral de Chile; Valdivia Chile
| | - Andrea X. Silva
- AUSTRALomics, Vicerrectoría de Investigación, Desarrollo y Creación Artística; Universidad Austral de Chile; Valdivia Chile
| | - Cristian Molina
- AUSTRALomics, Vicerrectoría de Investigación, Desarrollo y Creación Artística; Universidad Austral de Chile; Valdivia Chile
| | - Kenneth B. Storey
- Department of Biology and Institute of Biochemistry; Carleton University; Ottawa Ontario Canada
| | - Francisco Bozinovic
- Departamento de Ecología; Center of Applied Ecology and Sustainability (CAPES); Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
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1319
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Patil PG, Bohra A, Satheesh NSJ, Dubey J, Pandey P, Dutta D, Singh F, Singh IP, Singh NP. Validation of QTLs for plant ideotype, earliness and growth habit traits in pigeonpea ( Cajanus cajan Millsp.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1245-1259. [PMID: 30425438 PMCID: PMC6214447 DOI: 10.1007/s12298-018-0584-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 07/07/2018] [Accepted: 07/17/2018] [Indexed: 06/09/2023]
Abstract
Pigeonpea productivity is greatly constrained by poor plant ideotype of existing Indian cultivars. Enhancing pigeonpea yield demands a renewed focus on restructuring the ideal plant type by using more efficient approaches like genomic tools. Therefore, the present study aims to identify and validate a set of QTLs/gene(s) presumably associated with various plant ideotype traits in pigeonpea. A total of 133 pigeonpea germplasms were evaluated along with four checks in the augmented design for various ideotype traits i.e. initiation of flowering (IF), days to 50% flowering (DFF), days to maturity (DM), plant height (PH), primary branches (PB), seeds per pod (SP) and pod length (PL). We observed significant genetic diversity in the germplasm lines for these traits. The genetic control of IF, DFF, DM and PH renders these traits suitable for detection of marker trait associations. By using residual maximum likelihood algorithm, we obtained appropriate variance-covariance structures for modeling heterogeneity, correlation of genetic effects and non-genetic residual effects. The estimates of genetic correlations indicated a strong association among earliness traits. The best linear unbiased prediction values were calculated for individual traits, and association analysis was performed in a panel of 95 diverse genotypes with 19 genic SSRs. Out of five QTL-flanking SSRs used here for validation, only ASSR295 could show significant association with FDR and Bonferroni corrections, and accounted for 15.4% IF, 14.2% DFF and 16.2% DM of phenotypic variance (PV). Remaining SSR markers (ASSR1486, ASSR206 and ASSR408) could not qualify false discovery rate (FDR) and Bonferroni criteria, hence declared as false positives. Additionally, we identified two highly significant SSR markers, ASSR8 and ASSR390 on LG 1 and LG 2, respectively. The SSR marker ASSR8 explained up to 22 and 11% PV for earliness traits and PB respectively, whereas ASSR390 controlled up to 17% PV for earliness traits. The validation and identification of new QTLs in pigeonpea across diverse genetic backgrounds brightens the prospects for marker-assisted selection to improve yield gains in pigeonpea.
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Affiliation(s)
- Prakash G. Patil
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
- Present Address: ICAR-National Research Centre on Pomegranate, Solapur, 413 255 India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Naik S. J. Satheesh
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Jyotirmay Dubey
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Praveen Pandey
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Dibendu Dutta
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Farindra Singh
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - I. P. Singh
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - N. P. Singh
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
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1320
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Giri BR, Li H, Chen Y, Cheng G. Preliminary evaluation of neoblast-like stem cell factor and transcript expression profiles in Schistosoma japonicum. Acta Trop 2018; 187:57-64. [PMID: 30055172 DOI: 10.1016/j.actatropica.2018.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 11/18/2022]
Abstract
Neoblast-like stem cell factors and transcripts are essential for cell proliferation, self-renewal, and differentiation. Recent studies have demonstrated that nanos, sox, and vasa-like transcription factors are associated with neoblast-like stem cells in Schistosoma mansoni and play crucial roles in the regulation of worm development. However, these neoblast-like stem cell factors and transcripts and their expression profiles remain unknown in Schistosoma japonicum. In this study, we identified orthologs of 11 neoblast-like stem cell factors and transcripts in S. japonicum using bioinformatics and confirmed them by PCR. The expression profiles of neoblast-like stem cell factors and transcripts revealed that some of them were highly expressed in certain stages. Sex-based expression analysis revealed that nanos, polo-like kinase, PCNA, cyclin B, and H2A showed significantly higher expression in female worms, whereas ago and bruli showed higher expression in male worms. In addition, we noted that ago, bruli, and pp32 exhibited higher expression in the testes, while nanos, polo-like kinase, cyclin B, H2A, and H2B showed notable higher expression in both isolated ovaries and testes. Our preliminary results are expected to provide important information about the regulatory roles of these stem cell factors in parasite development and sexual maturation.
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Affiliation(s)
- Bikash Ranjan Giri
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, 518 Ziyue Road, 200241, Shanghai, China
| | - Huimin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, 518 Ziyue Road, 200241, Shanghai, China
| | - Yongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, 518 Ziyue Road, 200241, Shanghai, China
| | - Guofeng Cheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture, 518 Ziyue Road, 200241, Shanghai, China.
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1321
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Somuncu ÖS, Coşkun Y, Ballica B, Temiz AF, Somuncu D. In vitro artificial skin engineering by decellularized placental scaffold for secondary skin problems of meningomyelocele. J Clin Neurosci 2018; 59:291-297. [PMID: 30385168 DOI: 10.1016/j.jocn.2018.10.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/07/2018] [Indexed: 11/18/2022]
Abstract
BACKGROUND Meningomyelocele (MMC) is a condition that is originated by the fusion defect of the neural tube. It is a congenital anomaly and can be characterized by spinal cord defects and impaired skin integrity. It is very important to close the skin openings via three-dimensional artificial skin like construction for preventing infection and maintaining the healthy skin structure. Therefore, we aim to generate artificial skin like structures formed by the own cells of donor for treating the MMC-related skin disorder. METHODS In this study, waste placental tissues were collected and decellularization process was applied. Decellularized and normal placental tissues were compared by immunohistochemistry (IHC). Donor's own placental stem cells were seeded onto biological scaffold and were differentiated into skin related cell types. Finally, gene expressions were evaluated, and the structural integrity were analyzed with IHC. Tube formation assay was also performed for examining the angiogenesis formation of the tissue in order to evaluate the possibility of a healthy organ development. RESULTS Characterization experiments proved that the decellularized skin preserved a normal skin 3D construction and vasculature along with significant ECM arrangements. The well-kept placental ECM scaffold was cytocompatible, supportive of mesenchymal cell types. Native organ related scaffold is expected to carry a huge influence in skin tissue engineering via delivering a niche for skin-based cells and even for stem/progenitor cells. Regarding to the data obtained from this study, in vivo investigation the skin-like structure in animal models is thought to be the next step as a future prospect. CONCLUSION This study is a reference investigation for skin engineering based on placental stem cells and biological scaffolds.
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Affiliation(s)
| | - Yeşim Coşkun
- Bahçeşehir University, Faculty of Medicine, Department of Pediatrics, Turkey
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1322
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Ivanyi-Nagy R, Ahmed SM, Peter S, Ramani PD, Ong PF, Dreesen O, Dröge P. The RNA interactome of human telomerase RNA reveals a coding-independent role for a histone mRNA in telomere homeostasis. eLife 2018; 7:40037. [PMID: 30355447 PMCID: PMC6249008 DOI: 10.7554/elife.40037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/24/2018] [Indexed: 12/26/2022] Open
Abstract
Telomerase RNA (TR) provides the template for DNA repeat synthesis at telomeres and is essential for genome stability in continuously dividing cells. We mapped the RNA interactome of human TR (hTR) and identified a set of non-coding and coding hTR-interacting RNAs, including the histone 1C mRNA (HIST1H1C). Disruption of the hTR-HIST1H1C RNA association resulted in markedly increased telomere elongation without affecting telomerase enzymatic activity. Conversely, over-expression of HIST1H1C led to telomere attrition. By using a combination of mutations to disentangle the effects of histone 1 RNA synthesis, protein expression, and hTR interaction, we show that HIST1H1C RNA negatively regulates telomere length independently of its protein coding potential. Taken together, our data provide important insights into a surprisingly complex hTR-RNA interaction network and define an unexpected non-coding RNA role for HIST1H1C in regulating telomere length homeostasis, thus offering a glimpse into the mostly uncharted, vast space of non-canonical messenger RNA functions.
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Affiliation(s)
- Roland Ivanyi-Nagy
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Syed Moiz Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Peh Fern Ong
- Cell Ageing, Skin Research Institute Singapore, Singapore, Singapore
| | - Oliver Dreesen
- Cell Ageing, Skin Research Institute Singapore, Singapore, Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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1323
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Alazem M, Tseng KC, Chang WC, Seo JK, Kim KH. Elements Involved in the Rsv3-Mediated Extreme Resistance against an Avirulent Strain of Soybean Mosaic Virus. Viruses 2018; 10:E581. [PMID: 30355968 PMCID: PMC6267276 DOI: 10.3390/v10110581] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 01/06/2023] Open
Abstract
Extreme resistance (ER) is a type of R-gene-mediated resistance that rapidly induces a symptomless resistance phenotype, which is different from the phenotypical R-resistance manifested by the programmed cell death, accumulation of reactive oxygen species, and hypersensitive response. The Rsv3 gene in soybean cultivar L29 is responsible for ER against the avirulent strain G5H of soybean mosaic virus (SMV), but is ineffective against the virulent strain G7H. Rsv3-mediated ER is achieved through the rapid accumulation of callose, which arrests SMV-G5H at the point of infection. Callose accumulation, however, may not be the lone mechanism of this ER. Analyses of RNA-seq data obtained from infected soybean plants revealed a rapid induction of the abscisic acid pathway at 8 h post infection (hpi) in response to G5H but not to G7H, which resulted in the down-regulation of transcripts encoding β-1,3 glucanases that degrade callose in G5H-infected but not G7H-infected plants. In addition, parts of the autophagy and the small interfering (si) RNA pathways were temporally up-regulated at 24 hpi in response to G5H but not in response to G7H. The jasmonic acid (JA) pathway and many WRKY factors were clearly up-regulated only in G7H-infected plants. These results suggest that ER against SMV-G5H is achieved through the quick and temporary induction of ABA, autophagy, and the siRNA pathways, which rapidly eliminate G5H. The results also suggest that suppression of the JA pathway in the case of G5H is important for the Rsv3-mediated ER.
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Affiliation(s)
- Mazen Alazem
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
| | - Kuan-Chieh Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
| | - Wen-Chi Chang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
| | - Jang-Kyun Seo
- Department of International Agricultural Technology and Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
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1324
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Tyler CJ, Pérez-Jeldres T, Ehinger E, Capaldo B, Karuppuchamy T, Boyer JD, Patel D, Dulai P, Boland BS, Lannigan J, Eckmann L, Ernst PB, Sandborn WJ, Ho SB, Rivera-Nieves J. Implementation of Mass Cytometry as a Tool for Mechanism of Action Studies in Inflammatory Bowel Disease. Inflamm Bowel Dis 2018; 24:2366-2376. [PMID: 29889233 PMCID: PMC6185553 DOI: 10.1093/ibd/izy214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 12/12/2022]
Abstract
Background Novel therapeutics for inflammatory bowel disease (IBD) are under development, yet mechanistic readouts at the tissue level are lacking. Techniques to assess intestinal immune composition could represent a valuable tool for mechanism of action (MOA) studies of novel drugs. Mass cytometry enables analysis of intestinal inflammatory cell infiltrate and corresponding molecular fingerprints with unprecedented resolution. Here, we aimed to optimize the methodology for isolation and cryopreservation of cells from intestinal tissue to allow for the potential implementation of mass cytometry in MOA studies. Methods We investigated key technical issues, including minimal tissue requirements, cell isolation protocols, and cell storage, using intestinal biopsies and peripheral blood from healthy individuals. High-dimensional mass cytometry was employed for the analyses of biopsy-derived intestinal cellular subsets. Results Dithiothreitol and mechanical dissociation decreased epithelial cell contamination and allowed for isolation of adequate cell numbers from 2 to 4 colonic or ileal biopsies (6 × 104±2 × 104) after a 20-minute collagenase digestion, allowing for reliable detection of most major immune cell subsets. Biopsies and antibody-labeled mononuclear cells could be cryopreserved for later processing and acquisition (viability > 70%; P < 0.05). Conclusions Mass cytometry represents a unique tool for deep immunophenotyping intestinal cell composition. This technique has the potential to facilitate analysis of drug actions at the target tissue by identifying specific cellular subsets and their molecular signatures. Its widespread implementation may impact not only IBD research but also other gastrointestinal conditions where inflammatory cells play a role in pathogenesis.
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Affiliation(s)
- Christopher J Tyler
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
- VA San Diego Healthcare System, San Diego, California
| | - Tamara Pérez-Jeldres
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
- VA San Diego Healthcare System, San Diego, California
- Universidad Catolica de Chile, Santiago, Chile
| | - Erik Ehinger
- Flow Cytometry Core Facility, La Jolla Institute of Allergy and Immunology, La Jolla, California
| | - Brian Capaldo
- Flow Cytometry Core Facility, University of Virginia, Charlottesville, Virginia
| | - Thangaraj Karuppuchamy
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
- VA San Diego Healthcare System, San Diego, California
| | - Joshua D Boyer
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
- VA San Diego Healthcare System, San Diego, California
| | - Derek Patel
- VA San Diego Healthcare System, San Diego, California
| | - Parambir Dulai
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
- VA San Diego Healthcare System, San Diego, California
| | - Brigid S Boland
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
| | - Joanne Lannigan
- Flow Cytometry Core Facility, University of Virginia, Charlottesville, Virginia
| | - Lars Eckmann
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
| | - Peter B Ernst
- Division of Comparative Pathology, Department of Pathology, University of California San Diego, La Jolla, California
- Chiba University–UC San Diego Program in Mucosal Immunology, Allergy and Vaccines, San Diego, California
| | | | - Samuel B Ho
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
- VA San Diego Healthcare System, San Diego, California
| | - Jesús Rivera-Nieves
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, California
- VA San Diego Healthcare System, San Diego, California
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1325
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Faraji S, Rasouli SH, Kazemitabar SK. Genome-wide exploration of C2H2 zinc finger family in durum wheat (Triticum turgidum ssp. Durum): insights into the roles in biological processes especially stress response. Biometals 2018; 31:1019-1042. [PMID: 30288657 DOI: 10.1007/s10534-018-0146-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/22/2018] [Indexed: 11/30/2022]
Abstract
C2H2 type of zinc finger transcription factors (C2H2-ZFP TFs) play crucial roles in plant developments and stress response. Regarding its importance, genome-wide study of C2H2-ZFs were performed in multiple important plant species, but any such investigation was not fulfilled in Triticum turgidum ssp. Durum (durum wheat) as an important nutritional crop. The present study identified 122 C2H2-ZFs in durum wheat and physically mapped them onto the genome. The phylogenetic analysis classified these TFs into six major groups. Genes structure and conserved motifs assay showed TtC2H2-ZF involvement in the important cellular functions. Comparative phylogeny between durum wheat TtC2H2-ZF genes and the orthologs in rice revealed the evolutionary relationships of C2H2-ZF proteins. The gene ontology and promoter cis-element analysis indicated that most of TtC2H2-ZF genes are involved in multiple molecular functions including metal ion-binding and various stimuli responses. Further, the miRNAs targeting TtC2H2-ZF transcripts, homology modeling and proteins interaction network were also demonstrated, suggesting the vital cellular functions of TtC2H2-ZFs during various circumstances. The expression heatmap demonstrated differential and tissue-specific expression patterns of these genes. Expression profiling of this gene family members in response to dehydration and heat stresses showed differential expression pattern of these genes at multiple time points of stresses. This study can prepare a comprehensive overview of the durum wheat C2H2-ZF gene family and may provide a new perspective on the evolution of them, which will form the basis for further investigation of the roles of this family members and future genetic engineering studies in crops.
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Affiliation(s)
- Sahar Faraji
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
| | - Seyyed Hamidreza Rasouli
- Department of Entrepreneurship Technology, Faculty of Management, Payame Noor University (PNU), Babol, Iran
| | - Seyyed Kamal Kazemitabar
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
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1326
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Speidel JT, Xu M, Abdel-Rahman SZ. Promoter Haplotypes of the ABCB1 Gene Encoding the P-Glycoprotein Differentially Affect Its Promoter Activity by Altering Transcription Factor Binding. DNA Cell Biol 2018; 37:973-981. [PMID: 30277801 DOI: 10.1089/dna.2018.4376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Promoter single nucleotide polymorphisms (SNPs) of the ABCB1 gene, encoding the placental efflux transporter P-glycoprotein, can alter its expression and affect fetal exposure to therapeutics and environmental xenobiotics. SNPs are not arrayed as independent variants but as combinations forming defined haplotypes. Recently, we defined the haplotypes encompassing ABCB1 promoter SNPs and found that ABCB1 haplotypes differentially affect its promoter activity. The mechanism(s) by which ABCB1 haplotypes alter its promoter activity are not known. We hypothesize that the haplotype-dependent differences in ABCB1 promoter activity are due to haplotype-specific alterations in transcription factor (TF) binding. To test our hypothesis, we used a TF binding profile array and determined whether differences in TF binding exist across different ABCB1 haplotypes. TFs showing significant haplotype binding differences were mechanistically evaluated using small interfering RNA (siRNA) in cultured human placental cells. Our data indicate significant haplotype-dependent differences in TF binding. Our siRNA studies showed that the regulatory effects of TFs on promoter activity are also haplotype dependent. Our data provide a mechanistic explanation for the differential effects of ABCB1 haplotypes on its promoter activity and underscore the importance of evaluating genetic variants in the context of haplotypes rather than individual SNPs when investigating their effects on gene/protein expression and disease risk.
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Affiliation(s)
- Jordan T Speidel
- 1 Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas.,2 Maternal-Fetal Pharmacology and Biodevelopment Laboratories, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas
| | - Meixiang Xu
- 2 Maternal-Fetal Pharmacology and Biodevelopment Laboratories, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas
| | - Sherif Z Abdel-Rahman
- 2 Maternal-Fetal Pharmacology and Biodevelopment Laboratories, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas
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1327
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A glance of genetic relations in the Balkan populations utilizing network analysis based on in silico assigned Y-DNA haplogroups. ANTHROPOLOGICAL REVIEW 2018. [DOI: 10.2478/anre-2018-0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study is to provide an insight into Balkan populations’ genetic relations utilizing in silico analysis of Y-STR haplotypes and performing haplogroup predictions together with network analysis of the same haplotypes for visualization of the relations between chosen haplotypes and Balkan populations in general. The population dataset used in this study was obtained using 23, 17, 12, 9 and 7 Y-STR loci for 13 populations. The 13 populations include: Bosnia and Herzegovina (B&H), Croatia, Macedonia, Slovenia, Greece, Romany (Hungary), Hungary, Serbia, Montenegro, Albania, Kosovo, Romania and Bulgaria. The overall dataset contains a total of 2179 samples with 1878 different haplotypes.
I2a was detected as the major haplogroup in four out of thirteen analysed Balkan populations. The four populations (B&H, Croatia, Montenegro and Serbia) which had I2a as the most prevalent haplogroup were all from the former Yugoslavian republic. The remaining two major populations from former Yugoslavia, Macedonia and Slovenia, had E1b1b and R1a haplogroups as the most prevalent, respectively.
The populations with E1b1b haplogroup as the most prevalent one are Macedonian, Romanian, as well as Albanian populations from Kosovo and Albania. The I2a haplogroup cluster is more compact when compared to E1b1b and R1b haplogroup clusters, indicating a larger degree of homogeneity within the haplotypes that belong to the I2a haplogroup. Our study demonstrates that a combination of haplogroup prediction and network analysis represents an effective approach to utilize publicly available Y-STR datasets for population genetics.
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1328
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Martin-Mateos R, De Assuncao TM, Arab JP, Jalan-Sakrikar N, Yaqoob U, Greuter T, Verma VK, Mathison AJ, Cao S, Lomberk G, Mathurin P, Urrutia R, Huebert RC, Shah VH. Enhancer of Zeste Homologue 2 Inhibition Attenuates TGF-β Dependent Hepatic Stellate Cell Activation and Liver Fibrosis. Cell Mol Gastroenterol Hepatol 2018; 7:197-209. [PMID: 30539787 PMCID: PMC6282644 DOI: 10.1016/j.jcmgh.2018.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Transdifferentiation of hepatic stellate cells (HSCs) into myofibroblasts is a key event in the pathogenesis of liver fibrosis. Transforming growth factor β (TGF-β) and platelet-derived growth factor (PDGF) are canonical HSC activators after liver injury. The aim of this study was to analyze the epigenetic modulators that differentially control TGF-β and PDGF signaling pathways. METHODS We performed a transcriptomic comparison of HSCs treated with TGF-β or PDGF-BB using RNA sequencing. Among the targets that distinguish these 2 pathways, we focused on the histone methyltransferase class of epigenetic modulators. RESULTS Enhancer of zeste homolog 2 (EZH2) was expressed differentially, showing significant up-regulation in HSCs activated with TGF-β but not with PDGF-BB. Indeed, EZH2 inhibition using either a pharmacologic (GSK-503) or a genetic (small interfering RNA) approach caused a significant attenuation of TGF-β-induced fibronectin, collagen 1α1, and α-smooth muscle actin, both at messenger RNA and protein levels. Conversely, adenoviral overexpression of EZH2 in HSCs resulted in a significant stimulation of fibronectin protein and messenger RNA levels in TGF-β-treated cells. Finally, we conducted in vivo experiments with mice chronically treated with carbon tetrachloride or bile duct ligation. Administration of GSK-503 to mice receiving either carbon tetrachloride or bile duct ligation led to attenuated fibrosis as assessed by Trichrome and Sirius red stains, hydroxyproline, and α-smooth muscle actin/collagen protein assays. CONCLUSIONS TGF-β and PDGF share redundant and distinct transcriptomic targets, with the former predominating in HSC activation. The EZH2 histone methyltransferase is preferentially involved in the TGF-β as opposed to the PDGF signaling pathway. Inhibition of EZH2 attenuates fibrogenic gene transcription in TGF-β-treated HSCs and reduces liver fibrosis in vivo. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE119606 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119606).
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Affiliation(s)
- Rosa Martin-Mateos
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Ramón y Cajal University Hospital, Madrid, Spain
| | | | - Juan Pablo Arab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Departamento de Gastroenterologia, Escuela de Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | | | - Usman Yaqoob
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas Greuter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Vikas K Verma
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Angela J Mathison
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin; Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Sheng Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Gwen Lomberk
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Philippe Mathurin
- Service Maladie de l'Appareil Digestif, INSERM U995 Université Lille 2, Centre Hospitalier Régionale Universitaire (CHRU) de Lille, France
| | - Raul Urrutia
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin; Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert C Huebert
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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1329
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ICOSL-augmented adenoviral-based vaccination induces a bipolar Th17/Th1 T cell response against unglycosylated MUC1 antigen. Vaccine 2018; 36:6262-6269. [PMID: 30219366 DOI: 10.1016/j.vaccine.2018.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/18/2018] [Accepted: 09/07/2018] [Indexed: 01/14/2023]
Abstract
Cellular immunity established via immunotherapy holds the potential to eliminate solid tumors. Yet, cancer vaccines have failed to induce tumor-reactive T cells of sufficient quality to control disease. The inducible T cell costimulator (ICOS) pathway has been implicated in both the selective induction of immunity over tolerance as well as licensing of IL-17-polarized cellular immunity. Herein, we evaluated the ability of ICOS ligand (ICOSL) to augment the immunogenicity of adenoviral-based vaccination targeting the unglycosylated MUC1 peptide antigen. Vaccination disrupted immunotolerance in a transgenic mouse model recognizing human MUC1 as a self-antigen, inducing robust MUC1-specific immunity. Augmenting vaccination with ICOSL induced a bipolar Th17/Th1 effector profile, marked by increased MUC1-specific IL-17A production and RORγt expression in CD4+ but not CD8+ T cells which predominantly expressed IFNγ/IL-2 and T-bet. The polarization and maintenance of Th17 cells established following ICOSL augmented vaccination was highly durable, with elevated IL-17A and RORγt levels detected in CD4+ T cells up to 10 months after initial immunization. Furthermore, provision of ICOSL significantly enhanced MUC1-specific IgG antibody in response to immunization. ICOSL signaling dramatically influenced CD4+ T cell phenotype, altering gene expression of transcription factors and regulators of effector function following immunization. Interestingly, ICOSL augmentation failed to alter the transcriptional profile of CD8+ T cells following immunization, affecting the magnitude, but not distribution, of gene expression. Collectively, ICOSL supports the induction of durable, antigen-specific Th17/Th1-mediated immunity in vivo, establishing a vaccination platform to enhance CD4+ T cell-mediated antitumor immunity and providing a crucial component of an effective cancer vaccine.
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1330
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Casalino-Matsuda SM, Wang N, Ruhoff PT, Matsuda H, Nlend MC, Nair A, Szleifer I, Beitel GJ, Sznajder JI, Sporn PHS. Hypercapnia Alters Expression of Immune Response, Nucleosome Assembly and Lipid Metabolism Genes in Differentiated Human Bronchial Epithelial Cells. Sci Rep 2018; 8:13508. [PMID: 30202079 PMCID: PMC6131151 DOI: 10.1038/s41598-018-32008-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/31/2018] [Indexed: 12/19/2022] Open
Abstract
Hypercapnia, the elevation of CO2 in blood and tissues, commonly occurs in severe acute and chronic respiratory diseases, and is associated with increased risk of mortality. Recent studies have shown that hypercapnia adversely affects innate immunity, host defense, lung edema clearance and cell proliferation. Airway epithelial dysfunction is a feature of advanced lung disease, but the effect of hypercapnia on airway epithelium is unknown. Thus, in the current study we examined the effect of normoxic hypercapnia (20% CO2 for 24 h) vs normocapnia (5% CO2), on global gene expression in differentiated normal human airway epithelial cells. Gene expression was assessed on Affymetrix microarrays, and subjected to gene ontology analysis for biological process and cluster-network representation. We found that hypercapnia downregulated the expression of 183 genes and upregulated 126. Among these, major gene clusters linked to immune responses and nucleosome assembly were largely downregulated, while lipid metabolism genes were largely upregulated. The overwhelming majority of these genes were not previously known to be regulated by CO2. These changes in gene expression indicate the potential for hypercapnia to impact bronchial epithelial cell function in ways that may contribute to poor clinical outcomes in patients with severe acute or advanced chronic lung diseases.
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Affiliation(s)
- S Marina Casalino-Matsuda
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.
| | - Naizhen Wang
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Peder T Ruhoff
- Department of Technology and Innovation, University of Southern Denmark, Odense, Denmark
| | - Hiroaki Matsuda
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Physical Sciences & Engineering, Wilbur Wright College, Chicago, Illinois, United States of America
| | - Marie C Nlend
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Division of Protein and Cellular Analysis, Thermo Fisher Scientific, Rockford, Illinois, United States of America
| | - Aisha Nair
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Chemistry, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Greg J Beitel
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Jacob I Sznajder
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Peter H S Sporn
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
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1331
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Lin YT, Whitman WB, Coleman DC, Chiu CY. Effects of Reforestation on the Structure and Diversity of Bacterial Communities in Subtropical Low Mountain Forest Soils. Front Microbiol 2018; 9:1968. [PMID: 30186273 PMCID: PMC6110939 DOI: 10.3389/fmicb.2018.01968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/02/2018] [Indexed: 11/15/2022] Open
Abstract
Reforestation with different tree species could alter soil properties and in turn affect the bacterial community. However, the effects of long-term reforestation on bacterial community structure and diversity of subtropical forest soils are poorly understood. In the current study, we applied error-corrected barcoded pyrosequencing to characterize the differences in the soil bacterial community in a low mountain, subtropical forest subjected to reforestation. The communities were sampled in the summer and winter from a native broadleaved forest (BROAD-Nat) and two adjacent coniferous plantations, a Calocedrus formosana forest of 80 years (CONIF-80) and a Cunninghamia konishii forest of 40 years (CONIF-40). The soil bacterial communities among three forest types were dominated by Acidobacteria and Alphaproteobacteria. The distribution of abundant genera among communities was different. Based on the Shannon diversity index, the bacterial alpha diversity of CONIF-40 community was significantly higher than that in the CONIF-80 and BROAD-Nat soils. In both of the coniferous plantations, the soil bacterial diversity in summer was also higher than that in winter. Distribution of some abundant phylogenetic groups, K-shuff and redundancy analysis of beta diversity among communities showed that the bacterial structure of three soil communities differed between two seasons. These results suggest that seasonal differences influence the diversity and structure of bacterial soil communities and that the communities remain different even after a long period of reforestation.
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Affiliation(s)
- Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - David C Coleman
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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1332
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Takaoka Y, Iwahashi M, Chini A, Saito H, Ishimaru Y, Egoshi S, Kato N, Tanaka M, Bashir K, Seki M, Solano R, Ueda M. A rationally designed JAZ subtype-selective agonist of jasmonate perception. Nat Commun 2018; 9:3654. [PMID: 30194307 PMCID: PMC6128907 DOI: 10.1038/s41467-018-06135-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 08/05/2018] [Indexed: 12/21/2022] Open
Abstract
The phytohormone 7-iso-(+)-jasmonoyl-L-isoleucine (JA-Ile) mediates plant defense responses against herbivore and pathogen attack, and thus increases plant resistance against foreign invaders. However, JA-Ile also causes growth inhibition; and therefore JA-Ile is not a practical chemical regulator of plant defense responses. Here, we describe the rational design and synthesis of a small molecule agonist that can upregulate defense-related gene expression and promote pathogen resistance at concentrations that do not cause growth inhibition in Arabidopsis. By stabilizing interactions between COI1 and JAZ9 and JAZ10 but no other JAZ isoforms, the agonist leads to formation of JA-Ile co-receptors that selectively activate the JAZ9-EIN3/EIL1-ORA59 signaling pathway. The design of a JA-Ile agonist with high selectivity for specific protein subtypes may help promote the development of chemical regulators that do not cause a tradeoff between growth and defense.
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Grants
- JPMJPR16Q4 Japan Science and Technology Agency (JST)
- JPMJCR13B4 JST | Core Research for Evolutional Science and Technology (CREST)
- 23102012 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 26282207 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 17H06407 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 17H00885 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
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Affiliation(s)
- Yousuke Takaoka
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency, Tokyo, 102-0076, Japan
| | - Mana Iwahashi
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Andrea Chini
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049, Madrid, Spain
| | - Hiroaki Saito
- Center for Biosystems Dynamics Research, RIKEN, Suita, 565-0874, Japan
| | - Yasuhiro Ishimaru
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Syusuke Egoshi
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Nobuki Kato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Roberto Solano
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049, Madrid, Spain
| | - Minoru Ueda
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan.
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1333
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Jehn J, Gebert D, Pipilescu F, Stern S, Kiefer JST, Hewel C, Rosenkranz D. PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation. Commun Biol 2018; 1:137. [PMID: 30272016 PMCID: PMC6128900 DOI: 10.1038/s42003-018-0141-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/17/2018] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that PIWI genes and piRNAs are ubiquitously expressed in mollusks, similar to the situation in arthropods. We describe lineage-specific adaptations of transposon composition in piRNA clusters in the great pond snail and the pacific oyster, likely reflecting differential transposon activity in gastropods and bivalves. We further show that different piRNA clusters with unique transposon composition are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs presumably bound to different PIWI paralogs participate in homotypic and heterotypic ping-pong amplification loops in a tissue- and sex-specific manner. Together with recent findings from other animal species, our results support the idea that somatic piRNA expression represents the ancestral state in metazoans.
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Affiliation(s)
- Julia Jehn
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Frank Pipilescu
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Sarah Stern
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Julian Simon Thilo Kiefer
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany.
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1334
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Raman V, Aryal UK, Hedrick V, Ferreira RM, Fuentes Lorenzo JL, Stashenko EE, Levy M, Levy MM, Camarillo IG. Proteomic Analysis Reveals That an Extract of the Plant Lippia origanoides Suppresses Mitochondrial Metabolism in Triple-Negative Breast Cancer Cells. J Proteome Res 2018; 17:3370-3383. [DOI: 10.1021/acs.jproteome.8b00255] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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1335
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Franci G, Folliero V, Cammarota M, Zannella C, Sarno F, Schiraldi C, de Lera AR, Altucci L, Galdiero M. Epigenetic modulator UVI5008 inhibits MRSA by interfering with bacterial gyrase. Sci Rep 2018; 8:13117. [PMID: 30177735 PMCID: PMC6120918 DOI: 10.1038/s41598-018-31135-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/23/2018] [Indexed: 02/08/2023] Open
Abstract
The impact of multi-drug resistant bacterial strains on human health is reaching worrisome levels. Over 2 million people are infected by resistant bacteria, and more than 700,000 people die each year because of the continuous spread of resistant strains. The development of new antibiotics and the prudent use of existing ones to prolong their lifespan require a constant effort by drug industries and healthcare workers. The re-purposing of existing drugs for use as antimicrobial agents would streamline the development of new antibacterial strategies. As part of this effort, we screened a panel of drugs previously characterized to be epigenetic modulators/pro-apoptotic/differentiative drugs. We selected a few compounds that alter Gram-positive growth. Among these, UVI5008, a derivative of the natural compound psammaplin A (Psa_A), was identified. The interaction of Psa_A with the DNA gyrase enzyme has been shown, and here, we hypothesized and confirmed the gyrase-specific activity by biochemical assays. UVI5008 exhibited growth inhibition activity against Staphylococcus aureus via structural modification of the cell wall, which was observed by SEM electron microscopy. Based on our findings, we propose UVI5008 as an alternative antibacterial compound against methicillin-resistant (Met.R) S. aureus strains.
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Affiliation(s)
- Gianluigi Franci
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Veronica Folliero
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Marcella Cammarota
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Carla Zannella
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Federica Sarno
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Chiara Schiraldi
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IBIV, Vigo, Spain
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy.
| | - Massimiliano Galdiero
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy.
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1336
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Melaine N, Com E, Bellaud P, Guillot L, Lagarrigue M, Morrice NA, Guével B, Lavigne R, Velez de la Calle JF, Dojahn J, Pineau C. Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins. J Proteome Res 2018; 17:4197-4210. [DOI: 10.1021/acs.jproteome.8b00387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathalie Melaine
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Pascale Bellaud
- H2P2 Core Facility, UMS BioSit, Univ Rennes, Rennes F-35040, France
| | - Laetitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Mélanie Lagarrigue
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Nick A. Morrice
- Sciex, Phoenix House Lakeside Drive Centre Park, Warrington WA1 1RX, U.K
| | - Blandine Guével
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | | | - Jörg Dojahn
- Sciex, Landwehrstr. 54, 64293 Darmstadt, Germany
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
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1337
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Genetics and Expression Profile of the Tubulin Gene Superfamily in Breast Cancer Subtypes and Its Relation to Taxane Resistance. Cancers (Basel) 2018; 10:cancers10080274. [PMID: 30126203 PMCID: PMC6116153 DOI: 10.3390/cancers10080274] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 01/15/2023] Open
Abstract
Taxanes are a class of chemotherapeutic agents that inhibit cell division by disrupting the mitotic spindle through the stabilization of microtubules. Most breast cancer (BC) tumors show resistance against taxanes partially due to alterations in tubulin genes. In this project we investigated tubulin isoforms in BC to explore any correlation between tubulin alterations and taxane resistance. Genetic alteration and expression profiling of 28 tubulin isoforms in 6714 BC tumor samples from 4205 BC cases were analyzed. Protein-protein, drug-protein and alterations neighbor genes in tubulin pathways were examined in the tumor samples. To study correlation between promoter activity and expression of the tubulin isoforms in BC, we analyzed the ChIP-seq enrichment of active promoter histone mark H3K4me3 and mRNA expression profile of MCF-7, ZR-75-30, SKBR-3 and MDA-MB-231 cell lines. Potential correlation between tubulin alterations and taxane resistance, were investigated by studying the expression profile of taxane-sensitive and resistant BC tumors also the MDA-MB-231 cells acquired resistance to paclitaxel. All genomic data were obtained from public databases. Results showed that TUBD1 and TUBB3 were the most frequently amplified and deleted tubulin genes in the BC tumors respectively. The interaction analysis showed physical interactions of α-, β- and γ-tubulin isoforms with each other. The most of FDA-approved tubulin inhibitor drugs including taxanes target only β-tubulins. The analysis also revealed sex tubulin-interacting neighbor proteins including ENCCT3, NEK2, PFDN2, PTP4A3, SDCCAG8 and TBCE which were altered in at least 20% of the tumors. Three of them are tubulin-specific chaperons responsible for tubulin protein folding. Expression of tubulin genes in BC cell lines were correlated with H3K4me3 enrichment on their promoter chromatin. Analyzing expression profile of BC tumors and tumor-adjacent normal breast tissues showed upregulation of TUBA1A, TUBA1C, TUBB and TUBB3 and downregulation of TUBB2A, TUBB2B, TUBB6, TUBB7P pseudogene, and TUBGCP2 in the tumor tissues compared to the normal breast tissues. Analyzing taxane-sensitive versus taxane-resistant tumors revealed that expression of TUBB3 and TUBB6 was significantly downregulated in the taxane-resistant tumors. Our results suggest that downregulation of tumor βIII- and βV-tubulins is correlated with taxane resistance in BC. Based on our results, we conclude that aberrant protein folding of tubulins due to mutation and/or dysfunction of tubulin-specific chaperons may be potential mechanisms of taxane resistance. Thus, we propose studying the molecular pathology of tubulin mutations and folding in BC and their impacts on taxane resistance.
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1338
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Genetics and Expression Profile of the Tubulin Gene Superfamily in Breast Cancer Subtypes and Its Relation to Taxane Resistance. Cancers (Basel) 2018. [DOI: 10.10.3390/cancers10080274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Taxanes are a class of chemotherapeutic agents that inhibit cell division by disrupting the mitotic spindle through the stabilization of microtubules. Most breast cancer (BC) tumors show resistance against taxanes partially due to alterations in tubulin genes. In this project we investigated tubulin isoforms in BC to explore any correlation between tubulin alterations and taxane resistance. Genetic alteration and expression profiling of 28 tubulin isoforms in 6714 BC tumor samples from 4205 BC cases were analyzed. Protein-protein, drug-protein and alterations neighbor genes in tubulin pathways were examined in the tumor samples. To study correlation between promoter activity and expression of the tubulin isoforms in BC, we analyzed the ChIP-seq enrichment of active promoter histone mark H3K4me3 and mRNA expression profile of MCF-7, ZR-75-30, SKBR-3 and MDA-MB-231 cell lines. Potential correlation between tubulin alterations and taxane resistance, were investigated by studying the expression profile of taxane-sensitive and resistant BC tumors also the MDA-MB-231 cells acquired resistance to paclitaxel. All genomic data were obtained from public databases. Results showed that TUBD1 and TUBB3 were the most frequently amplified and deleted tubulin genes in the BC tumors respectively. The interaction analysis showed physical interactions of α-, β- and γ-tubulin isoforms with each other. The most of FDA-approved tubulin inhibitor drugs including taxanes target only β-tubulins. The analysis also revealed sex tubulin-interacting neighbor proteins including ENCCT3, NEK2, PFDN2, PTP4A3, SDCCAG8 and TBCE which were altered in at least 20% of the tumors. Three of them are tubulin-specific chaperons responsible for tubulin protein folding. Expression of tubulin genes in BC cell lines were correlated with H3K4me3 enrichment on their promoter chromatin. Analyzing expression profile of BC tumors and tumor-adjacent normal breast tissues showed upregulation of TUBA1A, TUBA1C, TUBB and TUBB3 and downregulation of TUBB2A, TUBB2B, TUBB6, TUBB7P pseudogene, and TUBGCP2 in the tumor tissues compared to the normal breast tissues. Analyzing taxane-sensitive versus taxane-resistant tumors revealed that expression of TUBB3 and TUBB6 was significantly downregulated in the taxane-resistant tumors. Our results suggest that downregulation of tumor βIII- and βV-tubulins is correlated with taxane resistance in BC. Based on our results, we conclude that aberrant protein folding of tubulins due to mutation and/or dysfunction of tubulin-specific chaperons may be potential mechanisms of taxane resistance. Thus, we propose studying the molecular pathology of tubulin mutations and folding in BC and their impacts on taxane resistance.
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1339
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Mahalingam R. Temporal Analyses of Barley Malting Stages Using Shotgun Proteomics. Proteomics 2018; 18:e1800025. [DOI: 10.1002/pmic.201800025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/08/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Ramamurthy Mahalingam
- United States Department of Agriculture; Agricultural Research Service; Cereal Crops Research Unit; 502 Walnut Street 53726 Madison WI USA
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1340
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Sundararajan A, Rane HS, Ramaraj T, Sena J, Howell AB, Bernardo SM, Schilkey FD, Lee SA. Cranberry-derived proanthocyanidins induce a differential transcriptomic response within Candida albicans urinary biofilms. PLoS One 2018; 13:e0201969. [PMID: 30089157 PMCID: PMC6082538 DOI: 10.1371/journal.pone.0201969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/25/2018] [Indexed: 11/18/2022] Open
Abstract
Candida albicans is one of the most common causes of hospital-acquired urinary tract infections (UTIs). However, azoles are poorly active against biofilms, echinocandins do not achieve clinically useful urinary concentrations, and amphotericin B exhibits severe toxicities. Thus, novel strategies are needed to prevent Candida UTIs, which are often associated with urinary catheter biofilms. We previously demonstrated that cranberry-derived proanthocyanidins (PACs) prevent C. albicans biofilm formation in an in vitro urinary model. To elucidate functional pathways unique to urinary biofilm development and PAC inhibition, we investigated the transcriptome of C. albicans in artificial urine (AU), with and without PACs. C. albicans biofilm and planktonic cells were cultivated with or without PACs. Genome-wide expression analysis was performed by RNA sequencing. Differentially expressed genes were determined using DESeq2 software; pathway analysis was performed using Cytoscape. Approximately 2,341 of 6,444 total genes were significantly expressed in biofilm relative to planktonic cells. Functional pathway analysis revealed that genes involved in filamentation, adhesion, drug response and transport were up-regulated in urinary biofilms. Genes involved in carbon and nitrogen metabolism and nutrient response were down-regulated. In PAC-treated urinary biofilms compared to untreated control biofilms, 557 of 6,444 genes had significant changes in gene expression. Genes downregulated in PAC-treated biofilms were implicated in iron starvation and adhesion pathways. Although urinary biofilms share key features with biofilms formed in other environments, many genes are uniquely expressed in urinary biofilms. Cranberry-derived PACs interfere with the expression of iron acquisition and adhesion genes within urinary biofilms.
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Affiliation(s)
- Anitha Sundararajan
- National Center for Genome Resources, Santa Fe, NM, United States of America
| | - Hallie S. Rane
- Section of Infectious Diseases, New Mexico VA Healthcare System, Albuquerque, NM, United States of America
| | | | - Johnny Sena
- National Center for Genome Resources, Santa Fe, NM, United States of America
| | - Amy B. Howell
- Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers, The State University of New Jersey, Chatsworth, NJ, United States of America
| | - Stella M. Bernardo
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM, United States of America
| | - Faye D. Schilkey
- National Center for Genome Resources, Santa Fe, NM, United States of America
| | - Samuel A. Lee
- Section of Infectious Diseases, New Mexico VA Healthcare System, Albuquerque, NM, United States of America
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM, United States of America
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1341
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Access to Urban Green Space in Cities of the Global South: A Systematic Literature Review. URBAN SCIENCE 2018. [DOI: 10.3390/urbansci2030067] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This review examines disparities in access to urban green space (UGS) based on socioeconomic status (SES) and race-ethnicity in Global South cities. It was motivated by documented human health and ecosystem services benefits of UGS in Global South countries and UGS planning barriers in rapidly urbanizing cities. Additionally, another review of Global North UGS studies uncovered that high-SES and White people have access to a higher quantity of higher quality UGSs than low-SES and racial-ethnic minority people but that no clear differences exist regarding who lives closer to UGS. Thus, we conducted a systematic review to uncover (1) whether UGS inequities in Global North cities are evident in Global South cities and (2) whether inequities in the Global South vary between continents. Through the PRISMA approach and five inclusion criteria, we identified 46 peer-reviewed articles that measured SES or racial-ethnic disparities in access to UGS in Global South cities. We found inequities for UGS quantity (high-SES people are advantaged in 85% of cases) and UGS proximity (74% of cases). Inequities were less consistent for UGS quality (65% of cases). We also found that UGS inequities were consistent across African, Asian, and Latin American cities. These findings suggest that Global South cities experience similar inequities in UGS quantity and quality as Global North cities, but that the former also face inequities in UGS proximity.
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1342
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Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling. Cell Metab 2018; 28:300-309.e4. [PMID: 29937373 PMCID: PMC6082711 DOI: 10.1016/j.cmet.2018.05.025] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/05/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022]
Abstract
Recruitment of brown/beige adipocytes (BAs) in white adipose tissue (WAT) involves proliferation and differentiation of adipocyte stem cells (ASCs) in concert with close interactions with resident immune cells. To deconvolve stromal cell heterogeneity in a comprehensive and unbiased fashion, we performed single-cell RNA sequencing (scRNA-seq) of >33,000 stromal/vascular cells from epididymal WAT (eWAT) and inguinal WAT (iWAT) under control conditions and during β3-adrenergic receptor (ADRB3) activation. scRNA-seq identified distinct ASC subpopulations in eWAT and iWAT that appeared to be differentially poised to enter the adipogenic pathway. ADRB3 activation triggered the dramatic appearance of proliferating ASCs in eWAT, whose differentiation into BAs could be inferred from a single time point. scRNA-seq identified various immune cell types in eWAT, including a proliferating macrophage subpopulation that occupies adipogenic niches. These results demonstrate the power of scRNA-seq to deconstruct adipogenic niches and suggest novel functional interactions among resident stromal cell subpopulations.
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1343
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Meyer DN, Baker BB, Baker TR. Ancestral TCDD Exposure Induces Multigenerational Histologic and Transcriptomic Alterations in Gonads of Male Zebrafish. Toxicol Sci 2018; 164:603-612. [PMID: 29788325 PMCID: PMC6061693 DOI: 10.1093/toxsci/kfy115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), the classic aryl hydrocarbon receptor (AhR) agonist, is a potent environmental toxicant and endocrine-disrupting chemical (EDC) with known developmental toxicity in humans, rodents, and fish. Early life exposure to some EDCs, including TCDD, is linked to the occurrence of adult-onset and multigenerational disease. Previous work exposing juvenile F0 zebrafish (Danio rerio) to 50 ppt (parts per trillion) TCDD during reproductive development has shown male-mediated transgenerational decreases in fertility (F0-F2) and histologic and transcriptomic alterations in F0 testes. Here, we analyzed male germline alterations in F1 and F2 adult fish, looking for changes in testicular histology and gene expression inherited through the male lineage that could account for decreased reproductive capacity. Testes of TCDD-lineage F1 fish displayed an increase in spermatogonia (immature germ cells) and decrease in spermatozoa (mature germ cells). No histological changes were present in F2 fish. Transcriptomic analysis of exposed F1 and F2 testes revealed alterations in lipid and glucose metabolism, oxidation, xenobiotic response, and sperm cell development and maintenance genes, all of which are implicated in fertility outcomes. Overall, we found that differential expression of reproductive genes and reduced capacity of sperm cells to mature could account for the reproductive defects previously seen in TCDD-exposed male zebrafish and their descendants, providing insight into the distinct multigenerational effects of toxicant exposure.
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Affiliation(s)
- Danielle N Meyer
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Bridget B Baker
- Institute of Environmental Health Sciences, Center for Urban Responses to Environmental Stressors
- Division of Laboratory Animal Resources, Wayne State University, Detroit, Michigan 48202
| | - Tracie R Baker
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan 48201
- Institute of Environmental Health Sciences, Center for Urban Responses to Environmental Stressors
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1344
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Thériault R, Raz A. Patterns of bronchial challenge testing in Canada. CANADIAN JOURNAL OF RESPIRATORY THERAPY : CJRT = REVUE CANADIENNE DE LA THERAPIE RESPIRATOIRE : RCTR 2018; 54:06. [PMID: 31297005 PMCID: PMC6591799 DOI: 10.29390/cjrt-2018-006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Bronchial challenge testing (BCT) measures airway hyperresponsiveness; asthma guidelines recommend using BCT when symptoms manifest despite normal spirometry. Improper application of these guidelines commonly results in the misdiagnosis of asthma. Yet, statistics concerning BCT remain largely obscure. The current paper addresses this gap and explores how various health variables may elucidate adherence to asthma guidelines and patterns of BCT across Canadian provinces. METHODS Using the Access to Information Act, medical financial claims for BCT (or equivalent procedures) were requested from each of the Canadian provinces and territories. Based on the available information (from provinces only), correlations between frequency of BCT claims and medical demographics (e.g., prevalence of respirologists, health expenditures) are reported. RESULTS Controlling for population or for people with asthma, physicians from Québec claim four times more BCT per year than those in other provinces; physicians from Alberta close to eight-fold fewer. The number of respirologists per capita and BCT per capita correlated moderately, r(132) = 0.582, p < 0.001, [95% CI 0.421, 0.716]. Excluding "outliers" (i.e., British Columbia, Alberta, and Saskatchewan) greatly strengthened this correlation, r(87) = 0.930, p < 0.001, [95% CI 0.883, 0.958]. DISCUSSION These findings demonstrate that provinces vary in their use of BCT. This result seems to stem, at least in part, from differences in the prevalence of respirologists. Interestingly, geographic region appears to wield a strong influence; in the correlation between number of tests and number of respirologists, physicians from Western provinces (i.e., Alberta, Saskatchewan, and British Columbia) administered fewer tests than their Eastern colleagues. Given the association between inadequate application of BCT and misdiagnosis of asthma, physicians should pay special attention to the Canadian guidelines when considering an asthma diagnosis.
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Affiliation(s)
- Rémi Thériault
- Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Amir Raz
- Faculty of Medicine, McGill University, Montréal, QC, Canada
- Institute for Community and Family Psychiatry, Montréal, QC, Canada
- The Lady Davis Institute for Medical Research at the Jewish General Hospital, Montréal, QC, Canada
- Institute for Interdisciplinary Behavioral and Brain Sciences, Chapman University, Irvine, CA, USA
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1345
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Natoli R, Mason E, Jiao H, Chuah A, Patel H, Fernando N, Valter K, Wells CA, Provis J, Rutar M. Dynamic Interplay of Innate and Adaptive Immunity During Sterile Retinal Inflammation: Insights From the Transcriptome. Front Immunol 2018; 9:1666. [PMID: 30073000 PMCID: PMC6058037 DOI: 10.3389/fimmu.2018.01666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/04/2018] [Indexed: 01/09/2023] Open
Abstract
The pathogenesis of many retinal degenerations, such as age-related macular degeneration (AMD), is punctuated by an ill-defined network of sterile inflammatory responses. The delineation of innate and adaptive immune milieu among the broad leukocyte infiltrate, and the gene networks, which construct these responses, are poorly described in the eye. Using photo-oxidative damage in a rodent model of subretinal inflammation, we employed a novel RNA-sequencing framework to map the global gene network signature of retinal leukocytes. This revealed a previously uncharted interplay of adaptive immunity during subretinal inflammation, including prolonged enrichment of myeloid and lymphocyte migration, antigen presentation, and the alternative arm of the complement cascade involving Factor B. We demonstrate Factor B-deficient mice are protected against macrophage infiltration and subretinal inflammation. Suppressing the drivers of retinal leukocyte proliferation, or their capacity to elicit complement responses, may help preserve retinal structure and function during sterile inflammation in diseases such as AMD.
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Affiliation(s)
- Riccardo Natoli
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Elizabeth Mason
- The Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC, Australia
| | - Haihan Jiao
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Aaron Chuah
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Hardip Patel
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Nilisha Fernando
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Krisztina Valter
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Christine A Wells
- The Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC, Australia
| | - Jan Provis
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Matt Rutar
- The Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC, Australia
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1346
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Vicente CSL, Mondal SI, Akter A, Ozawa S, Kikuchi T, Hasegawa K. Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica. PLoS One 2018; 13:e0200512. [PMID: 29990378 PMCID: PMC6039017 DOI: 10.1371/journal.pone.0200512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/27/2018] [Indexed: 11/18/2022] Open
Abstract
The successful adaptation of cockroaches is, in part, dependent of the activity of their obligatory endosymbionts, Blattabacterium spp., which are involved in uric acid degradation, nitrogen assimilation and nutrient provisioning. Their strategic localization, within bacteriocytes in the proximities of uric acid storage cells (urocytes), highlights their importance in the recycling of nitrogen from urea and ammonia, end-products not secreted by their host insects. In this study, we present the complete genome sequence of two new Blattabacterium spp. from Periplaneta fuliginosa (BPfu) and P. japonica (BPja), and detailed comparison with other Blattabacterium strains from different cockroach species. The genomes of BPfu and BPja show a high degree of stability as showed with for other Blattabacterium representatives, only presenting a 19-kb fragment inversion between BPja and BPfu. In fact, the phylogenomics showed BPja as an ancestor species of BPfu, BPLAN (P. americana) and BBor (Blatta orientalis), in congruence with their host cockroach phylogeny. Their functional profile is similar and closest to the omnivorous strain BBge (Blattella germanica). Interesting, BPja possesses the complete set of enzymes involved sulfate assimilatory pathway only found in BBge and BMda (Mastotermes darwiniensis). The newly sequenced genomes of BPja and BPfu emphasise the remarkable stability of Blattabacterium genomes supported by their long-term coevolution and obligatory lifestyle in their host insect.
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Affiliation(s)
- Cláudia S. L. Vicente
- NemaLab/ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
| | - Shakhinur Islam Mondal
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Kumargaon, Sylhet, Bangladesh
| | - Arzuba Akter
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Kumargaon, Sylhet, Bangladesh
| | - Sota Ozawa
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
| | - Tasei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Koichi Hasegawa
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
- * E-mail:
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1347
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Karakasheva TA, Lin EW, Tang Q, Qiao E, Waldron TJ, Soni M, Klein-Szanto AJ, Sahu V, Basu D, Ohashi S, Baba K, Giaccone ZT, Walker SR, Frank DA, Wileyto EP, Long Q, Dunagin MC, Raj A, Diehl JA, Wong KK, Bass AJ, Rustgi AK. IL-6 Mediates Cross-Talk between Tumor Cells and Activated Fibroblasts in the Tumor Microenvironment. Cancer Res 2018; 78:4957-4970. [PMID: 29976575 DOI: 10.1158/0008-5472.can-17-2268] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 01/06/2018] [Accepted: 06/28/2018] [Indexed: 12/18/2022]
Abstract
The tumor microenvironment (TME) plays a major role in the pathogenesis of multiple cancer types, including upper-gastrointestinal (GI) cancers that currently lack effective therapeutic options. Cancer-associated fibroblasts (CAF) are an essential component of the TME, contributing to tumorigenesis by secreting growth factors, modifying the extracellular matrix, supporting angiogenesis, and suppressing antitumor immune responses. Through an unbiased approach, we have established that IL-6 mediates cross-talk between tumor cells and CAF not only by supporting tumor cell growth, but also by promoting fibroblast activation. As a result, IL-6 receptor (IL6Rα) and downstream effectors offer opportunities for targeted therapy in upper-GI cancers. IL-6 loss suppressed tumorigenesis in physiologically relevant three-dimensional (3D) organotypic and 3D tumoroid models and murine models of esophageal cancer. Tocilizumab, an anti-IL6Rα antibody, suppressed tumor growth in vivo in part via inhibition of STAT3 and MEK/ERK signaling. Analysis of a pan-cancer TCGA dataset revealed an inverse correlation between IL-6 and IL6Rα overexpression and patient survival. Therefore, we expanded evaluation of tocilizumab to head and neck squamous cell carcinoma patient-derived xenografts and gastric adenocarcinoma xenografts, demonstrating suppression of tumor growth and altered STAT3 and ERK1/2 gene signatures. We used small-molecule inhibitors of STAT3 and MEK1/2 signaling to suppress tumorigenesis in the 3D organotypic model of esophageal cancer. We demonstrate that IL6 is a major contributor to the dynamic cross-talk between tumor cells and CAF in the TME. Our findings provide a translational rationale for inhibition of IL6Rα and downstream signaling pathways as a novel targeted therapy in oral-upper-GI cancers.Significance: These findings demonstrate the interaction of esophageal cancer and cancer-associated fibroblasts through IL-6 signaling, providing rationale for a novel therapeutic approach to target these cancers. Cancer Res; 78(17); 4957-70. ©2018 AACR.
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Affiliation(s)
- Tatiana A Karakasheva
- Division of Gastroenterology, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Eric W Lin
- Division of Gastroenterology, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Qiaosi Tang
- Division of Gastroenterology, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Edmund Qiao
- Division of Gastroenterology, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Todd J Waldron
- Division of Gastroenterology, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Monica Soni
- Division of Gastroenterology, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Varun Sahu
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Department of Otolaryngology - Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Devraj Basu
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Department of Otolaryngology - Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Surgery Service, Philadelphia Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Shinya Ohashi
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kiichiro Baba
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Zachary T Giaccone
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Sarah R Walker
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David A Frank
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - E Paul Wileyto
- Department of Biostatistics, Epidemiology and Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Qi Long
- Department of Biostatistics, Epidemiology and Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Margaret C Dunagin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
| | - K K Wong
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam J Bass
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Anil K Rustgi
- Division of Gastroenterology, Department of Medicine, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania. .,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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1348
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Hanish BJ, Hackney Price JF, Kaneko I, Ma N, van der Vaart A, Wagner CE, Jurutka PW, Marshall PA. A novel gene expression analytics-based approach to structure aided design of rexinoids for development as next-generation cancer therapeutics. Steroids 2018; 135:36-49. [PMID: 29704526 PMCID: PMC5977990 DOI: 10.1016/j.steroids.2018.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 12/20/2022]
Abstract
Rexinoids are powerful ligands that bind to retinoid-X-receptors (RXRs) and show great promise as therapeutics for a wide range of diseases, including cancer. However, only one rexinoid, bexarotene (Targretin TM) has been successfully transitioned from the bench to the clinic and used to treat cutaneous T-cell lymphoma (CTCL). Our goal is to develop novel potent rexinoids with a less untoward side effect profile than bexarotene. To this end, we have synthesized a wide array of rexinoids with EC50 values and biological activity similar to bexarotene. In order to determine their suitability for additional downstream analysis, and to identify potential candidate analogs for clinical translation, we treated human CTCL cells in culture and employed microarray technology to assess gene expression profiles. We analyzed twelve rexinoids and found they could be stratified into three distinct categories based on their gene expression: similar to bexarotene, moderately different from bexarotene, and substantially different from bexarotene. Surprisingly, small changes in the structure of the bexarotene parent compound led to marked differences in gene expression profiles. Furthermore, specific analogs diverged markedly from our hypothesis in expression of genes expected to be important for therapeutic promise. However, promoter analysis of genes whose expression was analyzed indicates general regulatory trends along structural frameworks. Our results suggest that certain structural motifs, particularly the basic frameworks found in analog 4 and analog 9, represent important starting points to exploit in generating additional rexinoids for future study and therapeutic applications.
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Affiliation(s)
- Bentley J Hanish
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States
| | - Jennifer F Hackney Price
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States
| | - Ichiro Kaneko
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States; University of Arizona College of Medicine-Phoenix, Department of Basic Medical Sciences, Phoenix, AZ, United States; Department of Molecular Nutrition, Institution of Health Bioscience, University of Tokushima Graduate School, Kuramoto-cho, Japan
| | - Ning Ma
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Carl E Wagner
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States
| | - Peter W Jurutka
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States; University of Arizona College of Medicine-Phoenix, Department of Basic Medical Sciences, Phoenix, AZ, United States; University of Arizona Cancer Center, Tucson, AZ, United States
| | - Pamela A Marshall
- New College of Interdisciplinary Arts and Sciences, Arizona State University, Glendale, AZ, United States.
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1349
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Grygoryev D, Rountree MR, Rwatambuga F, Ohlrich A, Kukino A, Butler MP, Allen CN, Turker MS. Rapid Response and Slow Recovery of the H3K4me3 Epigenomic Marker in the Liver after Light-mediated Phase Advances of the Circadian Clock. J Biol Rhythms 2018; 33:363-375. [PMID: 29888643 DOI: 10.1177/0748730418779958] [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: 11/17/2022]
Abstract
Mammalian tissues display circadian rhythms in transcription, translation, and histone modifications. Here we asked how an advance of the light-dark cycle alters daily rhythms in the liver epigenome at the H3K4me3 (trimethylation of lysine 4 on histone 3) modification, which is found at active and poised gene promoters. H3K4me3 levels were first measured at 4 time points (zeitgeber time [ZT] 3, 8, 15, and 20) during a normal 12L:12D light-dark cycle. Peak levels were observed during the early dark phase at ZT15 and dropped to low levels around lights-on (ZT0) between ZT20 and ZT3. A 6-h phase advance at ZT18 (new lights-on after only 6 h of darkness) led to a transient extension of peak H3K4me3 levels. Although locomotor activity reentrained within a week after the phase advance, H3K4me3 rhythms failed to do so, with peak levels remaining in the light phase at the 1-week recovery time point. Eight weekly phase advances, with 1-week recovery times between each phase advance, further disrupted the H3K4me3 rhythms. Finally, we used the mPer2Luc knockin mouse to determine whether the phase advance also disrupted Per2 protein expression. Similar to the results from the histone work, we found both a rapid response to the phase advance and a delayed recovery, the latter in sync with H3K4me3 levels. A model to explain these results is offered.
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Affiliation(s)
- Dmytro Grygoryev
- 1 These authors contributed equally to this study.,Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon
| | - Michael R Rountree
- 1 These authors contributed equally to this study.,Nzumbe Inc., Portland, Oregon
| | - Furaha Rwatambuga
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon
| | - Anna Ohlrich
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon
| | - Ayaka Kukino
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon
| | - Matthew P Butler
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon.,Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Charles N Allen
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon.,Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Mitchell S Turker
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
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1350
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Bassett B, Waibel B, White A, Hansen H, Stephens D, Koelper A, Larsen EM, Kim C, Glanzer A, Lavis LD, Hoops GC, Johnson RJ. Measuring the Global Substrate Specificity of Mycobacterial Serine Hydrolases Using a Library of Fluorogenic Ester Substrates. ACS Infect Dis 2018; 4:904-911. [PMID: 29648787 PMCID: PMC5993602 DOI: 10.1021/acsinfecdis.7b00263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M. smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.
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Affiliation(s)
- Braden Bassett
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Brent Waibel
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Alex White
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Heather Hansen
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Dominique Stephens
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Andrew Koelper
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Erik M. Larsen
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Charles Kim
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr., Ashburn, VA 20147-2439 (USA)
| | - Adam Glanzer
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Luke D. Lavis
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr., Ashburn, VA 20147-2439 (USA)
| | - Geoffrey C. Hoops
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
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