1251
|
Identification of CD5/Cyclin D1 Double-negative Pleomorphic Mantle Cell Lymphoma. Am J Surg Pathol 2019; 44:232-240. [DOI: 10.1097/pas.0000000000001390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
1252
|
Marimuthu SK, Nagarajan K, Perumal SK, Palanisamy S, Subbiah L. Insilico Alpha-Helical Structural Recognition of Temporin Antimicrobial Peptides and Its Interactions with Middle East Respiratory Syndrome-Coronavirus. Int J Pept Res Ther 2019; 26:1473-1483. [PMID: 32206049 PMCID: PMC7088259 DOI: 10.1007/s10989-019-09951-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
Many antimicrobial peptides (AMPs) have multiple antimicrobial immunity effects. One such class of peptides is temporins. Temporins are the smallest (AMPs) found in nature and are highly active against gram-positive bacteria. Nowadays, there was a rapid increase in the availability of the 3D structure of proteins in PDB (protein data bank). The conserved residues and 3D structural conformations of temporins (AMPs) were still unknown. The present study explores the sequence analysis, alpha-helical structural conformations of temporins. The sequence of temporins was deracinated from APD3 database, the three-dimensional structure was constructed by homology modeling studies. The sequence analysis results show that the conserved residues among the peptide sequences, the maximum of the sequences are 70% alike to each other. The secondary structure prediction results revealed that 99% of temporin (AMPs) exhibited in alpha-helical form. The 3D structure speculated using RAMPAGE exposes the alpha-helical conformation in all temporins (AMPs). The phylogenetic analysis reveals the evolutionary relationships of temporins (AMPs), which are branched into seven clusters. As a result, we identified a list of potential temporin AMPs which docked to the antiviral protein (MERS-CoV), it shows good protein-peptide binding. This computational approach may serve as a good model for the rationale design of temporin based antibiotics.
Collapse
Affiliation(s)
- Sathish Kumar Marimuthu
- Department of Pharmaceutical Technology, University College of Engineering, Anna University, Bharathidasan Institute of Technology (BIT) Campus, Tiruchirappalli, 620024 Tamilnadu India
| | - Krishnanand Nagarajan
- Department of Pharmaceutical Technology, University College of Engineering, Anna University, Bharathidasan Institute of Technology (BIT) Campus, Tiruchirappalli, 620024 Tamilnadu India
| | - Sathish Kumar Perumal
- Department of Pharmaceutical Technology, University College of Engineering, Anna University, Bharathidasan Institute of Technology (BIT) Campus, Tiruchirappalli, 620024 Tamilnadu India
| | - Selvamani Palanisamy
- Department of Pharmaceutical Technology, University College of Engineering, Anna University, Bharathidasan Institute of Technology (BIT) Campus, Tiruchirappalli, 620024 Tamilnadu India
| | - Latha Subbiah
- Department of Pharmaceutical Technology, University College of Engineering, Anna University, Bharathidasan Institute of Technology (BIT) Campus, Tiruchirappalli, 620024 Tamilnadu India
| |
Collapse
|
1253
|
Burgess STG, Marr EJ, Bartley K, Nunn FG, Down RE, Weaver RJ, Prickett JC, Dunn J, Rombauts S, Van Leeuwen T, Van de Peer Y, Nisbet AJ. A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression. BMC Genomics 2019; 20:756. [PMID: 31640546 PMCID: PMC6806590 DOI: 10.1186/s12864-019-6082-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/05/2019] [Indexed: 02/04/2023] Open
Abstract
Background Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack of P. ovis transcriptomic and genomic resources. Results Building on the recent publication of the P. ovis draft genome, here we present a genomic analysis and transcriptomic atlas of gene expression in P. ovis revealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis of P. ovis allergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novel P. ovis multigene families including known allergens and novel genes with high levels of stage-specific expression. Conclusions The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draft P. ovis genome.
Collapse
Affiliation(s)
- Stewart T G Burgess
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK.
| | - Edward J Marr
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK
| | - Kathryn Bartley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK
| | - Francesca G Nunn
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK
| | | | | | | | - Jackie Dunn
- Fera Science Ltd, Sand Hutton, York, YO41 1LZ, UK
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Alasdair J Nisbet
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK
| |
Collapse
|
1254
|
Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. MICROBIOME 2019; 7:135. [PMID: 31630686 DOI: 10.1101/670067v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/22/2023]
Abstract
The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
Collapse
Affiliation(s)
- Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
| |
Collapse
|
1255
|
Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. MICROBIOME 2019; 7:135. [PMID: 31630686 PMCID: PMC6802176 DOI: 10.1186/s40168-019-0752-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/20/2023]
Abstract
The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
Collapse
Affiliation(s)
- Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
| |
Collapse
|
1256
|
Abd El-Hamid MI, Abd El-Aziz NK, Samir M, El-Naenaeey ESY, Abo Remela EM, Mosbah RA, Bendary MM. Genetic Diversity of Campylobacter jejuni Isolated From Avian and Human Sources in Egypt. Front Microbiol 2019; 10:2353. [PMID: 31681217 PMCID: PMC6813243 DOI: 10.3389/fmicb.2019.02353] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
Campylobacter jejuni (C. jejuni) are able to colonise and infect domestic poultry and also pose a risk for humans. The aim of this study was to determine the extent of genotypic diversity among C. jejuni isolates recovered from avian and human sources in Egypt. Furthermore, the short variable region (SVR) of flagellin A (flaA) gene was analysed for the presence of allelic variants. Our results showed that C. jejuni isolates differ in their capacity to harbour each of the virulence genes alone or when present in various combinations. The flaA gene was detected in all C. jejuni strains and none of the strains had all the studied virulence genes together. When considering C. jejuni strains from the investigated sources, the cdtC gene was the most similar, while the cdtB and iam genes were the most dissimilar. We could identify 13 novel alleles in the analysed strains. The analyses of virulence gene patterns, flaA gene sequences and allelic variants showed that C. jejuni strains from different sources overlapped largely suggesting potential involvement of poultry in transmitting C. jejuni to humans. We also found that the strains isolated from the same host were highly heterogeneous, with chicken strains exhibiting the highest diversity. Moreover, the human strains were clustered closer to chicken ones than to those from pigeon. The results of this study should be taken into consideration when assessing the epidemiology and risk potential of Egyptian C. jejuni not only in poultry, but also in humans.
Collapse
Affiliation(s)
- Marwa I. Abd El-Hamid
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Norhan K. Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Mohamed Samir
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - El-sayed Y. El-Naenaeey
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Etab M. Abo Remela
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
- Department of Biology, College of Science, Taibah University, Medina, Saudi Arabia
| | - Rasha A. Mosbah
- Fellow Pharmacist at Zagazig University Hospital, Zagazig, Egypt
| | - Mahmoud M. Bendary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| |
Collapse
|
1257
|
Aliouat A, Hatin I, Bertin P, François P, Stierlé V, Namy O, Salhi S, Jean-Jean O. Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes. RNA Biol 2019; 17:227-239. [PMID: 31619139 PMCID: PMC6973328 DOI: 10.1080/15476286.2019.1674595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
Collapse
Affiliation(s)
- Affaf Aliouat
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pierre Bertin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Pauline François
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Vérène Stierlé
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Samia Salhi
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS, Biological Adaptation and Aging, B2A, 75005 Paris, France
| |
Collapse
|
1258
|
Identification of novel Nrf2 target genes as prognostic biomarkers in colitis-associated colorectal cancer in Nrf2-deficient mice. Life Sci 2019; 238:116968. [PMID: 31628914 DOI: 10.1016/j.lfs.2019.116968] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/03/2019] [Accepted: 10/13/2019] [Indexed: 02/06/2023]
Abstract
AIMS Colorectal cancer (CRC) is the third most common cancer worldwide. Nuclear factor erythroid 2-related factor 2 (Nrf2), a master regulator of many cytoprotective genes, plays a protective role in carcinogenesis. Recent studies have identified a specific gene-expression signature regulated by the Nrf2 pathway in lung adenocarcinoma and head-and-neck squamous cell cancer. However, the roles of Nrf2 in the development of colitis-associated colorectal cancer (CACC) have not been well characterized. Nrf2 target genes as prognostic biomarkers in CACC remain to be explored. Thus, this work aimed to identify the molecular changes that occur during mouse CACC progression to facilitate the development of diagnostic and prognostic biomarkers. MAIN METHODS The CACC model was established using azoxymethane (AOM) with dextran sulfate sodium salt (DSS) in BALB/c mice for 3 weeks to induce colitis-associated adenoma (CAA, early stage) and for 9 weeks to induce colitis-associated carcinoma (CAC, late stage). Using RNA-sequencing and bioinformatics analyses we examined the mRNA expression profiles of 6 groups: wild-type control (WT-C), WT-CAA, WT-CAC, Nrf2 knockout control (Nrf2KO-C), Nrf2KO-CAA, and Nrf2KO-CAC. KEY FINDINGS In the AOM/DSS model of colitis-associated tumorigenesis, Nrf2-/- mice showed a phenotype similar to WT mice, but with significantly more tumors and a much higher percentage of adenocarcinomas. We identified 47 novel Nrf2 genes via gene expression profiling of tumor samples. Survival analysis showed that 23 of these genes were biomarkers of a poor prognosis in colon cancer patients. SIGNIFICANCE Nrf2 target genes deserve exploration as prognostic and therapeutic targets for CRC.
Collapse
|
1259
|
Shuaib M, Parsi KM, Thimma M, Adroub SA, Kawaji H, Seridi L, Ghosheh Y, Fort A, Fallatah B, Ravasi T, Carninci P, Orlando V. Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells. Cell Syst 2019; 9:446-458.e6. [PMID: 31629687 DOI: 10.1016/j.cels.2019.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/29/2019] [Accepted: 09/12/2019] [Indexed: 12/21/2022]
Abstract
The impact of mammalian RNA interference components, particularly, Argonaute proteins, on chromatin organization is unexplored. Recent reports indicate that AGO1 association with chromatin appears to influence gene expression. To uncover the role of AGO1 in the nucleus, we used a combination of genome-wide approaches in control and AGO1-depleted HepG2 cells. We found that AGO1 strongly associates with active enhancers and RNA being produced at those sites. Hi-C analysis revealed AGO1 enrichment at the boundaries of topologically associated domains (TADs). By Hi-C in AGO1 knockdown cells, we observed changes in chromatin organization, including TADs and A/B compartment mixing, specifically in AGO1-bound regions. Distinct groups of genes and especially eRNA transcripts located within differentially interacting loci showed altered expression upon AGO1 depletion. Moreover, AGO1 association with enhancers is dependent on eRNA transcription. Collectively, our data suggest that enhancer-associated AGO1 contributes to the fine-tuning of chromatin architecture and gene expression in human cells.
Collapse
Affiliation(s)
- Muhammad Shuaib
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Krishna Mohan Parsi
- IRCSS Fondazione, Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy
| | - Manjula Thimma
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Sabir Abdu Adroub
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Loqmane Seridi
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Yanal Ghosheh
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Bodor Fallatah
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia; IRCSS Fondazione, Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy.
| |
Collapse
|
1260
|
Wu H, Ma T, Kang M, Ai F, Zhang J, Dong G, Liu J. A high-quality Actinidia chinensis (kiwifruit) genome. HORTICULTURE RESEARCH 2019; 6:117. [PMID: 31645971 PMCID: PMC6804796 DOI: 10.1038/s41438-019-0202-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/04/2019] [Accepted: 09/02/2019] [Indexed: 05/04/2023]
Abstract
Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C data. The high-quality assembled genome is 653 Mb long, with 0.76% heterozygosity. At least 43% of the genome consists of repetitive sequences, and the most abundant long terminal repeats were further identified and account for 23.38% of our novel genome. It has clear improvements in contiguity, accuracy, and gene annotation over the two previous versions and contains 40,464 annotated protein-coding genes, of which 94.41% are functionally annotated. Moreover, further analyses of genetic collinearity revealed that the kiwifruit genome has undergone two whole-genome duplications: one affecting all Ericales families near the K-T extinction event and a recent genus-specific duplication. The reference genome presented here will be highly useful for further molecular elucidation of diverse traits and for the breeding of this horticultural crop, as well as evolutionary studies with related taxa.
Collapse
Affiliation(s)
- Haolin Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Fandi Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Junlin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Guanyong Dong
- The Limited Agriculture Company of Xinyuan Sacred Fruit, Shifang, Deyang, 618409 Sichuan China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065 China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000 China
| |
Collapse
|
1261
|
Ryan MC, Stucky M, Wakefield C, Melott JM, Akbani R, Weinstein JN, Broom BM. Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. F1000Res 2019; 8. [PMID: 32269754 PMCID: PMC7111501 DOI: 10.12688/f1000research.20590.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/12/2020] [Indexed: 01/17/2023] Open
Abstract
Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology. Construction of a heat map generally requires the assistance of a biostatistician or bioinformatics analyst capable of working in R or a similar programming language to transform the study data, perform hierarchical clustering, and generate the heat map. Our web-based Interactive Heat Map Builder can be used by investigators with no bioinformatics experience to generate high-caliber, publication quality maps. Preparation of the data and construction of a heat map is rarely a simple linear process. Our tool allows a user to move back and forth iteratively through the various stages of map generation to try different options and approaches. Finally, the heat map the builder creates is available in several forms, including an interactive Next-Generation Clustered Heat Map that can be explored dynamically to investigate the results more fully.
Collapse
Affiliation(s)
| | - Mark Stucky
- In Silico Solutions, Fairfax, VA, 22031, USA
| | - Chris Wakefield
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James M Melott
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bradley M Broom
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
1262
|
Ryan MC, Stucky M, Wakefield C, Melott JM, Akbani R, Weinstein JN, Broom BM. Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. F1000Res 2019; 8:ISCB Comm J-1750. [PMID: 32269754 PMCID: PMC7111501 DOI: 10.12688/f1000research.20590.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/12/2020] [Indexed: 11/15/2023] Open
Abstract
Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology. Construction of a heat map generally requires the assistance of a biostatistician or bioinformatics analyst capable of working in R or a similar programming language to transform the study data, perform hierarchical clustering, and generate the heat map. Our web-based Interactive Heat Map Builder can be used by investigators with no bioinformatics experience to generate high-caliber, publication quality maps. Preparation of the data and construction of a heat map is rarely a simple linear process. Our tool allows a user to move back and forth iteratively through the various stages of map generation to try different options and approaches. Finally, the heat map the builder creates is available in several forms, including an interactive Next-Generation Clustered Heat Map that can be explored dynamically to investigate the results more fully.
Collapse
Affiliation(s)
| | - Mark Stucky
- In Silico Solutions, Fairfax, VA, 22031, USA
| | - Chris Wakefield
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James M. Melott
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N. Weinstein
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bradley M. Broom
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
1263
|
Expression Profiling of Candidate Genes in Sugar Beet Leaves Treated with Leonardite-Based Biostimulant. High Throughput 2019; 8:ht8040018. [PMID: 31614507 PMCID: PMC6970231 DOI: 10.3390/ht8040018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/02/2022] Open
Abstract
Leonardite-based biostimulants are a large class of compounds, including humic acid substances. Foliar application of biostimulants at field level improves plant growth, yield and quality through metabolic changes and stimulation of plant proton pumps. The present study aimed at identifying optimum dosage of BLACKJAK, a humic acid-based substance, which is able to modify genes involved in sugar beet growth. Thirty-three genes belonging to various biochemical pathway categories were tested in leaves of treated sugar beet (Beta vulgaris L.) samples to assess gene expression profiling in response to BLACKJAK. Seedlings of a diploid and multigerm variety were grown in plastic pots and sprayed with two dilutions of BLACKJAK (dilution 1:500–1.0 mg C L−1 and dilution 1:1000–0.5 mg C L−1). Leaf samples were collected after 24, 48, and 72 h treatment with BLACKJAK for each dilution. RNA was extracted and the quantification of gene expression was performed while using an OpenArray platform. Results of analysis of variance demonstrated that, 15 genes out of a total of 33 genes tested with OpenArray qPCR were significantly affected by treatment and exposure time. Analysis for annotation of gene products and pathways revealed that genes belonging to the mitochondrial respiratory pathways, nitrogen and hormone metabolisms, and nutrient uptake were up-regulated in the BLACKJAK treated samples. Among the up-regulated genes, Bv_PHT2;1 and Bv_GLN1 expression exerted a 2-fold change in 1:1000 and 1:500 BLACKJAK concentrations. Overall, the gene expression data in the BLACKJAK treated leaves demonstrated the induction of plant growth–related genes that were contributed almost to amino acid and nitrogen metabolism, plant defense system, and plant growth.
Collapse
|
1264
|
Dysregulated liver lipid metabolism and innate immunity associated with hepatic steatosis in neonatal BBdp rats and NOD mice. Sci Rep 2019; 9:14594. [PMID: 31601915 PMCID: PMC6787248 DOI: 10.1038/s41598-019-51143-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
In a previous study we reported that prediabetic rats have a unique gene signature that was apparent even in neonates. Several of the changes we observed, including enhanced expression of pro-inflammatory genes and dysregulated UPR and metabolism genes were first observed in the liver followed by the pancreas. In the present study we investigated further early changes in hepatic innate immunity and metabolism in two models of type 1 diabetes (T1D), the BBdp rat and NOD mouse. There was a striking increase in lipid deposits in liver, particularly in neonatal BBdp rats, with a less striking but significant increase in neonatal NOD mice in association with dysregulated expression of lipid metabolism genes. This was associated with a decreased number of extramedullary hematopoietic clusters as well as CD68+ macrophages in the liver of both models. In addition, PPARɣ and phosphorylated AMPKα protein were decreased in neonatal BBdp rats. BBdp rats displayed decreased expression of antimicrobial genes in neonates and decreased M2 genes at 30 days. This suggests hepatic steatosis could be a common early feature in development of T1D that impacts metabolic homeostasis and tolerogenic phenotype in the prediabetic liver.
Collapse
|
1265
|
Renschler G, Richard G, Valsecchi CIK, Toscano S, Arrigoni L, Ramírez F, Akhtar A. Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling. Genes Dev 2019; 33:1591-1612. [PMID: 31601616 PMCID: PMC6824461 DOI: 10.1101/gad.328971.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 09/09/2019] [Indexed: 11/30/2022]
Abstract
In this study, Renschler et al. set out to analyze the impact of genomic rearrangements on genome topology using the Drosophila genus and X chromosome dosage compensation as a model. The authors developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. Their data provides unique insights into genome topology evolution. RA Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs), and spatial contacts between high-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservation at various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarily flexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential processes such as dosage compensation of the X chromosome.
Collapse
Affiliation(s)
- Gina Renschler
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Gautier Richard
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany.,IGEPP, INRA, Agrocampus Ouest, Université Rennes, 35600 Le Rheu, France
| | | | - Sarah Toscano
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| | - Fidel Ramírez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany
| |
Collapse
|
1266
|
Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers. Sci Rep 2019; 9:14450. [PMID: 31595011 PMCID: PMC6783451 DOI: 10.1038/s41598-019-50978-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.
Collapse
|
1267
|
Leiva-Rebollo R, Labella AM, Borrego JJ, Castro D. Immune gene expression in gilthead seabream (Sparus aurata) after Lymphocystis disease virus (LCDV-Sa) challenge resulting in asymptomatic infection. J Appl Microbiol 2019; 128:41-53. [PMID: 31529740 DOI: 10.1111/jam.14454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/04/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022]
Abstract
AIMS To determine the immune gene expression response of gilthead seabream (Sparus aurata) that is experimentally infected with the lymphocystivirus LCDV-Sa. METHODS AND RESULTS Viral DNA and transcripts were detected by qPCR in all samples from fish injected with LCDV-Sa, demonstrating that the virus establish a systemic and asymptomatic infection. The expression of 23 immune-related genes was also analysed by RT-qPCR in the head kidney (HK) and intestine at several times post-infection (dpi). In HK, the expression of five type I interferon (IFN)-related genes (ifn, irf3, mx2, mx3 and isg15), il10 and ck10 was upregulated at 1-3 dpi, while genes related to the inflammation process (tnfα, il1ß, il6, casp1) were not differentially expressed or even downregulated. The expression profile in the intestine was different regarding type I INF-related genes. An upregulated c3 and ighm expression was observed in both HK and intestine at 3-8 dpi. Finally, the transcription of nccrp1 and mhcIIα was induced in HK, whereas tcrβ expression was downregulated in both organs. CONCLUSIONS LCDV-Sa seems to trigger an immune response in gilthead seabream characterized by a partial activation of type I IFN system and a lack of systemic inflammatory response which may be related to viral persistence. SIGNIFICANCE AND IMPACT OF THE STUDY The immune response observed in gilthead seabream infected by LCDV-Sa could be implicated in the establishment of an asymptomatic persistent infection.
Collapse
Affiliation(s)
- R Leiva-Rebollo
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - A M Labella
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - J J Borrego
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - D Castro
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| |
Collapse
|
1268
|
Dreyer A, Neugebauer F, Lohmann N, Rüdel H, Teubner D, Grotti M, Rauert C, Koschorreck J. Recent findings of halogenated flame retardants (HFR) in the German and Polar environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 253:850-863. [PMID: 31349194 DOI: 10.1016/j.envpol.2019.07.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
To get an overview about distribution, levels and temporal trends of polybrominated diphenyl ethers (PBDE) and halogenated flame retardants (HFR) of emerging concern, different types of environmental samples archived in the German Environment Specimen Bank as well as fish filet samples from the Arctic (n = 13) and Antarctica (n = 5) were analysed for 43 substances (24 PBDE, 19 HFR) using a multi-column clean-up and GC-API-MS/MS or GC-MS. Sample types were herring gull egg (n = 3), blue mussel (n = 3) and eelpout filet (n = 3) from the German North- and Baltic Sea, bream filet (n = 7), zebra mussel (n = 6) and suspended particulate matter (SPM, n = 7) from German freshwater ecosystems as well as tree leaves (n = 9)/shoots (n = 10), soil (n = 4), earthworm (n = 4) and deer liver (n = 7) as representatives of German terrestrial ecosystems. PBDE and emerging HFR were present in each investigated matrices from Germany and Polar regions showing their widespread distribution. The presence in Arctic and Antarctic fish samples confirms their long-range transport potential. Average concentrations of total emerging HFR were highest in SPM (26 ng g-1 dry weight (dw)), zebra mussel (10 ng g-1 dw) and herring gull egg (2.6 ng g-1 dw). Lowest levels were measured in fish filet samples from Antarctica (0.02 ng g-1 dw). Average total PBDE concentrations were highest in bream filet (154 ng g-1), herring gull egg (61 ng g-1 dw), SPM (21 ng g-1 dw), and zebra mussel 18 (ng g-1) and lowest in deer liver (0.04 ng g-1 dw). The patterns of non-fauna terrestrial samples (leaves, shoots, soil) as well as SPM were dominated by DBDPE and BDE209. Elevated proportions of DPTE and in most cases the absence of DBDPE characterized all fauna samples with the exception of Polar samples. Overall, emerging HFR appeared to be less bioaccumulative than PBDE. Temporal trends were generally decreasing with few exceptions such as DBDPE.
Collapse
Affiliation(s)
| | | | - Nina Lohmann
- Eurofins GfA Lab Service GmbH, 21079 Hamburg, Germany
| | - Heinz Rüdel
- Fraunhofer Institute for Molecular Biology and Applied Ecology (Fraunhofer IME), Schmallenberg, Germany
| | | | - Marco Grotti
- University of Genoa, Department of Chemistry and Industrial Chemistry, 16146 Genoa, Italy
| | | | | |
Collapse
|
1269
|
Wang L, Chua E, Sun F, Wan ZY, Ye B, Pang H, Wen Y, Yue GH. Mapping and Validating QTL for Fatty Acid Compositions and Growth Traits in Asian Seabass. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:643-654. [PMID: 31273567 DOI: 10.1007/s10126-019-09909-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
Asian seabass is an important food fish species. While improving growth, increasing the nutritional value is important, omega-3 fatty acids are indispensable to human health. Identifying and validating DNA markers associated with traits is the first step towards marker-assisted selection (MAS). We quantified 13 different fatty acids and three growth traits in 213 F2 Asian seabass from a family at the age 270 days post hatch, and screened QTL for these traits. The content of total fatty acids in 100 g flesh was 2.57 ± 0.80 g, while the proportions of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were 16.96 ± 2.20% and 5.42 ± 0.90%, respectively. A linkage map with 2424 SNPs was constructed and used for QTL mapping. For fatty acid compositions, 14 significant QTL were identified on three linkage groups (LG5, LG11 and LG14), with phenotypic variance explained (PVE) from 12.8 to 24.6%. Thirty-nine suggestive QTL were detected on 16 LGs. Two significant QTL for EPA were identified on LG5 and LG14, with PVE of 15.2% and 15.1%, respectively. No significant QTL was identified for DHA. For growth traits, six significant and 13 suggestive QTL were identified on two and seven LGs, respectively. Only a few significant QTL for fatty acids overlapped with previously mapped QTL for these traits, suggesting that most QTL detected in a family are family-specific and could only be used in MAS in the family per se. To facilitate population-wide molecular breeding, more powerful methods (e.g. GWAS) should be used to identify SNPs for genomic selection.
Collapse
Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Elaine Chua
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Fei Sun
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Hongyan Pang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yanfei Wen
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
| |
Collapse
|
1270
|
Pek RH, Yuan X, Rietzschel N, Zhang J, Jackson L, Nishibori E, Ribeiro A, Simmons W, Jagadeesh J, Sugimoto H, Alam MZ, Garrett L, Haldar M, Ralle M, Phillips JD, Bodine DM, Hamza I. Hemozoin produced by mammals confers heme tolerance. eLife 2019; 8:e49503. [PMID: 31571584 PMCID: PMC6773446 DOI: 10.7554/elife.49503] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/24/2019] [Indexed: 12/28/2022] Open
Abstract
Free heme is cytotoxic as exemplified by hemolytic diseases and genetic deficiencies in heme recycling and detoxifying pathways. Thus, intracellular accumulation of heme has not been observed in mammalian cells to date. Here we show that mice deficient for the heme transporter SLC48A1 (also known as HRG1) accumulate over ten-fold excess heme in reticuloendothelial macrophage lysosomes that are 10 to 100 times larger than normal. Macrophages tolerate these high concentrations of heme by crystallizing them into hemozoin, which heretofore has only been found in blood-feeding organisms. SLC48A1 deficiency results in impaired erythroid maturation and an inability to systemically respond to iron deficiency. Complete heme tolerance requires a fully-operational heme degradation pathway as haplo insufficiency of HMOX1 combined with SLC48A1 inactivation causes perinatal lethality demonstrating synthetic lethal interactions between heme transport and degradation. Our studies establish the formation of hemozoin by mammals as a previously unsuspected heme tolerance pathway.
Collapse
Affiliation(s)
- Rini H Pek
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkUnited States
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkUnited States
| | - Xiaojing Yuan
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkUnited States
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkUnited States
| | - Nicole Rietzschel
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkUnited States
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkUnited States
| | - Jianbing Zhang
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkUnited States
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkUnited States
| | - Laurie Jackson
- Department of MedicineUniversity of Utah School of MedicineSalt Lake CityUnited States
| | - Eiji Nishibori
- Faculty of Pure and Applied SciencesUniversity of TsukubaTsukubaJapan
- Tsukuba Research Center for Energy Materials ScienceUniversity of TsukabaTsukabaJapan
| | - Ana Ribeiro
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkUnited States
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkUnited States
| | - William Simmons
- Genetics and Molecular Biology BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Jaya Jagadeesh
- Genetics and Molecular Biology BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | | | - Md Zahidul Alam
- Department of Pathology and Laboratory MedicinePerelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Lisa Garrett
- NHGRI Embryonic Stem Cell and Transgenic Mouse CoreNational Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Malay Haldar
- Department of Pathology and Laboratory MedicinePerelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Martina Ralle
- Department of Molecular and Medical GeneticsOregon Health and Science UniversityPortlandUnited States
| | - John D Phillips
- Department of MedicineUniversity of Utah School of MedicineSalt Lake CityUnited States
| | - David M Bodine
- Genetics and Molecular Biology BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Iqbal Hamza
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkUnited States
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkUnited States
| |
Collapse
|
1271
|
Moll HP, Pranz K, Musteanu M, Grabner B, Hruschka N, Mohrherr J, Aigner P, Stiedl P, Brcic L, Laszlo V, Schramek D, Moriggl R, Eferl R, Moldvay J, Dezso K, Lopez-Casas PP, Stoiber D, Hidalgo M, Penninger J, Sibilia M, Győrffy B, Barbacid M, Dome B, Popper H, Casanova E. Afatinib restrains K-RAS-driven lung tumorigenesis. Sci Transl Med 2019; 10:10/446/eaao2301. [PMID: 29925635 DOI: 10.1126/scitranslmed.aao2301] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 03/19/2018] [Accepted: 05/11/2018] [Indexed: 12/14/2022]
Abstract
On the basis of clinical trials using first-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), it became a doctrine that V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-RAS) mutations drive resistance to EGFR inhibition in non-small cell lung cancer (NSCLC). Conversely, we provide evidence that EGFR signaling is engaged in K-RAS-driven lung tumorigenesis in humans and in mice. Specifically, genetic mouse models revealed that deletion of Egfr quenches mutant K-RAS activity and transiently reduces tumor growth. However, EGFR inhibition initiates a rapid resistance mechanism involving non-EGFR ERBB family members. This tumor escape mechanism clarifies the disappointing outcome of first-generation TKIs and suggests high therapeutic potential of pan-ERBB inhibitors. On the basis of various experimental models including genetically engineered mouse models, patient-derived and cell line-derived xenografts, and in vitro experiments, we demonstrate that the U.S. Food and Drug Administration-approved pan-ERBB inhibitor afatinib effectively impairs K-RAS-driven lung tumorigenesis. Our data support reconsidering the use of pan-ERBB inhibition in clinical trials to treat K-RAS-mutated NSCLC.
Collapse
Affiliation(s)
- Herwig P Moll
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
| | - Klemens Pranz
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria
| | - Monica Musteanu
- Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - Beatrice Grabner
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria
| | - Natascha Hruschka
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria
| | - Julian Mohrherr
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria
| | - Petra Aigner
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria
| | - Patricia Stiedl
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria
| | - Luka Brcic
- Institute of Pathology, Medical University of Graz, AT-8036 Graz, Austria
| | - Viktoria Laszlo
- Division of Thoracic Surgery, Department of Surgery and CCC, Medical University of Vienna, AT-1090 Vienna, Austria.,Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Daniel Schramek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, AT-1030 Vienna, Austria.,Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, ON-M5G 1X5 Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, ON-M5S 1A8 Toronto, Ontario, Canada
| | - Richard Moriggl
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Medical University of Vienna, AT-1210 Vienna, Austria.,Medical University of Vienna, AT-1090 Vienna, Austria
| | - Robert Eferl
- Institute of Cancer Research, Medical University of Vienna and CCC, AT-1090 Vienna, Austria
| | - Judit Moldvay
- Department of Tumor Biology, National Korányi Institute of Pulmonology, Semmelweis University, HU-1122 Budapest, Hungary
| | - Katalin Dezso
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, HU-1122 Budapest, Hungary
| | | | - Dagmar Stoiber
- Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria.,Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Manuel Hidalgo
- Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - Josef Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, AT-1030 Vienna, Austria
| | - Maria Sibilia
- Institute of Cancer Research, Medical University of Vienna and CCC, AT-1090 Vienna, Austria
| | - Balázs Győrffy
- MTA TK Lendület Cancer Biomarker Research Group, Institute of Enzymology and Second Department of Pediatrics, Semmelweis University, HU-1122 Budapest, Hungary
| | | | - Balázs Dome
- Division of Thoracic Surgery, Department of Surgery and CCC, Medical University of Vienna, AT-1090 Vienna, Austria.,Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, AT-1090 Vienna, Austria.,Department of Tumor Biology, National Korányi Institute of Pulmonology, Semmelweis University, HU-1122 Budapest, Hungary.,Department of Thoracic Surgery, National Institute of Oncology and Semmelweis University, HU-1122 Budapest, Hungary
| | - Helmut Popper
- Institute of Pathology, Medical University of Graz, AT-8036 Graz, Austria
| | - Emilio Casanova
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria. .,Ludwig Boltzmann Institute for Cancer Research, AT-1090 Vienna, Austria
| |
Collapse
|
1272
|
Koiwa J, Shiromizu T, Adachi Y, Ikejiri M, Nakatani K, Tanaka T, Nishimura Y. Generation of a Triple-Transgenic Zebrafish Line for Assessment of Developmental Neurotoxicity during Neuronal Differentiation. Pharmaceuticals (Basel) 2019; 12:E145. [PMID: 31554324 PMCID: PMC6958351 DOI: 10.3390/ph12040145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/19/2019] [Accepted: 09/22/2019] [Indexed: 12/15/2022] Open
Abstract
: The developing brain is extremely sensitive to many chemicals. Exposure to neurotoxicants during development has been implicated in various neuropsychiatric and neurological disorders, including autism spectrum disorders and schizophrenia. Various screening methods have been used to assess the developmental neurotoxicity (DNT) of chemicals, with most assays focusing on cell viability, apoptosis, proliferation, migration, neuronal differentiation, and neuronal network formation. However, assessment of toxicity during progenitor cell differentiation into neurons, astrocytes, and oligodendrocytes often requires immunohistochemistry, which is a reliable but labor-intensive and time-consuming assay. Here, we report the development of a triple-transgenic zebrafish line that expresses distinct fluorescent proteins in neurons (Cerulean), astrocytes (mCherry), and oligodendrocytes (mCitrine), which can be used to detect DNT during neuronal differentiation. Using in vivo fluorescence microscopy, we could detect DNT by 6 of the 10 neurotoxicants tested after exposure to zebrafish from 12 h to 5 days' post-fertilization. Moreover, the chemicals could be clustered into three main DNT groups based on the fluorescence pattern: (i) inhibition of neuron and oligodendrocyte differentiation and stimulation of astrocyte differentiation; (ii) inhibition of neuron and oligodendrocyte differentiation; and (iii) inhibition of neuron and astrocyte differentiation, which suggests that reporter expression reflects the toxicodynamics of the chemicals. Thus, the triple-transgenic zebrafish line developed here may be a useful tool to assess DNT during neuronal differentiation.
Collapse
Affiliation(s)
- Junko Koiwa
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
| | - Takashi Shiromizu
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
| | - Yuka Adachi
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
| | - Makoto Ikejiri
- Department of Central Laboratory, Mie University Hospital, Tsu, Mie 514-8507, Japan.
| | - Kaname Nakatani
- Department of Genomic Medicine, Mie University Hospital, Tsu, Mie 514-8507, Japan.
| | - Toshio Tanaka
- Department of Systems Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
| |
Collapse
|
1273
|
Deciphering the microbiome shift during fermentation of medicinal plants. Sci Rep 2019; 9:13461. [PMID: 31530872 PMCID: PMC6748931 DOI: 10.1038/s41598-019-49799-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
The importance of the human-microbiome relationship for positive health outcomes has become more apparent over the last decade. Influencing the gut microbiome via modification of diet represents a possibility of maintaining a healthy gut flora. Fermented food and lactic acid bacteria (LAB) display a preventive way to inhibit microbial dysbioses and diseases, but their ecology on plants is poorly understood. We characterized the microbiome of medicinal plants (Matricaria chamomilla L. and Calendula officinalis L.) using 16S rRNA gene profiling from leaves that were fermented over a six-week time course. The unfermented samples were characterized by a distinct phyllosphere microbiome, while the endosphere revealed a high similarity. During fermentation, significant microbial shifts were observed, whereby LAB were enhanced in all approaches but never numerically dominated. Among the LAB, Enterococcaceae were identified as the most dominant family in both plants. M. chamomilla community had higher relative abundances of Lactobacillaceae and Carnobacteriaceae, while C. officinalis showed a higher presence of Leuconostocaceae and Streptococcaceae. The natural leaf microbiome and the indigenous LAB communities of field-grown Asteraceae medicinal plants are plant-specific and habitat-specific and are subjected to significant shifts during fermentation. Leaf surfaces as well as leaf endospheres were identified as sources for biopreservative LAB.
Collapse
|
1274
|
Cosin-Roger J, Canet F, Macias-Ceja DC, Gisbert-Ferrándiz L, Ortiz-Masiá D, Esplugues JV, Alós R, Navarro F, Barrachina MD, Calatayud S. Autophagy Stimulation as a Potential Strategy Against Intestinal Fibrosis. Cells 2019; 8:cells8091078. [PMID: 31540207 PMCID: PMC6770118 DOI: 10.3390/cells8091078] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
We recently observed reduced autophagy in Crohn’s disease patients and an anti-inflammatory effect of autophagy stimulation in murine colitis, but both anti- and pro-fibrotic effects are associated with autophagy stimulation in different tissues, and fibrosis is a frequent complication of Crohn’s disease. Thus, we analyzed the effects of pharmacological modulation of autophagy in a murine model of intestinal fibrosis and detected that autophagy inhibition aggravates, while autophagy stimulation prevents, fibrosis. These effects are associated with changes in inflammation and in collagen degradation in primary fibroblasts. Thus, pharmacological stimulation of autophagy may be useful against intestinal fibrosis.
Collapse
Affiliation(s)
- Jesus Cosin-Roger
- Hospital Dr Peset, FISABIO, 46017 Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, 46010 Valencia, Spain
| | - Francisco Canet
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
| | - Dulce C Macias-Ceja
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
| | - Laura Gisbert-Ferrándiz
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
| | - Dolores Ortiz-Masiá
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, 46010 Valencia, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
| | - Juan V Esplugues
- Hospital Dr Peset, FISABIO, 46017 Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, 46010 Valencia, Spain
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
| | - Rafael Alós
- Departamento de Cirugía del Aparato Digestivo, Hospital La Fe, 46526 Valencia, Spain
| | - Francisco Navarro
- Departamento de Cirugía y Coloproctología, Hospital de Manises, 46940 Valencia, Spain
| | - María D Barrachina
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, 46010 Valencia, Spain.
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain.
| | - Sara Calatayud
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, 46010 Valencia, Spain
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
| |
Collapse
|
1275
|
Mohrherr J, Haber M, Breitenecker K, Aigner P, Moritsch S, Voronin V, Eferl R, Moriggl R, Stoiber D, Győrffy B, Brcic L, László V, Döme B, Moldvay J, Dezső K, Bilban M, Popper H, Moll HP, Casanova E. JAK-STAT inhibition impairs K-RAS-driven lung adenocarcinoma progression. Int J Cancer 2019; 145:3376-3388. [PMID: 31407334 PMCID: PMC6856680 DOI: 10.1002/ijc.32624] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/11/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
Oncogenic K‐RAS has been difficult to target and currently there is no K‐RAS‐based targeted therapy available for patients suffering from K‐RAS‐driven lung adenocarcinoma (AC). Alternatively, targeting K‐RAS‐downstream effectors, K‐RAS‐cooperating signaling pathways or cancer hallmarks, such as tumor‐promoting inflammation, has been shown to be a promising therapeutic strategy. Since the JAK–STAT pathway is considered to be a central player in inflammation‐mediated tumorigenesis, we investigated here the implication of JAK–STAT signaling and the therapeutic potential of JAK1/2 inhibition in K‐RAS‐driven lung AC. Our data showed that JAK1 and JAK2 are activated in human lung AC and that increased activation of JAK–STAT signaling correlated with disease progression and K‐RAS activity in human lung AC. Accordingly, administration of the JAK1/2 selective tyrosine kinase inhibitor ruxolitinib reduced proliferation of tumor cells and effectively reduced tumor progression in immunodeficient and immunocompetent mouse models of K‐RAS‐driven lung AC. Notably, JAK1/2 inhibition led to the establishment of an antitumorigenic tumor microenvironment, characterized by decreased levels of tumor‐promoting chemokines and cytokines and reduced numbers of infiltrating myeloid derived suppressor cells, thereby impairing tumor growth. Taken together, we identified JAK1/2 inhibition as promising therapy for K‐RAS‐driven lung AC. What's new? A drug that inhibits the JAK–STAT pathway may score a hit against K‐RAS driven lung cancer. Here, the authors Investigated the JAK STAT pathway as a possible target in lung adenocarcinoma because of its role in inflammation‐mediated tumorigenesis. First, they showed that JAK1 and JAK2 are both activated in lung adenocarcinoma patients with oncogenic mutations in K‐RAS. Next, they treated the tumors with ruxolitinib, which inhibits JAK1/2. The drug successfully slowed tumor proliferation and progression in immunocompetent mouse models. Furthermore, treatment with ruxolitinib reduced the tumor‐promoting factors present in the microenvironment.
Collapse
Affiliation(s)
- Julian Mohrherr
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
| | - Marcel Haber
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
| | - Kristina Breitenecker
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
| | - Petra Aigner
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
| | - Stefan Moritsch
- Institute of Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Viktor Voronin
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
| | - Robert Eferl
- Institute of Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Richard Moriggl
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
- Institute of Animal Breeding and GeneticsUniversity of Veterinary MedicineViennaAustria
- Medical University of ViennaViennaAustria
| | - Dagmar Stoiber
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
| | - Balázs Győrffy
- MTA TK Lendület Cancer Biomarker Research Group, Institute of Enzymology, and Second Department of PediatricsSemmelweis UniversityBudapestHungary
| | - Luka Brcic
- Diagnostic & Research Institute of PathologyMedical University of GrazGrazAustria
| | - Viktória László
- Division of Thoracic Surgery, Department of Surgery & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
| | - Balázs Döme
- Division of Thoracic Surgery, Department of Surgery & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
- Department of Biomedical Imaging and Image‐guided Therapy, Division of Molecular and Gender ImagingMedical University of ViennaViennaAustria
- Department of Tumor Biology, National Korányi Institute of PulmonologySemmelweis UniversityBudapestHungary
- Department of Thoracic SurgeryNational Institute of Oncology and Semmelweis UniversityBudapestHungary
| | - Judit Moldvay
- Department of Tumor Biology, National Korányi Institute of PulmonologySemmelweis UniversityBudapestHungary
- SE‐NAP Brain Metastasis Research Group, 2nd Department of PathologySemmelweis UniversityBudapestHungary
| | - Katalin Dezső
- First Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Martin Bilban
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
- Core FacilitiesMedical University of ViennaViennaAustria
| | - Helmut Popper
- Diagnostic & Research Institute of PathologyMedical University of GrazGrazAustria
| | - Herwig P. Moll
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
| | - Emilio Casanova
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC)Medical University of ViennaViennaAustria
- Ludwig Boltzmann Institute for Cancer Research (LBI‐CR)ViennaAustria
| |
Collapse
|
1276
|
Leal Zimmer FMA, Moura H, Barr JR, Ferreira HB. Intracellular changes of a swine tracheal cell line infected with a Mycoplasma hyopneumoniae pathogenic strain. Microb Pathog 2019; 137:103717. [PMID: 31494300 DOI: 10.1016/j.micpath.2019.103717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/13/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022]
Abstract
Mycoplasma hyopneumoniae is the etiological agent of enzootic pneumonia (EP), a widespread disease that causes major economic losses to the pig industry. The swine host response plays an important role in the outcome of M. hyopneumoniae infections. The whole proteome of newborn pig trachea (NPTr) epithelial cells infected with the M. hyopneumoniae pathogenic strain 7448 was analyzed using an LC-MS/MS approach to shed light on intracellular processes triggered in response to the pathogen. Overall, 853 swine protein species were identified, 156 of which were differentially represented in response to M. hyopneumoniae 7448 infection in comparison with non-infected control cells. These differentially represented proteins were categorized by function. Fifty-seven of them were assigned to the immune system and/or response to stimulus functional subcategories. Comparative expression analysis of these immune-related proteins in NPTr cells infected with attenuated or non-pathogenic mycoplasmas (M. hyopneumoniae J strain and M. flocculare, respectively) revealed proteins whose abundance was altered only in response to the pathogenic M. hyopneumoniae 7448 strain. Among these proteins, calcium homeostasis and endoplasmic reticulum stress-related biomarkers were detected, providing evidence of molecular mechanisms that might lead to swine cell apoptosis.
Collapse
Affiliation(s)
- Fernanda M A Leal Zimmer
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil
| | - Hercules Moura
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - John R Barr
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, Brazil.
| |
Collapse
|
1277
|
Human Immunodeficiency Virus (HIV) Infection and Use of Illicit Substances Promote Secretion of Semen Exosomes that Enhance Monocyte Adhesion and Induce Actin Reorganization and Chemotactic Migration. Cells 2019; 8:cells8091027. [PMID: 31484431 PMCID: PMC6770851 DOI: 10.3390/cells8091027] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/09/2019] [Accepted: 08/15/2019] [Indexed: 12/23/2022] Open
Abstract
Semen exosomes (SE) from HIV-uninfected (HIV−) individuals potently inhibit HIV infection in vitro. However, morphological changes in target cells in response to SE have not been characterized or have the effect of HIV infection or the use of illicit substances, specifically psychostimulants, on the function of SE been elucidated. The objective of this study was to evaluate the effect of HIV infection, psychostimulant use, and both together on SE-mediated regulation of monocyte function. SE were isolated from semen of HIV− and HIV-infected (HIV+) antiretroviral therapy (ART)-naive participants who reported either using or not using psychostimulants. The SE samples were thus designated as HIV−Drug−, HIV−Drug+, HIV+Drug−, and HIV+Drug+. U937 monocytes were treated with different SEs and analyzed for changes in transcriptome, morphometrics, actin reorganization, adhesion, and chemotaxis. HIV infection and/or use of psychostimulants had minimal effects on the physical characteristics of SE. However, different SEs had diverse effects on the messenger RNA signature of monocytes and rapidly induced monocyte adhesion and spreading. SE from HIV infected or psychostimulants users but not HIV−Drug− SE, stimulated actin reorganization, leading to the formation of filopodia-like structures and membrane ruffles containing F-actin and vinculin that in some cases were colocalized. All SE stimulated monocyte chemotaxis to HIV secretome and activated the secretion of matrix metalloproteinases, a phenotype exacerbated by HIV infection and psychostimulant use. SE-directed regulation of cellular morphometrics and chemotaxis depended on the donor clinical status because HIV infection and psychostimulant use altered SE function. Although our inclusion criteria specified the use of cocaine, humans are poly-drug and alcohol users and our study participants used psychostimulants, marijuana, opiates, and alcohol. Thus, it is possible that the effects observed in this study may be due to one of these other substances or due to an interaction between different substances.
Collapse
|
1278
|
Morroni L, Sartori D, Costantini M, Genovesi L, Magliocco T, Ruocco N, Buttino I. First molecular evidence of the toxicogenetic effects of copper on sea urchin Paracentrotus lividus embryo development. WATER RESEARCH 2019; 160:415-423. [PMID: 31163317 DOI: 10.1016/j.watres.2019.05.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
Bioassays with sea urchin embryos are widely used to define the environmental quality of marine waters. Anomalies during embryogenesis are generally considered as end-points, whereas a toxigenomic approach, despite it is wide use in other species, is yet in its infancy. In the present study we evaluated toxigenic effects induced by copper on the sea urchin Paracentrotus lividus embryo, combining morphological observations with gene expression analysis. Many anthropogenic activities release copper in the marine environment, with harmful effects on aquatic organisms. In the present study P. lidivus embryos were exposed to different concentrations of copper (24, 36, 48 μg/L) and the activation of fifty specific marker genes, involved in different biological processes (stress, skeletogenesis, development/differentiation, detoxification) was investigated at early blastula, late gastrula and pluteus stage. At blastula stage no morphological anomalies were found, with early down-regulation of genes involved in development/differentiation and a moderate up-regulation of some detoxification genes. At gastrula stage a slight increase in developmental anomalies (up to 19% of malformed embryos) was followed by an increased number of targeted genes belonging to the same two classes, relative to the blastula stage. At pluteus stage morphological anomalies increased in a dose dependent manner. All the analyzed genes were strongly up-regulated, stress and skeletogenic genes showing a "late response" and almost all genes were targeted by copper at all the concentrations tested. The present study represents the first molecular report on the potential negative effect of copper on P. lividus embryos in the environment. Gene expression analysis should be considered as a promising tool for future environmental biomonitoring programs.
Collapse
Affiliation(s)
- Lorenzo Morroni
- Institute for Environmental Protection and Research, ISPRA, Via del Cedro, 38, 57123, Livorno, Italy; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Davide Sartori
- Institute for Environmental Protection and Research, ISPRA, Via del Cedro, 38, 57123, Livorno, Italy
| | - Maria Costantini
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Lorenzo Genovesi
- Department of Aquatics, Acquario di Livorno, Costa Edutainment S.p.A, Piazzale Razzauti 1, 57127, Livorno, Italy
| | - Thomas Magliocco
- Department of Aquatics, Acquario di Livorno, Costa Edutainment S.p.A, Piazzale Razzauti 1, 57127, Livorno, Italy
| | - Nadia Ruocco
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Isabella Buttino
- Institute for Environmental Protection and Research, ISPRA, Via del Cedro, 38, 57123, Livorno, Italy; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| |
Collapse
|
1279
|
Lamichhane R, Schneider M, de la Harpe SM, Harrop TW, Hannaway RF, Dearden PK, Kirman JR, Tyndall JD, Vernall AJ, Ussher JE. TCR- or Cytokine-Activated CD8+ Mucosal-Associated Invariant T Cells Are Rapid Polyfunctional Effectors That Can Coordinate Immune Responses. Cell Rep 2019; 28:3061-3076.e5. [DOI: 10.1016/j.celrep.2019.08.054] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022] Open
|
1280
|
Scholz GE, Popescu AA, Taylor MI, Moulton V, Huber KT. OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression. Syst Biol 2019; 68:717-729. [PMID: 30668824 DOI: 10.1093/sysbio/syz004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method is based on representing introgression in terms of a certain "overlay" of the allele tree over the lineage trees, called an overlaid species forest (OSF). OSFs are similar to phylogenetic networks although a key difference is that they typically have multiple roots because each monophyletic group in the species tree has a different point of origin. Employing a new model for introgression, we derive an efficient algorithm for building OSFs called OSF-Builder that is guaranteed to return an optimal OSF in the sense that the number of potential introgression events is minimized. As well as using simulations to assess the performance of OSF-Builder, we illustrate its use on a butterfly data set in which introgression has been previously inferred. The OSF-Builder software is available for download from https://www.uea.ac.uk/computing/software/OSF-Builder.
Collapse
Affiliation(s)
| | | | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | |
Collapse
|
1281
|
Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS. The population genetics of structural variants in grapevine domestication. NATURE PLANTS 2019; 5:965-979. [PMID: 31506640 DOI: 10.1038/s41477-019-0507-8] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/26/2019] [Indexed: 05/20/2023]
Abstract
Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.
Collapse
Affiliation(s)
- Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA
| | | | - Edwin Solares
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Yuanda Lv
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Tengiz Beridze
- Institute of Molecular Genetics, Agricultural University of Georgia, Tbilisi, Georgia
| | - Dario Cantu
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
| |
Collapse
|
1282
|
L'Huillier AG, Ferreira VH, Ku T, Bahinskaya I, Kumar D, Humar A. Improving our mechanistic understanding of the indirect effects of CMV infection in transplant recipients. Am J Transplant 2019; 19:2495-2504. [PMID: 30916879 DOI: 10.1111/ajt.15371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/17/2019] [Accepted: 03/18/2019] [Indexed: 01/25/2023]
Abstract
Cytomegalovirus (CMV) is an immunomodulatory virus that indirectly increases the risk for bacterial, fungal, and viral infections. However, the pathogenesis of this phenomenon is poorly understood. We determined whether inflammatory responses to different Toll-like receptor (TLR) ligands are blunted during CMV infection in solid-organ transplant (SOT) patients. Peripheral blood mononuclear cells from 38 SOT patients with and without CMV were incubated in the presence of various viral, fungal, and bacterial TLR ligands. Cytokines were measured in the supernatant by multiplex enzyme-linked immunosorbent assay. Patients had blunted cytokine responses to bacterial, fungal, and viral ligands during CMV infection when compared to the absence of CMV infection. This was independent of viral load, clinical presentation of CMV infection or immunosuppression, supporting the clinical observation in SOT recipients that CMV infection increases susceptibility to bacterial, fungal, and other viral infections. Moreover, in the absence of CMV infection, patients with subsequent CMV infection had lower cytokines in response to TLR ligands compared to those without subsequent CMV infection, suggesting that inherent differences in patients not directly related to CMV also contribute to this increased susceptibility. In summary, these data provide novel ex vivo evidence to support indirect effects of CMV.
Collapse
Affiliation(s)
- Arnaud G L'Huillier
- Transplant Infectious Diseases and Multi-Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Victor H Ferreira
- Transplant Infectious Diseases and Multi-Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Terrance Ku
- Transplant Infectious Diseases and Multi-Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Ilona Bahinskaya
- Transplant Infectious Diseases and Multi-Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Deepali Kumar
- Transplant Infectious Diseases and Multi-Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Atul Humar
- Transplant Infectious Diseases and Multi-Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
1283
|
Martinez-Fierro ML, Garza-Veloz I, Rocha-Pizaña MR, Cardenas-Vargas E, Cid-Baez MA, Trejo-Vazquez F, Flores-Morales V, Villela-Ramirez GA, Delgado-Enciso I, Rodriguez-Sanchez IP, Ortiz-Castro Y. Serum cytokine, chemokine, and growth factor profiles and their modulation in inflammatory bowel disease. Medicine (Baltimore) 2019; 98:e17208. [PMID: 31567972 PMCID: PMC6756690 DOI: 10.1097/md.0000000000017208] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ulcerative colitis (UC) and Crohn disease (CD) are the most common forms of inflammatory bowel disease (IBD). Because these subtypes of IBD are characterized by periods of activity and remission, an understanding of the modulation of biochemical markers with the clinical features of IBD or its treatment, may be useful for determining the correct treatment protocol.This study aimed to evaluate the serum levels of 27 protein biomarkers to determine their association with IBD, correlation with clinical findings of disease, and modulation according to the pharmacologic therapy.A case-control study was carried out in Zacatecas, Mexico. The 27 protein profiles of serum from 53 participants (23 UC, 11 CD, and 19 controls) were evaluated using the Pro Human Cytokine 27-Plex immunoassay (Bio-Rad).Considering the controls as a reference, the group with IBD endoscopic activity showed higher serum levels of granulocyte colony-stimulating factor (G-CSF), interleukin 1 receptor antagonist (IL-1Ra), and platelet-derived growth factor BB (PDGF-BB) (P < .05). Interferon-induced protein 10 (IP-10) was associated with extraintestinal symptoms of disease (P = .041). Both PDGF-BB and interleukin 6 (IL-6) showed the strongest correlations with clinical features of IBD. Levels of IL-6, IL-7, and monocyte chemoattractant protein 1 were higher with 5-aminosalicylic acid (5-ASA) + Azathioprine therapy than controls (P < .05). Combined therapy with 5-ASA + Adalimumab led to the strongest changes in marker modulation: IL-4, IL-5, IL-15, and PDGF-BB, were upregulated (P < .05).Elevated serum levels of G-CSF, IL-1Ra, and PDGF-BB were associated with IBD endoscopic activity, and of IP-10 with extraintestinal manifestations of IBD. Combined therapy of 5-ASA + Adalimumab produced significant upregulation of IL-4, IL-5, IL-15, and PDGF-BB. This information may be useful for deciding on the course of pharmacologic therapy for patients with IBD and for generating new therapy alternatives to improve the outcome of patients with IBD.
Collapse
Affiliation(s)
- Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad Academica de Medicina Humana y CS
- Posgrado en Ingenieria y Tecnologia Aplicada, Unidad Academica de Ingenieria Electrica, Universidad Autonoma de Zacatecas, Zacatecas
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Unidad Academica de Medicina Humana y CS
- Posgrado en Ingenieria y Tecnologia Aplicada, Unidad Academica de Ingenieria Electrica, Universidad Autonoma de Zacatecas, Zacatecas
| | | | - Edith Cardenas-Vargas
- Molecular Medicine Laboratory, Unidad Academica de Medicina Humana y CS
- Hospital General Zacatecas “Luz González Cosío”, Servicios de Salud de Zacatecas
| | | | - Fabiola Trejo-Vazquez
- Molecular Medicine Laboratory, Unidad Academica de Medicina Humana y CS
- Hospital General de Zacatecas, Instituto de Seguridad y Servicios Sociales para los Trabajadores del Estado (ISSSTE)
| | - Virginia Flores-Morales
- Laboratorio de Sintesis Asimetrica y Bioenergetica (LSAyB), Ingenieria Quimica, Universidad Autonoma de Zacatecas, Zacatecas
| | - Gabriela A. Villela-Ramirez
- Molecular Medicine Laboratory, Unidad Academica de Medicina Humana y CS
- Posgrado en Ingenieria y Tecnologia Aplicada, Unidad Academica de Ingenieria Electrica, Universidad Autonoma de Zacatecas, Zacatecas
| | - Ivan Delgado-Enciso
- School of Medicine, University of Colima, and Cancerology State Institute, Colima State Health Services, Colima
| | - Iram P. Rodriguez-Sanchez
- Laboratorio de Fisiologia Molecular y Estructural, Facultad de Ciencias Biologicas, Universidad Autonoma de Nuevo Leon, Monterrey Nuevo Leon, Mexico
| | | |
Collapse
|
1284
|
Robinson K, Becker S, Xiao Y, Lyu W, Yang Q, Zhu H, Yang H, Zhao J, Zhang G. Differential Impact of Subtherapeutic Antibiotics and Ionophores on Intestinal Microbiota of Broilers. Microorganisms 2019; 7:microorganisms7090282. [PMID: 31443457 PMCID: PMC6780560 DOI: 10.3390/microorganisms7090282] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/05/2023] Open
Abstract
Antimicrobial growth promoters (AGPs) are commonly used in the livestock industry at subtherapeutic levels to improve production efficiency, which is achieved mainly through modulation of the intestinal microbiota. However, how different classes of AGPs, particularly ionophores, regulate the gut microbiota remains unclear. In this study, male Cobb broiler chickens were supplemented for 14 days with or without one of five commonly used AGPs including three classical antibiotics (bacitracin methylene disalicylate, tylosin, and virginiamycin) and two ionophores (monensin and salinomycin) that differ in antimicrobial spectrum and mechanisms. Deep sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed that two ionophores drastically reduced a number of rare bacteria resulting in a significant decrease in richness and a concomitant increase in evenness of the cecal microbiota, whereas three antibiotics had no obvious impact. Although each AGP modulated the gut microbiota differently, the closer the antibacterial spectrum of AGPs, the more similarly the microbiota was regulated. Importantly, all AGPs had a strong tendency to enrich butyrate- and lactic acid-producing bacteria, while reducing bile salt hydrolase-producing bacteria, suggestive of enhanced metabolism and utilization of dietary carbohydrates and lipids and improved energy harvest, which may collectively be responsible for the growth-promoting effect of AGPs.
Collapse
Affiliation(s)
- Kelsy Robinson
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Sage Becker
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yingping Xiao
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wentao Lyu
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qing Yang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Huiling Zhu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430000, China
| | - Hua Yang
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| |
Collapse
|
1285
|
Zhu J, Lau K, Puschmann R, Harmel RK, Zhang Y, Pries V, Gaugler P, Broger L, Dutta AK, Jessen HJ, Schaaf G, Fernie AR, Hothorn LA, Fiedler D, Hothorn M. Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis. eLife 2019; 8:43582. [PMID: 31436531 PMCID: PMC6731061 DOI: 10.7554/elife.43582] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 08/21/2019] [Indexed: 12/15/2022] Open
Abstract
Many eukaryotic proteins regulating phosphate (Pi) homeostasis contain SPX domains that are receptors for inositol pyrophosphates (PP-InsP), suggesting that PP-InsPs may regulate Pi homeostasis. Here we report that deletion of two diphosphoinositol pentakisphosphate kinases VIH1/2 impairs plant growth and leads to constitutive Pi starvation responses. Deletion of phosphate starvation response transcription factors partially rescues vih1 vih2 mutant phenotypes, placing diphosphoinositol pentakisphosphate kinases in plant Pi signal transduction cascades. VIH1/2 are bifunctional enzymes able to generate and break-down PP-InsPs. Mutations in the kinase active site lead to increased Pi levels and constitutive Pi starvation responses. ATP levels change significantly in different Pi growth conditions. ATP-Mg2+ concentrations shift the relative kinase and phosphatase activities of diphosphoinositol pentakisphosphate kinases in vitro. Pi inhibits the phosphatase activity of the enzyme. Thus, VIH1 and VIH2 relay changes in cellular ATP and Pi concentrations to changes in PP-InsP levels, allowing plants to maintain sufficient Pi levels.
Collapse
Affiliation(s)
- Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Kelvin Lau
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Robert Puschmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Robert K Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Youjun Zhang
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Verena Pries
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Philipp Gaugler
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Larissa Broger
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Amit K Dutta
- Institute of Organic Chemistry, Freiburg im Breisgau, Germany
| | | | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Bonn, Germany
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ludwig A Hothorn
- Institute of Biostatistics, Leibniz University, Hannover, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| |
Collapse
|
1286
|
Rabee AE, Forster RJ, Elekwachi CO, Kewan KZ, Sabra E, Mahrous HA, Khamiss OA, Shawket SM. Composition of bacterial and archaeal communities in the rumen of dromedary camel using cDNA-amplicon sequencing. Int Microbiol 2019; 23:137-148. [PMID: 31432356 DOI: 10.1007/s10123-019-00093-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 06/30/2019] [Accepted: 07/21/2019] [Indexed: 11/25/2022]
Abstract
The camel is known to survive in harsh environmental conditions, due to its higher digestive efficiency of high-fiber diets compared with other ruminants. However, limited data are available on the microbial community in the rumen of a camel. In this study, the Illumina sequencing of V4 region of 16S rRNA genes based on RNA isolation was employed to get insight into the bacterial and archaeal communities associated with liquid and solid rumen fractions in eight camels under different feeding systems. Camels in group C1 were fed Egyptian clover hay plus concentrates mixture and camels of group C2 were fed fresh Egyptian clover. The results showed that liquid fraction has higher operational taxonomic units (OTUs) than solid fraction, and camel group C1 showed a higher microbial diversity than C2. The UniFrac analysis indicated that the microbial communities in camel groups are distinct. Moreover, phylum Firmicutes and Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community with a significant difference in the relative abundance between camel groups. Dominant bacterial genera were Prevotella, Fibrobacteres, Ruminococcus, and Butyrivibrio. There were many negative and positive correlations between and within bacterial and archaeal genera. The composition of microbial community in the rumen of a camel is similar to other ruminants with differences in the abundance.
Collapse
Affiliation(s)
- Alaa E Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt.
| | | | | | - Khaled Z Kewan
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Hoda A Mahrous
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Omaima A Khamiss
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Safinaze M Shawket
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| |
Collapse
|
1287
|
Selles B, Moseler A, Rouhier N, Couturier J. Rhodanese domain-containing sulfurtransferases: multifaceted proteins involved in sulfur trafficking in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4139-4154. [PMID: 31055601 DOI: 10.1093/jxb/erz213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 04/29/2019] [Indexed: 05/25/2023]
Abstract
Sulfur is an essential element for the growth and development of plants, which synthesize cysteine and methionine from the reductive assimilation of sulfate. Besides its incorporation into proteins, cysteine is the building block for the biosynthesis of numerous sulfur-containing molecules and cofactors. The required sulfur atoms are extracted either directly from cysteine by cysteine desulfurases or indirectly after its catabolic transformation to 3-mercaptopyruvate, a substrate for sulfurtransferases (STRs). Both enzymes are transiently persulfidated in their reaction cycle, i.e. the abstracted sulfur atom is bound to a reactive cysteine residue in the form of a persulfide group. Trans-persulfidation reactions occur when sulfur atoms are transferred to nucleophilic acceptors such as glutathione, proteins, or small metabolites. STRs form a ubiquitous, multigenic protein family. They are characterized by the presence of at least one rhodanese homology domain (Rhd), which usually contains the catalytic, persulfidated cysteine. In this review, we focus on Arabidopsis STRs, presenting the sequence characteristics of all family members as well as their biochemical and structural features. The physiological functions of particular STRs in the biosynthesis of molybdenum cofactor, thio-modification of cytosolic tRNAs, arsenate tolerance, cysteine catabolism, and hydrogen sulfide formation are also discussed.
Collapse
Affiliation(s)
| | - Anna Moseler
- Université de Lorraine, Inra, IAM, Nancy, France
| | | | | |
Collapse
|
1288
|
Barnhill EC, Crucello A, Houserova D, King VM, Amin SV, Roberts JT, Zambrano ME, DeMeis JD, Dahmer DJ, Ijaz Z, Barchie AA, Watters BC, Prusak JE, Dean MA, Holton NW, Ferreira-Filho JA, Sant'Ana AS, Spector MP, Borchert GM. Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium. RNA Biol 2019; 16:1643-1657. [PMID: 31390935 DOI: 10.1080/15476286.2019.1653680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Noncoding RNA (ncRNA) modulation of gene expression has now been ubiquitously observed across all domains of life. An increasingly apparent role of ncRNAs is to coordinate changes in gene expressions in response to environmental stress. Salmonella enterica, a common food-born pathogen, is known for its striking ability to survive, adapt, and thrive in various unfavourable environments which makes it a particularly difficult pathogen to eliminate as well as an interesting model in which to study ncRNA contributions to cellular stress response. Mounting evidence now suggests that small RNAs (sRNAs) represent key regulators of Salmonella stress adaptation. Approximately 50-500 nucleotides in length, sRNAs regulate gene expression through complementary base pairing with molecular targets and have recently been suggested to outnumber protein-coding genes in bacteria. In this work, we employ small RNA transcriptome sequencing to characterize changes in the sRNA profiles of Salmonella in response to desiccation. In all, we identify 102 previously annotated sRNAs significantly differentially expressed during desiccation; and excitingly, 71 novel sRNAs likewise differentially expressed. Small transcript northern blotting and qRT-PCRs confirm the identities and expressions of several of our novel sRNAs, and computational analyses indicate the majority are highly conserved and structurally related to characterized sRNAs. Predicted sRNA targets include several proteins necessary for desiccation survival and this, in part, suggests a role for desiccation-regulated sRNAs in this stress response. Furthermore, we find individual knock-outs of two of the novel sRNAs identified herein, either sRNA1320429 or sRNA3981754, significantly impairs the ability of Salmonella to survive desiccation, confirming their involvements (and suggesting the potential involvements of other sRNAs we identify in this work) in the Salmonella response to desiccation.
Collapse
Affiliation(s)
| | - Aline Crucello
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Food Science, University of Campinas , Campinas , Brazil
| | | | - Valeria M King
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Molecular and Cell Biology, University of California Berkeley , Berkeley , CA , USA
| | - Shivam V Amin
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Pharmacology, USA College of Medicine , Mobile , AL , USA
| | - Justin T Roberts
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine , Aurora , CO , USA
| | | | - Jeffrey D DeMeis
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - Donavon J Dahmer
- Department of Biomedical Sciences, University of South Alabama , Mobile , AL , USA
| | - Zara Ijaz
- Department of Biomedical Sciences, University of South Alabama , Mobile , AL , USA
| | - Addison A Barchie
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - Brianna C Watters
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - James E Prusak
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - Meghan A Dean
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | | | - Jaire A Ferreira-Filho
- Center for Molecular Biology and Genetic Engineering, University of Campinas , Campinas , Brazil
| | | | - Michael P Spector
- Department of Biomedical Sciences, University of South Alabama , Mobile , AL , USA
| | - Glen M Borchert
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Pharmacology, USA College of Medicine , Mobile , AL , USA
| |
Collapse
|
1289
|
The Small RNA Repertoire of Small Extracellular Vesicles Isolated From Donor Kidney Preservation Fluid Provides a Source for Biomarker Discovery for Organ Quality and Posttransplantation Graft Function. Transplant Direct 2019; 5:e484. [PMID: 31579812 PMCID: PMC6739040 DOI: 10.1097/txd.0000000000000929] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/11/2019] [Indexed: 02/07/2023] Open
Abstract
Supplemental Digital Content is available in the text. Delayed graft function (DGF) after kidney transplantation is negatively associated with long-term graft function and survival. Kidney function after transplantation depends on multiple factors, both donor- and recipient-associated. Prediction of posttransplantation graft function would allow timely intervention to optimize patient care and survival. Currently, graft-based predictions can be made based on histological and molecular analyses of 0-hour biopsy samples. However, such analyses are currently not implemented, as biopsy samples represent only a very small portion of the entire graft and are not routinely analyzed in all transplantation centers. Alternatives are thus required.
Collapse
|
1290
|
Li C, Lee MK, Gao F, Webster S, Di H, Duan J, Yang CY, Bhopal N, Peinado N, Pryhuber G, Smith SM, Borok Z, Bellusci S, Minoo P. Secondary crest myofibroblast PDGFRα controls the elastogenesis pathway via a secondary tier of signaling networks during alveologenesis. Development 2019; 146:dev.176354. [PMID: 31331942 PMCID: PMC6703710 DOI: 10.1242/dev.176354] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
Postnatal alveolar formation is the most important and the least understood phase of lung development. Alveolar pathologies are prominent in neonatal and adult lung diseases. The mechanisms of alveologenesis remain largely unknown. We inactivated Pdgfra postnatally in secondary crest myofibroblasts (SCMF), a subpopulation of lung mesenchymal cells. Lack of Pdgfra arrested alveologenesis akin to bronchopulmonary dysplasia (BPD), a neonatal chronic lung disease. The transcriptome of mutant SCMF revealed 1808 altered genes encoding transcription factors, signaling and extracellular matrix molecules. Elastin mRNA was reduced, and its distribution was abnormal. Absence of Pdgfra disrupted expression of elastogenic genes, including members of the Lox, Fbn and Fbln families. Expression of EGF family members increased when Tgfb1 was repressed in mouse. Similar, but not identical, results were found in human BPD lung samples. In vitro, blocking PDGF signaling decreased elastogenic gene expression associated with increased Egf and decreased Tgfb family mRNAs. The effect was reversible by inhibiting EGF or activating TGFβ signaling. These observations demonstrate the previously unappreciated postnatal role of PDGFA/PDGFRα in controlling elastogenic gene expression via a secondary tier of signaling networks composed of EGF and TGFβ.
Collapse
Affiliation(s)
- Changgong Li
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Matt K Lee
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Feng Gao
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Sha Webster
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Helen Di
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Jiang Duan
- Department of Pediatrics, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Chang-Yo Yang
- Department of Pediatrics, Chang Gung Children's Hospital and Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33305, Taiwan
| | - Navin Bhopal
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Neil Peinado
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Susan M Smith
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Zea Borok
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Saverio Bellusci
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA.,Excellence Cluster Cardio-Pulmonary System (ECCPS), Universities of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-University Giessen, German Center for Lung Research (DZL), 35392, Giessen, Germany
| | - Parviz Minoo
- Department of Pediatrics, Division of Newborn Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| |
Collapse
|
1291
|
Hori A, Shimoda M, Naoi Y, Kagara N, Tanei T, Miyake T, Shimazu K, Kim SJ, Noguchi S. Vasculogenic mimicry is associated with trastuzumab resistance of HER2-positive breast cancer. Breast Cancer Res 2019; 21:88. [PMID: 31387614 PMCID: PMC6683360 DOI: 10.1186/s13058-019-1167-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Background Trastuzumab is a drug that targets the receptor tyrosine kinase HER2 and is essential for the treatment of HER2-positive breast cancer. Resistance to the drug leads to severe consequences, including disease recurrence, tumor enlargement, and metastasis. We hypothesized that trastuzumab treatment might be associated with phenotypic switching in HER2-positive breast cancer cells (BCCs), enabling them to escape and survive the effect of trastuzumab. Methods We conducted comprehensive immunophenotyping to detect phenotypic changes in HER2-positive BCCs treated with trastuzumab, based on criteria determined a priori. Based on immunophenotyping results, we characterized the vascular phenotypes of HER2-positive BCCs by western blotting, real-time RT-PCR, and tube formation assay. The vascular phenotype of tumor cells from clinical samples was evaluated by staining with periodic acid-Schiff and an anti-CD31 antibody. We explored small molecule inhibitors that suppress tube formation and determined the inhibitory mechanism. Results Out of 242 cell surface antigens, 9 antigens were significantly upregulated and 3 were significantly downregulated by trastuzumab treatment. All upregulated antigens were related to endothelial and stem cell phenotypes, suggesting that trastuzumab treatment might be correlated to switching to a vascular phenotype, namely, vasculogenic mimicry (VM). Several VM markers were upregulated in trastuzumab-treated cells, but these cells did not form tubes on Matrigel, a functional hallmark of VM. Upon analysis of three trastuzumab-resistant HER2-positive cell lines, we found that all three cell lines showed tube formation on Matrigel in the presence of angiogenic growth factors including EGF, FGF2, IGF1, or VEGF. Clinically, VM channels significantly increased in surviving cancer cell clusters of surgically removed tumors pretreated with trastuzumab and chemotherapy compared to both surgically removed tumors without prior systemic treatment and tumors biopsied before presurgical treatment with trastuzumab. Finally, we found that salinomycin completely suppressed VM in all three trastuzumab-resistant cell lines through disruption of actin cytoskeletal integrity. Conclusions VM promotes metastasis and worsens patient outcomes. The present study indicates that HER2-positive BCCs can exhibit VM in an angiogenic microenvironment after eventually acquiring trastuzumab resistance. The clinical finding supports this in vitro observation. Thus, targeting VM might provide a therapeutic benefit to patients with HER2-positive breast cancer. Electronic supplementary material The online version of this article (10.1186/s13058-019-1167-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ami Hori
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita, Osaka, 565-0871, Japan
| |
Collapse
|
1292
|
Chen L, Toke NH, Luo S, Vasoya RP, Aita R, Parthasarathy A, Tsai YH, Spence JR, Verzi MP. HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine. Development 2019; 146:dev.179432. [PMID: 31345929 DOI: 10.1242/dev.179432] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022]
Abstract
As embryos mature, cells undergo remarkable transitions that are accompanied by shifts in transcription factor regulatory networks. Mechanisms driving developmental transitions are incompletely understood. The embryonic intestine transitions from a rapidly proliferating tube with pseudostratified epithelium prior to murine embryonic day (E) 14.5 to an exquisitely folded columnar epithelium in fetal stages. We sought to identify factors driving mouse fetal intestinal maturation by mining chromatin accessibility data for transcription factor motifs. ATAC-seq accessible regions shift during tissue maturation, with CDX2 transcription factor motifs abundant at chromatin-accessible regions of the embryo. Hepatocyte nuclear factor 4 (HNF4) transcription factor motifs are the most abundant in the fetal stages (>E16.5). Genetic inactivation of Hnf4a and its paralog Hnf4g revealed that HNF4 factors are redundantly required for fetal maturation. CDX2 binds to and activates Hnf4 gene loci to elevate HNF4 expression at fetal stages. HNF4 and CDX2 transcription factors then occupy shared genomic regulatory sites to promote chromatin accessibility and gene expression in the maturing intestine. Thus, HNF4 paralogs are key components of an intestinal transcription factor network shift during the embryonic to fetal transition.
Collapse
Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Natalie H Toke
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Shirley Luo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Roshan P Vasoya
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Rohit Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Aditya Parthasarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA.,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| |
Collapse
|
1293
|
Boros Á, Orlovácz K, Pankovics P, Szekeres S, Földvári G, Fahsbender E, Delwart E, Reuter G. Diverse picornaviruses are prevalent among free-living and laboratory rats (Rattus norvegicus) in Hungary and can cause disseminated infections. INFECTION GENETICS AND EVOLUTION 2019; 75:103988. [PMID: 31377399 DOI: 10.1016/j.meegid.2019.103988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 12/28/2022]
Abstract
In this study, the full length genomes of three phylogenetically distant picornaviruses (family Picornaviridae) belonging to the genus Rosavirus (rat08/rRoB/HUN, MN116648), Kobuvirus (rat08/rAiA/HUN, MN116647), and Cardiovirus (rat08/rCaB/HUN, MN116646) were obtained from a single faecal sample of a free-living Norway rat (Rattus norvegicus) in Hungary using viral metagenomics and RT-PCR/Sanger sequencing. The acquired complete genomes were in silico analyzed in detail revealing the presence of a second minor open reading frame encoding an alternative Leader peptide (L*) in rat08/rCaB/HUN and a ca. 222 nt-long sequence repeat with compact secondary RNA structure in the 3' UTR of rat08/rRoB/HUN. The studied rat picornaviruses were frequently detectable by RT-PCR with relatively high viral loads ranged between 8.99E+02 and 1.29E+06 copies/ml in rat faecal samples collected from five geographically distant locations throughout Hungary. The VP1 sequence-based phylogenetic analyses show the presence of multiple, mostly location-specific lineages for all three picornaviruses. Rat rosavirus and rat cardiovirus were identified in spleen while rat cardiovirus was also detected in liver, muscle and kidney samples with variable copy numbers (6.42E+01-1.90E+05 copies/μg total RNA) suggesting extra-intestinal dissemination. Both viruses were also prevalent (70.0% and 18.2%) among two populations of laboratory rats ("Wistar-type" and "hooded-type") held in different, isolated laboratory animal units.
Collapse
Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Katalin Orlovácz
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Sándor Szekeres
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Gábor Földvári
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary; Evolutionary Systems Research Group MTA Centre for Ecological Research, Tihany, Hungary
| | | | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary.
| |
Collapse
|
1294
|
Maity S, Ambatipudi K. Quantitative proteomics of milk whey reveals breed and season specific variation in protein abundance in Holstein Friesian cow and Murrah buffalo. Res Vet Sci 2019; 125:244-252. [DOI: 10.1016/j.rvsc.2019.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/22/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
|
1295
|
Essential role of GEXP15, a specific Protein Phosphatase type 1 partner, in Plasmodium berghei in asexual erythrocytic proliferation and transmission. PLoS Pathog 2019; 15:e1007973. [PMID: 31348803 PMCID: PMC6685639 DOI: 10.1371/journal.ppat.1007973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/07/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022] Open
Abstract
The essential and distinct functions of Protein Phosphatase type 1 (PP1) catalytic subunit in eukaryotes are exclusively achieved through its interaction with a myriad of regulatory partners. In this work, we report the molecular and functional characterization of Gametocyte EXported Protein 15 (GEXP15), a Plasmodium specific protein, as a regulator of PP1. In vitro interaction studies demonstrated that GEXP15 physically interacts with PP1 through the RVxF binding motif in P. berghei. Functional assays showed that GEXP15 was able to increase PP1 activity and the mutation of the RVxF motif completely abolished this regulation. Immunoprecipitation assays of tagged GEXP15 or PP1 in P. berghei followed by immunoblot or mass spectrometry analyses confirmed their interaction and showed that they are present both in schizont and gametocyte stages in shared protein complexes involved in the spliceosome and proteasome pathways and known to play essential role in parasite development. Phenotypic analysis of viable GEXP15 deficient P. berghei blood parasites showed that they were unable to develop lethal infection in BALB/c mice or to establish experimental cerebral malaria in C57BL/6 mice. Further, although deficient parasites produced gametocytes they did not produce any oocysts/sporozoites indicating a high fitness cost in the mosquito. Global proteomic and phosphoproteomic analyses of GEXP15 deficient schizonts revealed a profound defect with a significant decrease in the abundance and an impact on phosphorylation status of proteins involved in regulation of gene expression or invasion. Moreover, depletion of GEXP15 seemed to impact mainly the abundance of some specific proteins of female gametocytes. Our study provides the first insight into the contribution of a PP1 regulator to Plasmodium virulence and suggests that GEXP15 affects both the asexual and sexual life cycle. In the absence of an effective vaccine and the emerging resistance to artemisinin combination therapy, malaria is still a significant threat to human health. Increasing our understanding of the specific mechanisms of the biology of Plasmodium is essential to propose new strategies to control this infection. Here, we demonstrated that GEXP15, a specific protein in Plasmodium, was able to interact with the Protein Phosphatase 1 and regulate its activity. We showed that both proteins are implicated in common protein complexes involved in the mRNA splicing and proteasome pathways. We reported that the deletion of GEXP15 leads to a loss of parasite virulence during asexual stages and a total abolishment of the capacity of deficient parasites to develop in the mosquito. We also found that this deletion affects both protein phosphorylation status and significantly decreases the expression of essential proteins in schizont and gametocyte stages. This study characterizes for the first time a novel molecular pathway through the control of PP1 by an essential and specific Plasmodium regulator, which may contribute to the discovery of new therapeutic targets to control malaria.
Collapse
|
1296
|
Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica. Microorganisms 2019; 7:microorganisms7070203. [PMID: 31323808 PMCID: PMC6681027 DOI: 10.3390/microorganisms7070203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/13/2019] [Accepted: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts.
Collapse
|
1297
|
A rapid dicrimination of wheat, walnut and hazelnut flour samples using chemometric algorithms on GC/MS data. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2019. [DOI: 10.1007/s11694-019-00216-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
1298
|
Slater RT, Frost LR, Jossi SE, Millard AD, Unnikrishnan M. Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms. Sci Rep 2019; 9:9903. [PMID: 31289293 PMCID: PMC6616478 DOI: 10.1038/s41598-019-46143-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/21/2019] [Indexed: 12/18/2022] Open
Abstract
The anaerobic gut pathogen, Clostridioides difficile, forms adherent biofilms that may play an important role in recurrent C. difficile infections. The mechanisms underlying C. difficile community formation and inter-bacterial interactions are nevertheless poorly understood. C. difficile produces AI-2, a quorum sensing molecule that modulates biofilm formation across many bacterial species. We found that a strain defective in LuxS, the enzyme that mediates AI-2 production, is defective in biofilm development in vitro. Transcriptomic analyses of biofilms formed by wild type (WT) and luxS mutant (luxS) strains revealed a downregulation of prophage loci in the luxS mutant biofilms compared to the WT. Detection of phages and eDNA within biofilms may suggest that DNA release by phage-mediated cell lysis contributes to C. difficile biofilm formation. In order to understand if LuxS mediates C. difficile crosstalk with other gut species, C. difficile interactions with a common gut bacterium, Bacteroides fragilis, were studied. We demonstrate that C. difficile growth is significantly reduced when co-cultured with B. fragilis in mixed biofilms. Interestingly, the absence of C. difficile LuxS alleviates the B. fragilis-mediated growth inhibition. Dual species RNA-sequencing analyses from single and mixed biofilms revealed differential modulation of distinct metabolic pathways for C. difficile WT, luxS and B. fragilis upon co-culture, indicating that AI-2 may be involved in induction of selective metabolic responses in B. fragilis. Overall, our data suggest that C. difficile LuxS/AI-2 utilises different mechanisms to mediate formation of single and mixed species communities.
Collapse
Affiliation(s)
- Ross T Slater
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Lucy R Frost
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Sian E Jossi
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Andrew D Millard
- University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Meera Unnikrishnan
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom.
| |
Collapse
|
1299
|
Evans HT, Benetatos J, van Roijen M, Bodea L, Götz J. Decreased synthesis of ribosomal proteins in tauopathy revealed by non-canonical amino acid labelling. EMBO J 2019; 38:e101174. [PMID: 31268600 PMCID: PMC6600635 DOI: 10.15252/embj.2018101174] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 01/06/2023] Open
Abstract
Tau is a scaffolding protein that serves multiple cellular functions that are perturbed in neurodegenerative diseases, including Alzheimer's disease (AD) and frontotemporal dementia (FTD). We have recently shown that amyloid-β, the second hallmark of AD, induces de novo protein synthesis of tau. Importantly, this activation was found to be tau-dependent, raising the question of whether FTD-tau by itself affects protein synthesis. We therefore applied non-canonical amino acid labelling to visualise and identify newly synthesised proteins in the K369I tau transgenic K3 mouse model of FTD. This revealed massively decreased protein synthesis in neurons containing pathologically phosphorylated tau, a finding confirmed in P301L mutant tau transgenic rTg4510 mice. Using quantitative SWATH-MS proteomics, we identified changes in 247 proteins of the de novo proteome of K3 mice. These included decreased synthesis of the ribosomal proteins RPL23, RPLP0, RPL19 and RPS16, a finding that was validated in both K3 and rTg4510 mice. Together, our findings present a potential pathomechanism by which pathological tau interferes with cellular functions through the dysregulation of ribosomal protein synthesis.
Collapse
Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Joseph Benetatos
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | | | - Liviu‐Gabriel Bodea
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| |
Collapse
|
1300
|
Diéguez-Hurtado R, Kato K, Giaimo BD, Nieminen-Kelhä M, Arf H, Ferrante F, Bartkuhn M, Zimmermann T, Bixel MG, Eilken HM, Adams S, Borggrefe T, Vajkoczy P, Adams RH. Loss of the transcription factor RBPJ induces disease-promoting properties in brain pericytes. Nat Commun 2019; 10:2817. [PMID: 31249304 PMCID: PMC6597568 DOI: 10.1038/s41467-019-10643-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
Sufficient vascular supply is indispensable for brain development and function, whereas dysfunctional blood vessels are associated with human diseases such as vascular malformations, stroke or neurodegeneration. Pericytes are capillary-associated mesenchymal cells that limit vascular permeability and protect the brain by preserving blood-brain barrier integrity. Loss of pericytes has been linked to neurodegenerative changes in genetically modified mice. Here, we report that postnatal inactivation of the Rbpj gene, encoding the transcription factor RBPJ, leads to alteration of cell identity markers in brain pericytes, increases local TGFβ signalling, and triggers profound changes in endothelial behaviour. These changes, which are not mimicked by pericyte ablation, imperil vascular stability and induce the acquisition of pathological landmarks associated with cerebral cavernous malformations. In adult mice, loss of Rbpj results in bigger stroke lesions upon ischemic insult. We propose that brain pericytes can acquire deleterious properties that actively enhance vascular lesion formation and promote pathogenic processes. Pericytes are perivascular cells essential for blood-brain barrier maintenance. Here Diéguez-Hurtado et al. show that depletion of the transcription factor RBPJ in pericytes affects their molecular identity and disturbs endothelial cell behaviour, inducing the formation of vascular lesions in the brain.
Collapse
Affiliation(s)
- Rodrigo Diéguez-Hurtado
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.,Faculty of Medicine, University of Münster, 48149, Münster, Germany
| | - Katsuhiro Kato
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | | | - Melina Nieminen-Kelhä
- Department of Neurosurgery, Charité-Universitätsmedizin, Charitéplatz 1, Berlin, 10117, Germany.,Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Hendrik Arf
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - M Gabriele Bixel
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | - Hanna M Eilken
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.,Bayer AG, Aprather Weg 18a, 42113, Wuppertal, Germany
| | - Susanne Adams
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité-Universitätsmedizin, Charitéplatz 1, Berlin, 10117, Germany. .,Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany.
| | - Ralf H Adams
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany. .,Faculty of Medicine, University of Münster, 48149, Münster, Germany.
| |
Collapse
|