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Erdmann J, Preusse M, Khaledi A, Pich A, Häussler S. Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa. Environ Microbiol 2018; 20:3952-3963. [DOI: 10.1111/1462-2920.14419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Jelena Erdmann
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Centre for Pharmacology and Toxicology; Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School; Hannover Germany
| | - Matthias Preusse
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Ariane Khaledi
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Andreas Pich
- Centre for Pharmacology and Toxicology; Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School; Hannover Germany
| | - Susanne Häussler
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
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52
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Onco-Multi-OMICS Approach: A New Frontier in Cancer Research. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9836256. [PMID: 30402498 PMCID: PMC6192166 DOI: 10.1155/2018/9836256] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/06/2018] [Indexed: 02/07/2023]
Abstract
The acquisition of cancer hallmarks requires molecular alterations at multiple levels including genome, epigenome, transcriptome, proteome, and metabolome. In the past decade, numerous attempts have been made to untangle the molecular mechanisms of carcinogenesis involving single OMICS approaches such as scanning the genome for cancer-specific mutations and identifying altered epigenetic-landscapes within cancer cells or by exploring the differential expression of mRNA and protein through transcriptomics and proteomics techniques, respectively. While these single-level OMICS approaches have contributed towards the identification of cancer-specific mutations, epigenetic alterations, and molecular subtyping of tumors based on gene/protein-expression, they lack the resolving-power to establish the casual relationship between molecular signatures and the phenotypic manifestation of cancer hallmarks. In contrast, the multi-OMICS approaches involving the interrogation of the cancer cells/tissues in multiple dimensions have the potential to uncover the intricate molecular mechanism underlying different phenotypic manifestations of cancer hallmarks such as metastasis and angiogenesis. Moreover, multi-OMICS approaches can be used to dissect the cellular response to chemo- or immunotherapy as well as discover molecular candidates with diagnostic/prognostic value. In this review, we focused on the applications of different multi-OMICS approaches in the field of cancer research and discussed how these approaches are shaping the field of personalized oncomedicine. We have highlighted pioneering studies from “The Cancer Genome Atlas (TCGA)” consortium encompassing integrated OMICS analysis of over 11,000 tumors from 33 most prevalent forms of cancer. Accumulation of huge cancer-specific multi-OMICS data in repositories like TCGA provides a unique opportunity for the systems biology approach to tackle the complexity of cancer cells through the unification of experimental data and computational/mathematical models. In future, systems biology based approach is likely to predict the phenotypic changes of cancer cells upon chemo-/immunotherapy treatment. This review is sought to encourage investigators to bring these different approaches together for interrogating cancer at molecular, cellular, and systems levels.
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53
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Wong KC. DNA Motif Recognition Modeling from Protein Sequences. iScience 2018; 7:198-211. [PMID: 30267681 PMCID: PMC6153143 DOI: 10.1016/j.isci.2018.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/08/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022] Open
Abstract
Although the existing works on DNA motif discovery on DNA sequences are plethoric, mechanistic knowledge to infer DNA motifs from protein sequences across multiple DNA-binding domain families without conducting any wet-lab experiments is still lacking. Therefore, the k-spectrum recognition modeling is proposed to address the issues at the highest possible resolutions. The k-spectrum model can capture DNA motif patterns from protein sequences at the resolution in which local sequence context and nucleotide dependency can be taken into account completely. Multiple evaluation metrics are adopted and measured on millions of k-mer binding intensities from 92 proteins across 5 DNA-binding families (i.e., bHLH, bZIP, ETS, Forkhead, and Homeodomain), demonstrating its competitive edges. In addition, it not only can contribute to DNA motif recognition modeling but also can help prioritize the observed or even unobserved binding of single nucleotide variants on transcription factor binding sites in a genome-wide manner. DNA motif modeling from protein is fundamental for understanding gene regulation A framework is proposed at the highest possible sequence resolution for the first time It is validated on millions of k-mer intensities from 92 proteins across 5 families It can prioritize the unobserved regulatory single nucleotide variants on DNA motifs
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Affiliation(s)
- Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong.
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Timmons JA, Atherton PJ, Larsson O, Sood S, Blokhin IO, Brogan RJ, Volmar CH, Josse AR, Slentz C, Wahlestedt C, Phillips SM, Phillips BE, Gallagher IJ, Kraus WE. A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease. Nucleic Acids Res 2018; 46:7772-7792. [PMID: 29986096 PMCID: PMC6125682 DOI: 10.1093/nar/gky570] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/23/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWAS), relying on hundreds of thousands of individuals, have revealed >200 genomic loci linked to metabolic disease (MD). Loss of insulin sensitivity (IS) is a key component of MD and we hypothesized that discovery of a robust IS transcriptome would help reveal the underlying genomic structure of MD. Using 1,012 human skeletal muscle samples, detailed physiology and a tissue-optimized approach for the quantification of coding (>18,000) and non-coding (>15,000) RNA (ncRNA), we identified 332 fasting IS-related genes (CORE-IS). Over 200 had a proven role in the biochemistry of insulin and/or metabolism or were located at GWAS MD loci. Over 50% of the CORE-IS genes responded to clinical treatment; 16 quantitatively tracking changes in IS across four independent studies (P = 0.0000053: negatively: AGL, G0S2, KPNA2, PGM2, RND3 and TSPAN9 and positively: ALDH6A1, DHTKD1, ECHDC3, MCCC1, OARD1, PCYT2, PRRX1, SGCG, SLC43A1 and SMIM8). A network of ncRNA positively related to IS and interacted with RNA coding for viral response proteins (P < 1 × 10-48), while reduced amino acid catabolic gene expression occurred without a change in expression of oxidative-phosphorylation genes. We illustrate that combining in-depth physiological phenotyping with robust RNA profiling methods, identifies molecular networks which are highly consistent with the genetics and biochemistry of human metabolic disease.
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Affiliation(s)
- James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, London, UK
- Scion House, Stirling University Innovation Park, Stirling, UK
| | | | - Ola Larsson
- Department of Oncology-Pathology, Science For Life Laboratory, Stockholm, Sweden
| | - Sanjana Sood
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - Robert J Brogan
- Scion House, Stirling University Innovation Park, Stirling, UK
| | | | | | - Cris Slentz
- Duke University School of Medicine, Durham, USA
| | - Claes Wahlestedt
- Department of Oncology-Pathology, Science For Life Laboratory, Stockholm, Sweden
| | | | | | - Iain J Gallagher
- Scion House, Stirling University Innovation Park, Stirling, UK
- School of Health Sciences and Sport, University of Stirling, Stirling, UK
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55
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The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock. PLoS Genet 2018; 14:e1007563. [PMID: 30059503 PMCID: PMC6085073 DOI: 10.1371/journal.pgen.1007563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 08/09/2018] [Accepted: 07/15/2018] [Indexed: 12/11/2022] Open
Abstract
RNA-binding proteins (RBPs) establish the cellular fate of a transcript, but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules. Using MS2 RNA tagging, we have purified proteins associated with individual mRNA species induced by osmotic stress, STL1 and GPD1. We found members of the Lsm1-7/Pat1 RBP complex to preferentially bind these mRNAs, relative to the non-stress induced mRNAs, HYP2 and ASH1. To assess the functional importance, we mutated components of the Lsm1-7/Pat1 RBP complex and analyzed the impact on expression of osmostress gene products. We observed a defect in global translation inhibition under osmotic stress in pat1 and lsm1 mutants, which correlated with an abnormally high association of both non-stress and stress-induced mRNAs to translationally active polysomes. Additionally, for stress-induced proteins normally triggered only by moderate or high osmostress, in the mutants the protein levels rose high already at weak hyperosmosis. Analysis of ribosome passage on mRNAs through co-translational decay from the 5’ end (5P-Seq) showed increased ribosome accumulation in lsm1 and pat1 mutants upstream of the start codon. This effect was particularly strong for mRNAs induced under osmostress. Thus, our results indicate that, in addition to its role in degradation, the Lsm1-7/Pat1 complex acts as a selective translational repressor, having stronger effect over the translation initiation of heavily expressed mRNAs. Binding of the Lsm1-7/Pat1p complex to osmostress-induced mRNAs mitigates their translation, suppressing it in conditions of weak or no stress, and avoiding a hyperresponse when triggered. When confronted with external physical or chemical stress, cells respond by increasing the mRNA output of a small number of genes required for stress survival, while shutting down the majority of other genes. Moreover, each mRNA is regulated under stress to either enhance or diminish its translation into proteins. The overall purpose is for the cell to optimize gene expression for survival and recovery during rapidly changing conditions. Much of this regulation is mediated by RNA-binding proteins. We have isolated proteins binding to specific mRNAs induced by stress, to investigate how they affect the stress response. We found members of one protein complex to be bound to stress-induced mRNAs. When mutants lacking these proteins were exposed to stress, ribosomes were more engaged with translating mRNAs than in the wild-type. In the mutants, it was also possible to trigger expression of stress proteins with only minimal stress levels. Tracing the passage of ribosomes over mRNAs, we saw that ribosomes accumulated around the start codon in the mutants. These findings indicate that the protein complex is required to moderate the stress response and prevent it from overreacting, which would be harmful for the cell.
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56
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Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP. Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma. J Thorac Oncol 2018; 13:1519-1529. [PMID: 30017829 DOI: 10.1016/j.jtho.2018.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/12/2018] [Accepted: 06/27/2018] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Despite apparently complete surgical resection, approximately half of resected early-stage lung cancer patients relapse and die of their disease. Adjuvant chemotherapy reduces this risk by only 5% to 8%. Thus, there is a need for better identifying who benefits from adjuvant therapy, the drivers of relapse, and novel targets in this setting. METHODS RNA sequencing and liquid chromatography/liquid chromatography-mass spectrometry proteomics data were generated from 51 surgically resected non-small cell lung tumors with known recurrence status. RESULTS We present a rationale and framework for the incorporation of high-content RNA and protein measurements into integrative biomarkers and show the potential of this approach for predicting risk of recurrence in a group of lung adenocarcinomas. In addition, we characterize the relationship between mRNA and protein measurements in lung adenocarcinoma and show that it is outcome specific. CONCLUSIONS Our results suggest that mRNA and protein data possess independent biological and clinical importance, which can be leveraged to create higher-powered expression biomarkers.
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Affiliation(s)
- Michael F Sharpnack
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Nilini Ranbaduge
- Department of Chemistry, The Ohio State University, Columbus, Ohio
| | - Arunima Srivastava
- Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio
| | | | - Simona G Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Celine Mascaux
- Department of Multidisciplinary Oncology and Therapeutic Innovations, Assistance Publique des Hôpitaux de Marseille, France; Aix-Marseille University, Marseille, France
| | - Wayne O Miles
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Robert Morris
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - James L Sharpnack
- Department of Statistics, University of California, Davis, California
| | - Joseph Amann
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Christopher A Maher
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio
| | - Vicki H Wysocki
- Department of Chemistry, The Ohio State University, Columbus, Ohio
| | - Ramaswami Govindan
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Parag Mallick
- Department of Radiology, Stanford University, Palo Alto, California
| | - Kevin R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - David P Carbone
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
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57
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Shifts in the relationship between mRNA and protein abundance of gill ion-transporters during smolt development and seawater acclimation in Atlantic salmon (Salmo salar). Comp Biochem Physiol A Mol Integr Physiol 2018; 221:63-73. [DOI: 10.1016/j.cbpa.2018.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 11/24/2022]
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58
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Antunes S, Couto J, Ferrolho J, Rodrigues F, Nobre J, Santos AS, Santos-Silva MM, de la Fuente J, Domingos A. Rhipicephalus bursa Sialotranscriptomic Response to Blood Feeding and Babesia ovis Infection: Identification of Candidate Protective Antigens. Front Cell Infect Microbiol 2018; 8:116. [PMID: 29780749 PMCID: PMC5945973 DOI: 10.3389/fcimb.2018.00116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/23/2018] [Indexed: 02/03/2023] Open
Abstract
Ticks are among the most prevalent blood-feeding arthropods, and they act as vectors and reservoirs for numerous pathogens. Sialotranscriptomic characterizations of tick responses to blood feeding and pathogen infections can offer new insights into the molecular interplay occurring at the tick-host-pathogen interface. In the present study, we aimed to identify and characterize Rhipicephalus bursa salivary gland (SG) genes that were differentially expressed in response to blood feeding and Babesia ovis infection. Our experimental approach consisted of RNA sequencing of SG from three different tick samples, fed-infected, fed-uninfected, and unfed-uninfected, for characterization and inter-comparison. Overall, 7,272 expressed sequence tags (ESTs) were constructed from unfed-uninfected, 13,819 ESTs from fed-uninfected, and 15,292 ESTs from fed-infected ticks. Two catalogs of transcripts that were differentially expressed in response to blood feeding and B. ovis infection were produced. Four genes coding for a putative vitellogenin-3, lachesin, a glycine rich protein, and a secreted cement protein were selected for RNA interference functional studies. A reduction of 92, 65, and 51% was observed in vitellogenin-3, secreted cement, and lachesin mRNA levels in SG, respectively. The vitellogenin-3 knockdown led to increased tick mortality, with 77% of ticks dying post-infestation. The reduction of the secreted cement protein-mRNA levels resulted in 46% of ticks being incapable of correctly attaching to the host and significantly lower female weights post-feeding in comparison to the control group. The lachesin knockdown resulted in a 70% reduction of the levels associated with B. ovis infection in R. bursa SG and 70% mortality. These results improved our understanding of the role of tick SG genes in Babesia infection/proliferation and tick feeding. Moreover, lachesin, vitellogenin-3, and secreted cement proteins were validated as candidate protective antigens for the development of novel tick and tick-borne disease control measures.
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Affiliation(s)
- Sandra Antunes
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Joana Couto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Joana Ferrolho
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Fábio Rodrigues
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - João Nobre
- Instituto Nacional de Investigação Agrária e Veterinária, Pólo de Santarém, Vale de Santarém, Portugal
| | - Ana S Santos
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Centro de Estudos de Vectores e Doenças Infecciosas Dr. Francisco Cambournac (CEVDI/INSA), Águas de Moura, Portugal
| | - M Margarida Santos-Silva
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Centro de Estudos de Vectores e Doenças Infecciosas Dr. Francisco Cambournac (CEVDI/INSA), Águas de Moura, Portugal
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Ana Domingos
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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59
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Ilicic M, Butler T, Zakar T, Paul JW. The expression of genes involved in myometrial contractility changes during ex situ culture of pregnant human uterine smooth muscle tissue. J Smooth Muscle Res 2018; 53:73-89. [PMID: 28652518 PMCID: PMC5487834 DOI: 10.1540/jsmr.53.73] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background: Ex situ analyses of human myometrial tissue has been used to
investigate the regulation of uterine quiescence and transition to a contractile
phenotype. Following concerns about the validity of cultured primary cells, we examined
whether myometrial tissue undergoes culture-induced changes ex situ that
may affect the validity of in vitro models. Objectives: To determine
whether human myometrial tissue undergoes culture-induced changes ex situ
in Estrogen receptor 1 (ESR1), Prostaglandin-endoperoxide synthase 2
(PTGS2) and Oxytocin receptor (OXTR) expression.
Additionally, to determine whether culture conditions approaching the in
vivo environment influence the expression of these key genes. Methods: Term
non-laboring human myometrial tissues were cultured in the presence of specific
treatments, including; serum supplementation, progesterone and estrogen, cAMP, PMA,
stretch or NF-κB inhibitors. ESR1, PTGS2 and
OXTR mRNA abundance after 48 h culture was determined using
quantitative RT-PCR. Results: Myometrial tissue in culture exhibited culture-induced
up-regulation of ESR1 and PTGS2 and down-regulation of
OXTR mRNA expression. Progesterone prevented culture-induced increase
in ESR1 expression. Estrogen further up-regulated PTGS2
expression. Stretch had no direct effect, but blocked the effects of progesterone and
estrogen on ESR1 and PTGS2 expression. cAMP had no
effect whereas PMA further up-regulated PTGS2 expression and prevented
decline of OXTR expression. Conclusion: Human myometrial tissue in
culture undergoes culture-induced gene expression changes consistent with transition
toward a laboring phenotype. Changes in ESR1, PTGS2 and
OXTR expression could not be controlled simultaneously. Until optimal
culture conditions are determined, results of in vitro experiments with
myometrial tissues should be interpreted with caution.
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Affiliation(s)
- Marina Ilicic
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.,Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW 2308, Australia.,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW 2305, Australia
| | - Trent Butler
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.,Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW 2308, Australia.,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW 2305, Australia
| | - Tamas Zakar
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.,Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW 2308, Australia.,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW 2305, Australia.,John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
| | - Jonathan W Paul
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.,Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW 2308, Australia.,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW 2305, Australia
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Schulz D, Zanotelli VRT, Fischer JR, Schapiro D, Engler S, Lun XK, Jackson HW, Bodenmiller B. Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry. Cell Syst 2018; 6:25-36.e5. [PMID: 29289569 PMCID: PMC5791659 DOI: 10.1016/j.cels.2017.12.001] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/06/2017] [Accepted: 12/01/2017] [Indexed: 01/18/2023]
Abstract
To build comprehensive models of cellular states and interactions in normal and diseased tissue, genetic and proteomic information must be extracted with single-cell and spatial resolution. Here, we extended imaging mass cytometry to enable multiplexed detection of mRNA and proteins in tissues. Three mRNA target species were detected by RNAscope-based metal in situ hybridization with simultaneous antibody detection of 16 proteins. Analysis of 70 breast cancer samples showed that HER2 and CK19 mRNA and protein levels are moderately correlated on the single-cell level, but that only HER2, and not CK19, has strong mRNA-to-protein correlation on the cell population level. The chemoattractant CXCL10 was expressed in stromal cell clusters, and the frequency of CXCL10-expressing cells correlated with T cell presence. Our flexible and expandable method will allow an increase in the information content retrieved from patient samples for biomedical purposes, enable detailed studies of tumor biology, and serve as a tool to bridge comprehensive genomic and proteomic tissue analysis.
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Affiliation(s)
- Daniel Schulz
- Insitute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Vito Riccardo Tomaso Zanotelli
- Insitute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; Systems Biology PhD Program, Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Jana Raja Fischer
- Insitute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Denis Schapiro
- Insitute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Stefanie Engler
- Insitute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Xiao-Kang Lun
- Insitute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Bernd Bodenmiller
- Insitute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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Integrated omics dissection of proteome dynamics during cardiac remodeling. Nat Commun 2018; 9:120. [PMID: 29317621 PMCID: PMC5760723 DOI: 10.1038/s41467-017-02467-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 11/29/2017] [Indexed: 11/08/2022] Open
Abstract
Transcript abundance and protein abundance show modest correlation in many biological models, but how this impacts disease signature discovery in omics experiments is rarely explored. Here we report an integrated omics approach, incorporating measurements of transcript abundance, protein abundance, and protein turnover to map the landscape of proteome remodeling in a mouse model of pathological cardiac hypertrophy. Analyzing the hypertrophy signatures that are reproducibly discovered from each omics data type across six genetic strains of mice, we find that the integration of transcript abundance, protein abundance, and protein turnover data leads to 75% gain in discovered disease gene candidates. Moreover, the inclusion of protein turnover measurements allows discovery of post-transcriptional regulations across diverse pathways, and implicates distinct disease proteins not found in steady-state transcript and protein abundance data. Our results suggest that multi-omics investigations of proteome dynamics provide important insights into disease pathogenesis in vivo.
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62
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Pla D, Petras D, Saviola AJ, Modahl CM, Sanz L, Pérez A, Juárez E, Frietze S, Dorrestein PC, Mackessy SP, Calvete JJ. Transcriptomics-guided bottom-up and top-down venomics of neonate and adult specimens of the arboreal rear-fanged Brown Treesnake, Boiga irregularis, from Guam. J Proteomics 2017; 174:71-84. [PMID: 29292096 DOI: 10.1016/j.jprot.2017.12.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
The Brown Treesnake (Boiga irregularis) is an arboreal, nocturnal, rear-fanged venomous snake native to northern and eastern regions of Australia, Papua New Guinea and the Solomon Islands. It was inadvertently introduced onto the island of Guam during the late 1940's to early 1950's, and it has caused massive declines and extirpations of the native bird, lizard, and mammal populations. In the current study, we report the characterization of the venom proteome of an adult and a neonate B. irregularis specimens from Guam by a combination of venom gland transcriptomic and venomic analyses. Venom gland transcriptomic analysis of an adult individual identified toxins belonging to 18 protein families, with three-finger toxin isoforms being the most abundantly expressed transcripts, comprising 94% of all venom protein transcript reads. Transcripts for PIII-metalloproteinases, C-type lectins, cysteine-rich secretory proteins, acetylcholinesterases, natriuretic peptides, ficolins, phospholipase A2 (PLA2) inhibitors, PLA2s, vascular endothelial growth factors, Kunitz-type protease inhibitors, cystatins, phospholipase Bs, cobra venom factors, waprins, SVMP inhibitors, matrix metalloproteinases, and hyaluronidases were also identified, albeit, at very low abundances ranging from 0.05% to 1.7% of the transcriptome. The venom proteomes of neonate and adult B. irregularis were also both overwhelmingly (78 and 84%, respectively) dominated by monomeric and dimeric 3FTxs, followed by moderately abundant (21% (N) and 13% (A)) CRISPs, low abundance (1% (N), 3% (A)) PIII-SVMPs, and very low abundance (<0.01%) PLA2 and SVMP inhibitors. The differences in relative toxin abundances identified between neonate and adult snakes likely correlates to shifts in prey preference between the two age classes, from nearly-exclusively lizards to lizards, birds and small mammals. Immunoaffinity antivenomics with experimentally designed rabbit anti-Brown Treesnake (anti-BTS) venom IgGs against homologous venom from adult snakes demonstrated that CRISPs, PIII-SVMPs, and 60-70% of 3FTxs were effectively immunocaptured. Western blot analysis showed that all venom proteins were recognized by anti-BTS IgGs, and cross-reactivity with other rear-fanged snake venoms was also observed. Incubation of anti-BTS venom IgGs with crude B. irregularis venom resulted in a significant decrease in proteolytic (SVMP) activity against azocasein. These results provide the first comparative venomic and anti-venomic analysis of neonate and adult B. irregularis from Guam, further highlighting evolutionary trends in venom composition among rear-fanged venomous snakes. SIGNIFICANCE PARAGRAPH The Brown Treesnake (Boiga irregularis) has caused extensive ecological and economic damage to the island of Guam where it has become a classic example of the negative impacts of invasive species. In the current study, we report the first combined transcriptomic and proteomic analysis of B. irregularis venom of Guam origin. The transcriptome of an adult snake contained toxin sequences belonging to 18 protein families, with three-finger toxin (3FTx) isoforms being the most abundant and representing 94% of all venom protein transcript reads. Our bottom-up and top-down venomic analyses confirmed that 3FTxs are the major components of B. irregularis venom, and a comparative analysis of neonate and adult venoms demonstrate a clear ontogenetic shift in toxin abundance, likely driven by dietary variation between the two age classes. Second-generation antivenomics and Western blot analysis using purified anti-Brown Treesnake rabbit serum IgGs (anti-BTS IgGs) showed strong immunoreactivity toward B. irregularis venom. Interestingly, our anti-BTS IgGs did not cross-react with 3FTxs found in several other rear-fanged snake venoms, or against 3FTxs in the venom of the elapid Ophiophagus hannah, indicating that epitopes in these 3FTx molecules are quite distinct.
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Affiliation(s)
- Davinia Pla
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Daniel Petras
- University of California San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Anthony J Saviola
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain; School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA
| | - Cassandra M Modahl
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA
| | - Libia Sanz
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Alicia Pérez
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Elena Juárez
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Seth Frietze
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA
| | - Pieter C Dorrestein
- University of California San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA.
| | - Juan J Calvete
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain.
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Smith JG. Molecular Epidemiology of Heart Failure: Translational Challenges and Opportunities. JACC Basic Transl Sci 2017; 2:757-769. [PMID: 30062185 PMCID: PMC6058947 DOI: 10.1016/j.jacbts.2017.07.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022]
Abstract
Heart failure (HF) is the end-stage of all heart disease and arguably constitutes the greatest unmet therapeutic need in cardiovascular medicine today. Classic epidemiological studies have established clinical risk factors for HF, but the cause remains poorly understood in many cases. Biochemical analyses of small case-control series and animal models have described a plethora of molecular characteristics of HF, but a single unifying pathogenic theory is lacking. Heart failure appears to result not only from cardiac overload or injury but also from a complex interplay among genetic, neurohormonal, metabolic, inflammatory, and other biochemical factors acting on the heart. Recent development of robust, high-throughput tools in molecular biology provides opportunity for deep molecular characterization of population-representative cohorts and HF cases (molecular epidemiology), including genome sequencing, profiling of myocardial gene expression and chromatin modifications, plasma composition of proteins and metabolites, and microbiomes. The integration of such detailed information holds promise for improving understanding of HF pathophysiology in humans, identification of therapeutic targets, and definition of disease subgroups beyond the current classification based on ejection fraction which may benefit from improved individual tailoring of therapy. Challenges include: 1) the need for large cohorts with deep, uniform phenotyping; 2) access to the relevant tissues, ideally with repeated sampling to capture dynamic processes; and 3) analytical issues related to integration and analysis of complex datasets. International research consortia have formed to address these challenges and combine datasets, and cohorts with up to 1 million participants are being collected. This paper describes the molecular epidemiology of HF and provides an overview of methods and tissue types and examples of published and ongoing efforts to systematically evaluate molecular determinants of HF in human populations.
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Affiliation(s)
- J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden.,Department of Heart Failure and Valvular Disease, Skåne University Hospital, Lund, Sweden.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
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64
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Li Y, Estep JA, Karginov FV. Transcriptome-wide Identification and Validation of Interactions between the miRNA Machinery and HuR on mRNA Targets. J Mol Biol 2017; 430:285-296. [PMID: 29273203 DOI: 10.1016/j.jmb.2017.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/28/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022]
Abstract
The 3' untranslated region (UTR) of mRNAs is the primary regulatory region that mediates post-transcriptional control by microRNAs and RNA-binding proteins in the cytoplasm. Aside from individual sequence-specific binding and regulation, examples of interaction between these factors at particular 3' UTR sites have emerged. However, the whole picture of such higher-order regulatory modules across the transcriptome is lacking. Here, we investigate the interactions between HuR, a ubiquitous RNA-binding protein, and Ago2, a core effector of the miRNA pathway, at the transcriptome-wide level. Using HITS-CLIP, we map HuR and miRNA binding sites on human 3' UTRs and assess their co-occurrence. In addition, we demonstrate global effects of HuR knockdown on Ago2 occupancy, suggesting a co-regulatory relationship. Focusing on sites of Ago2-HuR overlap, 13 candidates were screened in luciferase reporter assays. Eleven sites showed miRNA-dependent repression, as confirmed in Dicer-null cells. To test for HuR's role in co-regulation, we measured the reporters in HuR KO cells. Three of the miRNA sites demonstrated altered activities, indicating that HuR has an effect on miRNA repression at those sites. Our study presents an efficient search and validation system for studying miRNA-HuR interactions, which expands our understanding of the combinatorial post-transcriptional control of gene expression at the 3' UTR.
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Affiliation(s)
- Yahui Li
- Department of Molecular, Cell and Systems Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Jason A Estep
- Department of Molecular, Cell and Systems Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Fedor V Karginov
- Department of Molecular, Cell and Systems Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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Brown RE, Senniappan S, Hussain K, McGuire MF. Morphoproteomics and biomedical analytics coincide with clinical outcomes in supporting a constant but variable role for the mTOR pathway in the biology of congenital hyperinsulinism of infancy. Orphanet J Rare Dis 2017; 12:181. [PMID: 29246172 PMCID: PMC5732475 DOI: 10.1186/s13023-017-0735-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/06/2017] [Indexed: 11/10/2022] Open
Abstract
We first introduced the concept of the mTOR pathway’s involvement in congenital hyperinsulinism of infancy (CHI), based largely on morphoproteomic observations and clinical outcomes using sirolimus (rapamycin) as a therapeutic agent in infants refractory to octreotide and diazoxide treatment. Subsequent publications have verified the efficacy of such treatment in some cases but limited and variable in others. We present further evidence of a constant but variable role for the mTOR pathway in the biology of CHI and provide a strategy that allows for the short-term testing of sirolimus in individual CHI patients.
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Affiliation(s)
- Robert E Brown
- Department of Pathology and Laboratory Medicine, UT Health McGovern Medical School, Houston, TX, USA.
| | - Senthil Senniappan
- Department of Paediatric Endocrinology, Alder Hey Children's Hospital, Liverpool, L12 2AP, UK
| | - Khalid Hussain
- Department of Paediatric Medicine Division of Endocrinology, Sidra Medical & Research Center OPC, C6-337, PO Box 26999, Doha, Qatar
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66
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Li JJ, Chew GL, Biggin MD. Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them. Nucleic Acids Res 2017; 45:11821-11836. [PMID: 29040683 PMCID: PMC5714229 DOI: 10.1093/nar/gkx898] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/25/2017] [Indexed: 11/17/2022] Open
Abstract
Translation rate per mRNA molecule correlates positively with mRNA abundance. As a result, protein levels do not scale linearly with mRNA levels, but instead scale with the abundance of mRNA raised to the power of an ‘amplification exponent’. Here we show that to quantitate translational control, the translation rate must be decomposed into two components. One, TRmD, depends on the mRNA level and defines the amplification exponent. The other, TRmIND, is independent of mRNA amount and impacts the correlation coefficient between protein and mRNA levels. We show that in Saccharomyces cerevisiae TRmD represents ∼20% of the variance in translation and directs an amplification exponent of 1.20 with a 95% confidence interval [1.14, 1.26]. TRmIND constitutes the remaining ∼80% of the variance in translation and explains ∼5% of the variance in protein expression. We also find that TRmD and TRmIND are preferentially determined by different mRNA sequence features: TRmIND by the length of the open reading frame and TRmD both by a ∼60 nucleotide element that spans the initiating AUG and by codon and amino acid frequency. Our work provides more appropriate estimates of translational control and implies that TRmIND is under different evolutionary selective pressures than TRmD.
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Affiliation(s)
- Jingyi Jessica Li
- Department of Statistics and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Guo-Liang Chew
- Computational Biology Program, Public Health Sciences and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mark D Biggin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94708, USA
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Moreno-Navarrete JM, Rodríguez A, Becerril S, Valentí V, Salvador J, Frühbeck G, Fernández-Real JM. Increased Small Intestine Expression of Non-Heme Iron Transporters in Morbidly Obese Patients With Newly Diagnosed Type 2 Diabetes. Mol Nutr Food Res 2017; 62. [PMID: 29082606 DOI: 10.1002/mnfr.201700301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 08/04/2017] [Indexed: 01/01/2023]
Abstract
SCOPE To investigate intestinal markers of iron absorption in morbidly obese subjects according to glucose tolerance. METHODS AND RESULTS Gene expression of both non-heme (SLC40A1 (ferroportin), SLC11A2) and heme iron (SLC46A1 (HCP1), HMOX1) transporters is analyzed in 38 small intestine tissue samples [11 with normal glucose tolerance, 14 with glucose intolerance (GI), and 13 with newly diagnosed type 2 diabetes (T2D)]. SLC40A1 (r = 0.43, p = 0.008) and SLC11A2 (r = 0.35, p = 0.03) mRNA levels are positively correlated with ferritin-to-hepcidin ratio and with fasting glucose, being significantly increased in patients with T2D. Only ferroportin is negatively associated with serum hepcidin (r = -0.617, p < 0.0001). In multivariate regression analysis, fasting glucose contributes independently to intestinal SLC40A1 (p = 0.009) and SLC11A2 (p = 0.04) variance after controlling for age, sex, and BMI. When circulating hepcidin is incorporated into the model, fasting glucose contributes significantly and independently to intestinal SLC40A1 (p = 0.02), but not to SLC11A2 (p = 0.07) variance. SLC46A1 and HMOX1 are similar in all groups. CONCLUSION The expression of ferroportin and SLC11A2 is increased in the intestine of patients with T2D in association with iron stores and serum hepcidin levels. Increased intestinal iron absorption is a potential mechanism that could explain the increased body iron stores frequently observed in patients with T2D.
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Affiliation(s)
- José María Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Amaia Rodríguez
- Metabolic Research Laboratory, Clínica Universidad de Navarra, CIBEROBN, IdiSNA, Pamplona, Spain
| | - Sara Becerril
- Metabolic Research Laboratory, Clínica Universidad de Navarra, CIBEROBN, IdiSNA, Pamplona, Spain
| | - Víctor Valentí
- Department of Surgery, Clínica Universidad de Navarra, CIBEROBN, IdiSNA, Pamplona, Spain
| | - Javier Salvador
- Department of Endocrinology & Nutrition, Clínica Universidad de Navarra, CIBEROBN, IdiSNA, Pamplona, Spain
| | - Gema Frühbeck
- Metabolic Research Laboratory, Clínica Universidad de Navarra, CIBEROBN, IdiSNA, Pamplona, Spain.,Department of Endocrinology & Nutrition, Clínica Universidad de Navarra, CIBEROBN, IdiSNA, Pamplona, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
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Ainsworth S, Petras D, Engmark M, Süssmuth RD, Whiteley G, Albulescu LO, Kazandjian TD, Wagstaff SC, Rowley P, Wüster W, Dorrestein PC, Arias AS, Gutiérrez JM, Harrison RA, Casewell NR, Calvete JJ. The medical threat of mamba envenoming in sub-Saharan Africa revealed by genus-wide analysis of venom composition, toxicity and antivenomics profiling of available antivenoms. J Proteomics 2017; 172:173-189. [PMID: 28843532 DOI: 10.1016/j.jprot.2017.08.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/05/2017] [Accepted: 08/22/2017] [Indexed: 12/23/2022]
Abstract
Mambas (genus Dendroaspis) are among the most feared of the medically important elapid snakes found in sub-Saharan Africa, but many facets of their biology, including the diversity of venom composition, remain relatively understudied. Here, we present a reconstruction of mamba phylogeny, alongside genus-wide venom gland transcriptomic and high-resolution top-down venomic analyses. Whereas the green mambas, D. viridis, D. angusticeps, D. j. jamesoni and D. j. kaimosae, express 3FTx-predominant venoms, black mamba (D. polylepis) venom is dominated by dendrotoxins I and K. The divergent terrestrial ecology of D. polylepis compared to the arboreal niche occupied by all other mambas makes it plausible that this major difference in venom composition is due to dietary variation. The pattern of intrageneric venom variability across Dendroaspis represented a valuable opportunity to investigate, in a genus-wide context, the variant toxicity of the venom, and the degree of paraspecific cross-reactivity between antivenoms and mamba venoms. To this end, the immunological profiles of the five mamba venoms were assessed against a panel of commercial antivenoms generated for the sub-Saharan Africa market. This study provides a genus-wide overview of which available antivenoms may be more efficacious in neutralising human envenomings caused by mambas, irrespective of the species responsible. The information gathered in this study lays the foundations for rationalising the notably different potency and pharmacological profiles of Dendroaspis venoms at locus resolution. This understanding will allow selection and design of toxin immunogens with a view to generating a safer and more efficacious pan-specific antivenom against any mamba envenomation. BIOLOGICAL SIGNIFICANCE The mambas (genus Dendroaspis) comprise five especially notorious medically important venomous snakes endemic to sub-Saharan Africa. Their highly potent venoms comprise a high diversity of pharmacologically active peptides, including extremely rapid-acting neurotoxins. Previous studies on mamba venoms have focused on the biochemical and pharmacological characterisation of their most relevant toxins to rationalize the common neurological and neuromuscular symptoms of envenomings caused by these species, but there has been little work on overall venom composition or comparisons between them. Only very recently an overview of the composition of the venom of two Dendroaspis species, D. angusticeps and D. polylepis, has been unveiled through venomics approaches. Here we present the first genus-wide transcriptomic-proteomic analysis of mamba venom composition. The transcriptomic analyses described in this paper have contributed 29 (D. polylepis), 23 (D. angusticeps), 40 (D. viridis), 25 (D. j. jamesoni) and 21 (D. j. kaimosae), novel full-length toxin sequences to the non-redundant Dendroaspis sequence database. The mamba genus-wide venomic analysis demonstrated that major D. polylepis venom components are Kunitz-fold family toxins. This feature is unique in relation to the relatively conserved three-finger toxin (3FTx)-dominated venom compositions of the green mambas. Venom variation was interpreted in the context of dietary variation due to the divergent terrestrial ecology of D. polylepis compared to the arboreal niche occupied by all other mambas. Additionally, the degree of cross-reactivity conservation of mamba venoms was assessed by antivenomics against a panel of commercial antivenoms generated for the sub-Saharan Africa market. This study provides a genus-wide overview to infer which available antivenoms may be capable of neutralising human envenomings caused by mambas, irrespective of the species responsible. The information gathered in this study lays the foundations for rationalising the pharmacological profiles of mamba venoms at locus resolution. This understanding will contribute to the generation of a safer and more efficacious pan-Dendroaspis therapeutic antivenom against any mamba envenomation.
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Affiliation(s)
- Stuart Ainsworth
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Daniel Petras
- University of California San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Dr, La Jolla, CA 92093, USA; Technische Universität Berlin, Institut für Chemie, Straße des 17.Juni 124, 10623 Berlin, Germany
| | - Mikael Engmark
- Technical University of Denmark, Department of Bio and Health Informatics, 2800 Kgs. Lyngby, Denmark
| | - Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Straße des 17.Juni 124, 10623 Berlin, Germany
| | - Gareth Whiteley
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Laura-Oana Albulescu
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Taline D Kazandjian
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Simon C Wagstaff
- Bioinformatics Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Paul Rowley
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Wolfgang Wüster
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor LL57 2UW, United Kingdom
| | - Pieter C Dorrestein
- University of California San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Ana Silvia Arias
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - José M Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Robert A Harrison
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Nicholas R Casewell
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, United Kingdom.
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010, Valencia, Spain.
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Saltykova IV, Ogorodova LM, Ivanov VV, Bogdanov AO, Gereng EA, Perina EA, Brindley PJ, Sazonov AE. Carbonyl stress phenomena during chronic infection with Opisthorchis felineus. Parasitol Int 2017; 66:453-457. [PMID: 26773869 PMCID: PMC4938777 DOI: 10.1016/j.parint.2016.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/15/2015] [Accepted: 01/06/2016] [Indexed: 12/14/2022]
Abstract
Infection with the fish borne liver fluke Opisthorchis felineus is common in the Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Better understanding of the molecular pathogenesis of the biliary tract and liver during chronic opisthorchiasis can be expected to improve protection against and management of complications of this disease. We hypothesize that infection with O. felineus associates with formation of methylglyoxal and carbonyl stress in the liver and hence here we investigated the glyoxalase system and the receptor for advanced glycated end products (RAGE) in the liver of hamsters infected with this liver fluke. Expression of mRNA encoding glyoxalase 1 decreased at 8weeks of the infection and catalytic activity as well decreased at 8 and 12weeks after infection, and the expression of the glyoxalase 2 decreased until 36week post-infection, which associated with the decreasing activity of the enzyme at 8 and 12weeks post-infection. Glutathione levels in infected livers had decreased at week 8, whereas up-regulation of RAGE at mRNA levels was seen for the extended duration of the experimental infection of the hamsters. This outcome supported the notion of hepatic dicarbonyl stress during chronic opisthorchiasis. The inhibition of the glyoxalase system and accumulation of methylglyoxal at the early stages of the infection may underpin development of insulin resistance during opisthorchiasis.
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Affiliation(s)
- Irina V Saltykova
- Central Research Laboratory, Siberian State Medical University, 2 Moskovsky trakt, Tomsk 634050, Tomsk, Russian Federation; Laboratory of Catalytic Research, 49 Arkadiya Ivanova street, 634050 Tomsk, Tomsk State University, Russian Federation; Research Center for Neglected Diseases of Poverty, Department of Microbiology, Immunology and Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Ross Hall, 2300 I Street, NW, Washington, DC 20037, USA.
| | - Ludmilla M Ogorodova
- Central Research Laboratory, Siberian State Medical University, 2 Moskovsky trakt, Tomsk 634050, Tomsk, Russian Federation
| | - Vladimir V Ivanov
- Central Research Laboratory, Siberian State Medical University, 2 Moskovsky trakt, Tomsk 634050, Tomsk, Russian Federation
| | - Aleksandr O Bogdanov
- Central Research Laboratory, Siberian State Medical University, 2 Moskovsky trakt, Tomsk 634050, Tomsk, Russian Federation
| | - Elena A Gereng
- Central Research Laboratory, Siberian State Medical University, 2 Moskovsky trakt, Tomsk 634050, Tomsk, Russian Federation
| | - Ekaterina A Perina
- Central Research Laboratory, Siberian State Medical University, 2 Moskovsky trakt, Tomsk 634050, Tomsk, Russian Federation
| | - Paul J Brindley
- Research Center for Neglected Diseases of Poverty, Department of Microbiology, Immunology and Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Ross Hall, 2300 I Street, NW, Washington, DC 20037, USA
| | - Alexsey E Sazonov
- Central Research Laboratory, Siberian State Medical University, 2 Moskovsky trakt, Tomsk 634050, Tomsk, Russian Federation; Lomonosov Moscow State University, 1 Leninskie Gory, Moscow 119991, Russian Federation
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Smith JG, Gerszten RE. Emerging Affinity-Based Proteomic Technologies for Large-Scale Plasma Profiling in Cardiovascular Disease. Circulation 2017; 135:1651-1664. [PMID: 28438806 DOI: 10.1161/circulationaha.116.025446] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets. Obstacles for comprehensive proteomic profiling include the immense size and structural heterogeneity of the proteome, and the broad range of abundance levels, as well. Proteome-wide, untargeted profiling can be performed in tissues and cells with tandem mass spectrometry. However, applications to plasma are limited by the need for complex preanalytical sample preparation stages limiting sample throughput. Multiplexing of targeted methods based on capture and detection of specific proteins are therefore receiving increasing attention in plasma proteomics. Immunoaffinity assays are the workhorse for measuring individual proteins but have been limited for proteomic applications by long development times, cross-reactivity preventing multiplexing, specificity issues, and incomplete sensitivity to detect proteins in the lower range of the abundance spectrum (below picograms per milliliter). Emerging technologies to address these issues include nucleotide-labeled immunoassays and aptamer reagents that can be automated for efficient multiplexing of thousands of proteins at high sample throughput, coupling of affinity capture methods to mass spectrometry for improved specificity, and ultrasensitive detection systems to measure low-abundance proteins. In addition, proteomics can now be integrated with modern genomics tools to comprehensively relate proteomic profiles to genetic variants, which may both influence binding of affinity reagents and serve to validate the target specificity of affinity assays. The application of deep quantitative proteomic profiling to large cohorts has thus become increasingly feasible with emerging affinity methods. The aims of this article are to provide the broad readership of Circulation with a timely overview of emerging methods for affinity proteomics and recent progress in cardiovascular medicine based on such methods.
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Affiliation(s)
- J Gustav Smith
- From Molecular Epidemiology and Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skåne University Hospital, Lund, Sweden (J.G.S.); Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge (J.G.S., R.E.G.); and Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA (R.E.G.).
| | - Robert E Gerszten
- From Molecular Epidemiology and Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skåne University Hospital, Lund, Sweden (J.G.S.); Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge (J.G.S., R.E.G.); and Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA (R.E.G.).
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71
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Fortelny N, Overall CM, Pavlidis P, Freue GVC. Can we predict protein from mRNA levels? Nature 2017; 547:E19-E20. [PMID: 28748932 DOI: 10.1038/nature22293] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/01/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Nikolaus Fortelny
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabriela V Cohen Freue
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
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72
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Solute carriers affect Anopheles stephensi survival and Plasmodium berghei infection in the salivary glands. Sci Rep 2017; 7:6141. [PMID: 28733628 PMCID: PMC5522484 DOI: 10.1038/s41598-017-06317-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022] Open
Abstract
Malaria is caused by mosquito-borne Plasmodium spp. parasites that must infect and survive within mosquito salivary glands (SGs) prior to host transmission. Recent advances in transcriptomics and the complete genome sequencing of mosquito vectors have increased our knowledge of the SG genes and proteins involved in pathogen infection and transmission. Membrane solute carriers are key proteins involved in drug transport and are useful in the development of new interventions for transmission blocking. Herein, we applied transcriptomics analysis to compare SGs mRNA levels in Anopheles stephensi fed on non-infected and P. berghei-infected mice. The A. stephensi solute carriers prestinA and NDAE1 were up-regulated in response to infection. These molecules are predicted to interact with each other, and are reportedly involved in the maintenance of cell homeostasis. To further evaluate their functions in mosquito survival and parasite infection, these genes were knocked down by RNA interference. Knockdown of prestinA and NDAE1 resulted in reduction of the number of sporozoites in mosquito SGs. Moreover, NDAE1 knockdown strongly impacted mosquito survival, resulting in the death of half of the treated mosquitoes. Overall, our findings indicate the importance of prestinA and NDAE1 in interactions between mosquito SGs and Plasmodium, and suggest the need for further research.
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73
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Lopez CE, Sheehan HC, Vierra DA, Azzinaro PA, Meedel TH, Howlett NG, Irvine SQ. Proteomic responses to elevated ocean temperature in ovaries of the ascidian Ciona intestinalis. Biol Open 2017; 6:943-955. [PMID: 28500033 PMCID: PMC5550911 DOI: 10.1242/bio.024786] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 05/10/2017] [Indexed: 11/21/2022] Open
Abstract
Ciona intestinalis, a common sea squirt, exhibits lower reproductive success at the upper extreme of the water temperatures it experiences in coastal New England. In order to understand the changes in protein expression associated with elevated temperatures, and possible response to global temperature change, we reared C. intestinalis from embryos to adults at 18°C (a temperature at which they reproduce normally at our collection site in Rhode Island) and 22°C (the upper end of the local temperature range). We then dissected ovaries from animals at each temperature, extracted protein, and measured proteomic levels using shotgun mass spectrometry (LC-MS/MS). 1532 proteins were detected at a 1% false discovery rate present in both temperature groups by our LC-MS/MS method. 62 of those proteins are considered up- or down-regulated according to our statistical criteria. Principal component analysis shows a clear distinction in protein expression pattern between the control (18°C) group and high temperature (22°C) group. Similar to previous studies, cytoskeletal and chaperone proteins are upregulated in the high temperature group. Unexpectedly, we find evidence that proteolysis is downregulated at the higher temperature. We propose a working model for the high temperature response in C. intestinalis ovaries whereby increased temperature induces upregulation of signal transduction pathways involving PTPN11 and CrkL, and activating coordinated changes in the proteome especially in large lipid transport proteins, cellular stress responses, cytoskeleton, and downregulation of energy metabolism.
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Affiliation(s)
- Chelsea E Lopez
- Departments of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Hannah C Sheehan
- Departments of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - David A Vierra
- Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Paul A Azzinaro
- Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Thomas H Meedel
- Biology Department, Rhode Island College, Providence, RI 02908, USA
| | - Niall G Howlett
- Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Steven Q Irvine
- Departments of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
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74
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Jansen R, Hottenga JJ, Nivard MG, Abdellaoui A, Laport B, de Geus EJ, Wright FA, Penninx BWJH, Boomsma DI. Conditional eQTL analysis reveals allelic heterogeneity of gene expression. Hum Mol Genet 2017; 26:1444-1451. [PMID: 28165122 DOI: 10.1093/hmg/ddx043] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/27/2017] [Indexed: 11/14/2022] Open
Abstract
In recent years, multiple eQTL (expression quantitative trait loci) catalogs have become available that can help understand the functionality of complex trait-related single nucleotide polymorphisms (SNPs). In eQTL catalogs, gene expression is often strongly associated with multiple SNPs, which may reflect either one or multiple independent associations. Conditional eQTL analysis allows a distinction between dependent and independent eQTLs. We performed conditional eQTL analysis in 4,896 peripheral blood microarray gene expression samples. Our analysis showed that 35% of genes with a cis eQTL have at least two independent cis eQTLs; for several genes up to 13 independent cis eQTLs were identified. Also, 12% (671) of the independent cis eQTLs identified in conditional analyses were not significant in unconditional analyses. The number of GWAS catalog SNPs identified as eQTL in the conditional analyses increases with 24% as compared to unconditional analyses. We provide an online conditional cis eQTL mapping catalog for whole blood (https://eqtl.onderzoek.io/), which can be used to lookup eQTLs more accurately than in standard unconditional whole blood eQTL databases.
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Affiliation(s)
- Rick Jansen
- Department of Psychiatry, Vrije Universiteit Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Public Health, Amsterdam, The Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Public Health, Amsterdam, The Netherlands
| | - Abdel Abdellaoui
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Public Health, Amsterdam, The Netherlands
| | - Bram Laport
- Department of Psychiatry, Vrije Universiteit Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Eco J de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Public Health, Amsterdam, The Netherlands
| | - Fred A Wright
- Departments of Statistics and Biological Sciences, Bioinformatics Research Center, North Carolina State University, NC, USA
| | - Brenda W J H Penninx
- Department of Psychiatry, Vrije Universiteit Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Public Health, Amsterdam, The Netherlands
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75
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Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line. PLoS One 2017; 12:e0177336. [PMID: 28489927 PMCID: PMC5425217 DOI: 10.1371/journal.pone.0177336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/26/2017] [Indexed: 12/31/2022] Open
Abstract
We determine p53 protein abundances and cell to cell variation in two human cancer cell lines with single cell resolution, and show that the fractional width of the distributions is the same in both cases despite a large difference in average protein copy number. We developed a computational framework to identify dominant mechanisms controlling the variation of protein abundance in a simple model of gene expression from the summary statistics of single cell steady state protein expression distributions. Our results, based on single cell data analysed in a Bayesian framework, lends strong support to a model in which variation in the basal p53 protein abundance may be best explained by variations in the rate of p53 protein degradation. This is supported by measurements of the relative average levels of mRNA which are very similar despite large variation in the level of protein.
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76
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Ma J, Li X. High-throughput sequencing provides an insight into the hepatotoxicity mechanism of MC-LR in HepG2 cells. TOXIN REV 2017. [DOI: 10.1080/15569543.2017.1318403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Junguo Ma
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Xiaoyu Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
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77
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Modulation of Progesterone Receptor Isoform Expression in Pregnant Human Myometrium. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4589214. [PMID: 28540297 PMCID: PMC5433421 DOI: 10.1155/2017/4589214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/06/2017] [Indexed: 12/17/2022]
Abstract
Background. Regulation of myometrial progesterone receptor (PR) expression is an unresolved issue central to understanding the mechanism of functional progesterone withdrawal and initiation of labor in women. Objectives. To determine whether pregnant human myometrium undergoes culture-induced changes in PR isoform expression ex situ and, further, to determine if conditions approaching the in vivo environment stabilise PR isoform expression in culture. Methods. Term nonlaboring human myometrial tissues were cultured under specific conditions: serum supplementation, steroids, stretch, cAMP, PMA, PGF2α , NF-κB inhibitors, or TSA. Following 48 h culture, PR-T, PR-A, and PR-B mRNA levels were determined using qRT-PCR. PR-A/PR-B ratios were calculated. Results. PR-T and PR-A expression and the PR-A/PR-B ratio significantly increased in culture. Steroids prevented the culture-induced increase in PR-T and PR-A expression. Stretch blocked the effects of steroids on PR-T and PR-A expression. PMA further increased the PR-A/PR-B ratio, while TSA blocked culture-induced increases of PR-A expression and the PR-A/PR-B ratio. Conclusion. Human myometrial tissue in culture undergoes changes in PR gene expression consistent with transition toward a laboring phenotype. TSA maintained the nonlaboring PR isoform expression pattern. This suggests that preserving histone and/or nonhistone protein acetylation is critical for maintaining the progesterone dependent quiescent phenotype of human myometrium in culture.
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78
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Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics 2017; 16:959-981. [PMID: 28456751 DOI: 10.1074/mcp.mr117.000024] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 12/20/2022] Open
Abstract
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease. Many methods and tools have been developed or adapted to enable an array of integrative proteogenomic approaches and in this article, we systematically classify published methods and tools into four major categories, (1) Sequence-centric proteogenomics; (2) Analysis of proteogenomic relationships; (3) Integrative modeling of proteogenomic data; and (4) Data sharing and visualization. We provide a comprehensive review of methods and available tools in each category and highlight their typical applications.
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Affiliation(s)
- Kelly V Ruggles
- From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016
| | - Karsten Krug
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Xiaojing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Karl R Clauser
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Jing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Samuel H Payne
- **Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - David Fenyö
- ‡‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016; .,§§Institute for Systems Genetics, New York University School of Medicine, New York, New York 10016
| | - Bing Zhang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030; .,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - D R Mani
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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79
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Benet M, Miguel A, Carrasco F, Li T, Planells J, Alepuz P, Tordera V, Pérez-Ortín JE. Modulation of protein synthesis and degradation maintains proteostasis during yeast growth at different temperatures. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:794-802. [PMID: 28461260 DOI: 10.1016/j.bbagrm.2017.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 04/07/2017] [Accepted: 04/18/2017] [Indexed: 02/03/2023]
Abstract
To understand how cells regulate each step in the flow of gene expression is one of the most fundamental goals in molecular biology. In this work, we have investigated several protein turnover-related steps in the context of gene expression regulation in response to changes in external temperature in model yeast Saccharomyces cerevisiae. We have found that the regulation of protein homeostasis is stricter than mRNA homeostasis. Although global translation and protein degradation rates are found to increase with temperature, the increase of the catalytic activity of ribosomes is higher than the global translation rate suggesting that yeast cells adapt the amount of translational machinery to the constraints imposed by kinetics in order to minimize energy costs. Even though the transcriptional machinery is subjected to the same constraints, we observed interesting differences between transcription and translation, which may be related to the different energy costs of the two processes as well as the differential functions of mRNAs and proteins.
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Affiliation(s)
- Marta Benet
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Ana Miguel
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Fany Carrasco
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Tianlu Li
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Jordi Planells
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Paula Alepuz
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - Vicente Tordera
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain.
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80
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Ribosome profiling the cell cycle: lessons and challenges. Curr Genet 2017; 63:959-964. [PMID: 28451847 DOI: 10.1007/s00294-017-0698-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/31/2022]
Abstract
Understanding the causes and consequences of dynamic changes in the abundance and activity of cellular components during cell division is what most cell cycle studies are about. Here we focus on control of gene expression in the cell cycle at the level of translation. The advent of deep sequencing methodologies led to technologies that quantify the levels of all mRNAs that are bound by ribosomes and engaged in translation in the cell (Ingolia et al. Science 324:218-223, 2009). This approach has been applied recently to synchronous cell populations to find transcripts under translational control at different cell cycle phases (Blank et al. EMBO J 36:487-502, 2017; Stumpf et al. Mol Cell 52:574-582, 2013; Tanenbaum et al. Elife 4:e07957, 2015). These studies revealed new biology, but they also have limitations, pointing to challenges that need to be addressed in the future.
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81
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Arase M, Tamura Y, Kawasaki N, Isogaya K, Nakaki R, Mizutani A, Tsutsumi S, Aburatani H, Miyazono K, Koinuma D. Dynamics of chromatin accessibility during TGF-β-induced EMT of Ras-transformed mammary gland epithelial cells. Sci Rep 2017; 7:1166. [PMID: 28446749 PMCID: PMC5430828 DOI: 10.1038/s41598-017-00973-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/20/2017] [Indexed: 12/15/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is induced by transforming growth factor (TGF)-β and facilitates tumor progression. We here performed global mapping of accessible chromatin in the mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing. TGF-β and Ras altered chromatin accessibility either cooperatively or independently, and AP1, ETS, and RUNX binding motifs were enriched in the accessible chromatin regions of EpH4 and EpRas cells. Etv4, an ETS family oncogenic transcription factor, was strongly expressed and bound to more than one-third of the accessible chromatin regions in EpRas cells treated with TGF-β. While knockdown of Etv4 and another ETS family member Etv5 showed limited effects on the decrease in the E-cadherin abundance and stress fiber formation by TGF-β, gene ontology analysis showed that genes encoding extracellular proteins were most strongly down-regulated by Etv4 and Etv5 siRNAs. Accordingly, TGF-β-induced expression of Mmp13 and cell invasiveness were suppressed by Etv4 and Etv5 siRNAs, which were accompanied by the reduced chromatin accessibility at an enhancer region of Mmp13 gene. These findings suggest a mechanism of transcriptional regulation during Ras- and TGF-β-induced EMT that involves alterations of accessible chromatin, which are partly regulated by Etv4 and Etv5.
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Affiliation(s)
- Mayu Arase
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yusuke Tamura
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Natsumi Kawasaki
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kazunobu Isogaya
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ryo Nakaki
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Meguro-ku, Tokyo, 153-8904, Japan
| | - Anna Mizutani
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Meguro-ku, Tokyo, 153-8904, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Meguro-ku, Tokyo, 153-8904, Japan
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Daizo Koinuma
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
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82
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Becnel LB, Ochsner SA, Darlington YF, McOwiti A, Kankanamge WH, Dehart M, Naumov A, McKenna NJ. Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine. Sci Signal 2017; 10:10/476/eaah6275. [DOI: 10.1126/scisignal.aah6275] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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83
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Gonskikh Y, Polacek N. Alterations of the translation apparatus during aging and stress response. Mech Ageing Dev 2017; 168:30-36. [PMID: 28414025 DOI: 10.1016/j.mad.2017.04.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 01/03/2023]
Abstract
Aging is a biological process characterized by the irreversible and time-dependent deterioration of cell functions, tissues, and organs. Accumulating studies in a wide range of species from yeast to human revealed changes associated with the aging process to be conserved throughout evolution. The main characteristics of aging are (i) genomic instability, (ii) loss of telomere function, (iii) epigenetic changes,(iv) increased cellular senescence, (v) depletion of the stem cell pool, (vi) altered intercellular communication and (vii) loss of protein homeostasis. Among the multiple molecular mechanisms underlying aging, alterations of the translation machinery affecting the rate and selectivity of protein biosynthesis seem to play a central role. At the very heart of translation is the ribosome, a multifaceted and universally conserved RNA-protein particle responsible for accurate polypeptide synthesis and co-translational protein folding. Here we summarize and discuss recent developments on the contribution of altered translation and age-dependent modifications on the ribosome structure to aging and cellular senescence.
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Affiliation(s)
- Yulia Gonskikh
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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84
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Du Y, Deng W, Wang Z, Ning M, Zhang W, Zhou Y, Lo EH, Xing C. Differential subnetwork of chemokines/cytokines in human, mouse, and rat brain cells after oxygen-glucose deprivation. J Cereb Blood Flow Metab 2017; 37:1425-1434. [PMID: 27328691 PMCID: PMC5453462 DOI: 10.1177/0271678x16656199] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mice and rats are the most commonly used animals for preclinical stroke studies, but it is unclear whether targets and mechanisms are always the same across different species. Here, we mapped the baseline expression of a chemokine/cytokine subnetwork and compared responses after oxygen-glucose deprivation in primary neurons, astrocytes, and microglia from mouse, rat, and human. Baseline profiles of chemokines (CX3CL1, CXCL12, CCL2, CCL3, and CXCL10) and cytokines (IL-1α, IL-1β, IL-6, IL-10, and TNFα) showed significant differences between human and rodents. The response of chemokines/cytokines to oxygen-glucose deprivation was also significantly different between species. After 4 h oxygen-glucose deprivation and 4 h reoxygenation, human and rat neurons showed similar changes with a downregulation in many chemokines, whereas mouse neurons showed a mixed response with up- and down-regulated genes. For astrocytes, subnetwork response patterns were more similar in rats and mice compared to humans. For microglia, rat cells showed an upregulation in all chemokines/cytokines, mouse cells had many down-regulated genes, and human cells showed a mixed response with up- and down-regulated genes. This study provides proof-of-concept that species differences exist in chemokine/cytokine subnetworks in brain cells that may be relevant to stroke pathophysiology. Further investigation of differential gene pathways across species is warranted.
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Affiliation(s)
- Yang Du
- 1 Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.,3 Department of Geriatrics, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenjun Deng
- 4 Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zixing Wang
- 5 Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - MingMing Ning
- 4 Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Zhang
- 1 Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,3 Department of Geriatrics, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yiming Zhou
- 2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Eng H Lo
- 2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Changhong Xing
- 2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
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85
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Tan H, Yang K, Li Y, Shaw TI, Wang Y, Blanco DB, Wang X, Cho JH, Wang H, Rankin S, Guy C, Peng J, Chi H. Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation. Immunity 2017; 46:488-503. [PMID: 28285833 DOI: 10.1016/j.immuni.2017.02.010] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/09/2016] [Accepted: 01/10/2017] [Indexed: 01/08/2023]
Abstract
The molecular circuits by which antigens activate quiescent T cells remain poorly understood. We combined temporal profiling of the whole proteome and phosphoproteome via multiplexed isobaric labeling proteomics technology, computational pipelines for integrating multi-omics datasets, and functional perturbation to systemically reconstruct regulatory networks underlying T cell activation. T cell receptors activated the T cell proteome and phosphoproteome with discrete kinetics, marked by early dynamics of phosphorylation and delayed ribosome biogenesis and mitochondrial activation. Systems biology analyses identified multiple functional modules, active kinases, transcription factors and connectivity between them, and mitochondrial pathways including mitoribosomes and complex IV. Genetic perturbation revealed physiological roles for mitochondrial enzyme COX10-mediated oxidative phosphorylation in T cell quiescence exit. Our multi-layer proteomics profiling, integrative network analysis, and functional studies define landscapes of the T cell proteome and phosphoproteome and reveal signaling and bioenergetics pathways that mediate lymphocyte exit from quiescence.
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Affiliation(s)
- Haiyan Tan
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kai Yang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Timothy I Shaw
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yanyan Wang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Daniel Bastardo Blanco
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Xusheng Wang
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji-Hoon Cho
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hong Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sherri Rankin
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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86
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Engel T, Martinez-Villarreal J, Henke C, Jimenez-Mateos EM, Sanz-Rodriguez A, Alves M, Hernandez-Santana Y, Brennan GP, Kenny A, Campbell A, Lucas JJ, Henshall DC. Spatiotemporal progression of ubiquitin-proteasome system inhibition after status epilepticus suggests protective adaptation against hippocampal injury. Mol Neurodegener 2017; 12:21. [PMID: 28235423 PMCID: PMC5324261 DOI: 10.1186/s13024-017-0163-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 02/17/2017] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND The ubiquitin-proteasome-system (UPS) is the major intracellular pathway leading to the degradation of unwanted and/or misfolded soluble proteins. This includes proteins regulating cellular survival, synaptic plasticity and neurotransmitter signaling; processes controlling excitability thresholds that are altered by epileptogenic insults. Dysfunction of the UPS has been reported to occur in a brain region- and cell-specific manner and contribute to disease progression in acute and chronic brain diseases. Prolonged seizures, status epilepticus, may alter UPS function but there has been no systematic attempt to map when and where this occurs in vivo or to determine the consequences of proteasome inhibition on seizure-induced brain injury. METHOD To determine whether seizures lead to an impairment of the UPS, we used a mouse model of status epilepticus whereby seizures are triggered by an intra-amygdala injection of kainic acid. Status epilepticus in this model causes cell death in selected brain areas, in particular the ipsilateral CA3 subfield of the hippocampus, and the development of epilepsy after a short latent period. To monitor seizure-induced dysfunction of the UPS we used a UPS inhibition reporter mouse expressing the ubiquitin fusion degradation substrate ubiquitinG76V-green fluorescent protein. Treatment with the specific proteasome inhibitor epoxomicin was used to establish the impact of proteasome inhibition on seizure-induced pathology. RESULTS AND CONCLUSIONS Our studies show that status epilepticus induced by intra-amygdala kainic acid causes select spatio-temporal UPS inhibition which is most evident in damage-resistant regions of the hippocampus, including CA1 pyramidal and dentate granule neurons then appears later in astrocytes. In support of this exerting a beneficial effect, injection of mice with the proteasome inhibitor epoxomicin protected the normally vulnerable hippocampal CA3 subfield from seizure-induced neuronal death in the model. These studies reveal brain region- and cell-specific UPS impairment occurs after seizures and suggest UPS inhibition can protect against seizure-induced brain damage. Identifying networks or pathways regulated through the proteasome after seizures may yield novel target genes for the treatment of seizure-induced cell death and possibly epilepsy.
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Affiliation(s)
- Tobias Engel
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland.
| | - Jaime Martinez-Villarreal
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Christine Henke
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland.,Medical Clinic III, University Clinic Dresden, TU Dresden, Dresden, Germany
| | - Eva M Jimenez-Mateos
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Amaya Sanz-Rodriguez
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Mariana Alves
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Yasmina Hernandez-Santana
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Gary P Brennan
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Aidan Kenny
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Aoife Campbell
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
| | - Jose J Lucas
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - David C Henshall
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 111 St. Stephen's Green, Dublin, 02 YN77, Ireland
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87
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Masvidal L, Hulea L, Furic L, Topisirovic I, Larsson O. mTOR-sensitive translation: Cleared fog reveals more trees. RNA Biol 2017; 14:1299-1305. [PMID: 28277937 PMCID: PMC5711451 DOI: 10.1080/15476286.2017.1290041] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Translation is fundamental for many biologic processes as it enables cells to rapidly respond to stimuli without requiring de novo mRNA synthesis. The mammalian/mechanistic target of rapamycin (mTOR) is a key regulator of translation. Although mTOR affects global protein synthesis, translation of a subset of mRNAs appears to be exceptionally sensitive to changes in mTOR activity. Recent efforts to catalog these mTOR-sensitive mRNAs resulted in conflicting results. Whereas ribosome-profiling almost exclusively identified 5'-terminal oligopyrimidine (TOP) mRNAs as mTOR-sensitive, polysome-profiling suggested that mTOR also regulates translation of non-TOP mRNAs. This inconsistency was explained by analytical and technical biases limiting the efficiency of ribosome-profiling in detecting mRNAs showing differential translation. Moreover, genome-wide characterization of 5'UTRs of non-TOP mTOR-sensitive mRNAs revealed 2 subsets of transcripts which differ in their requirement for translation initiation factors and biologic functions. We summarize these recent advances and their impact on the understanding of mTOR-sensitive translation.
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Affiliation(s)
- Laia Masvidal
- a Department of Oncology-Pathology , Science for Life Laboratory, Karolinska Institutet , Stockholm , Sweden
| | - Laura Hulea
- b Lady Davis Institute, SMBD Jewish General Hospital , Montreal , Canada.,c Gerald-Bronfman Department of Oncology, Departments of Experimental Medicine , and Biochemistry McGill University , Montreal , Canada
| | - Luc Furic
- d Cancer Program , Biomedicine Discovery Institute and Department of Anatomy & Developmental Biology, Monash University , Victoria , Australia.,e Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre , Melbourne , Victoria , Australia
| | - Ivan Topisirovic
- b Lady Davis Institute, SMBD Jewish General Hospital , Montreal , Canada.,c Gerald-Bronfman Department of Oncology, Departments of Experimental Medicine , and Biochemistry McGill University , Montreal , Canada
| | - Ola Larsson
- a Department of Oncology-Pathology , Science for Life Laboratory, Karolinska Institutet , Stockholm , Sweden
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88
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Riebeling C, Jungnickel H, Luch A, Haase A. Systems Biology to Support Nanomaterial Grouping. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 947:143-171. [PMID: 28168668 DOI: 10.1007/978-3-319-47754-1_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.
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Affiliation(s)
- Christian Riebeling
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Harald Jungnickel
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andreas Luch
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andrea Haase
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany.
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89
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Wang H, Lan P, Shen RF. Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs. Proteomics 2016; 16:877-93. [PMID: 26749523 DOI: 10.1002/pmic.201500265] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 12/28/2015] [Accepted: 01/05/2016] [Indexed: 11/11/2022]
Abstract
Plants and other multicellular organisms consist of many types of specialized cells. Systems-wide exploration of large-scale information from singe cell level is essential to understand how cell works. Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, in the interaction with microbe, and in plant anchorage, and represent an ideal model to study the biology of a single cell type. Single cell sampling combined with omics approaches has been applied to study plant root hairs. This review emphasizes the integration of omics approaches towards understanding the systems biology of root hairs, unraveling the common and plant species-specific properties of root hairs, as well as the concordance of protein and transcript abundance. Understanding plant root hair biology by mining the integrated omics data will provide a way to know how a single cell differentiates, elongates, and functions, which might help molecularly modify crops for developing sustainable agriculture practices.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
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90
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Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016; 165:535-50. [PMID: 27104977 DOI: 10.1016/j.cell.2016.03.014] [Citation(s) in RCA: 1847] [Impact Index Per Article: 230.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 12/30/2022]
Abstract
The question of how genomic information is expressed to determine phenotypes is of central importance for basic and translational life science research and has been studied by transcriptomic and proteomic profiling. Here, we review the relationship between protein and mRNA levels under various scenarios, such as steady state, long-term state changes, and short-term adaptation, demonstrating the complexity of gene expression regulation, especially during dynamic transitions. The spatial and temporal variations of mRNAs, as well as the local availability of resources for protein biosynthesis, strongly influence the relationship between protein levels and their coding transcripts. We further discuss the buffering of mRNA fluctuations at the level of protein concentrations. We conclude that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
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Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Beyer
- Cellular Networks and Systems Biology, University of Cologne, CECAD, Joseph-Stelzmann-Strasse 26, Cologne 50931, Germany.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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91
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Re A, Waldron L, Quattrone A. Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites. PLoS Comput Biol 2016; 12:e1005198. [PMID: 27923063 PMCID: PMC5140048 DOI: 10.1371/journal.pcbi.1005198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 10/13/2016] [Indexed: 11/18/2022] Open
Abstract
Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5’ untranslated regions was strongly associated with improvement in predictive accuracy. On the basis of these observations, we propose that the recently discovered widespread uTISs in the human genome can be a previously unappreciated substrate of translational control mediated by RBPs. Gene expression is a dynamic program by which the information stored in the genome is rendered functional by production and degradation of two types of macromolecules, RNAs and proteins. mRNAs are templates for proteins; therefore we expect correspondence between quantities of mRNAs and proteins. Genome-wide studies instead indicate a marked discrepancy between them, when considering their steady-state levels or their variations across different conditions. We employed linear regression approaches with paired mRNA/protein datasets in order to develop a model predicting the protein level of a gene from both the mRNA level and the protein levels of RBPs inferred to bind the mRNA untranslated regions. The results of our analyses restricted the utility of RBPs to improve accuracy of predicted protein abundance to a small fraction of the total modelled genes, and identified a novel association of the improvement induced by RBPs with the presence of upstream translation sites. This finding suggests a new avenue of experimental studies aimed at exploring the hypothesis that RBPs could influence protein abundance by changing the preference for certain translation initiation sites.
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Affiliation(s)
- Angela Re
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Trento, Italy
- * E-mail: (AR); (LW); (AQ)
| | - Levi Waldron
- City University of New York Graduate School of Public Health and Health Policy, New York, New York, United States of America
- * E-mail: (AR); (LW); (AQ)
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Trento, Italy
- * E-mail: (AR); (LW); (AQ)
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92
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Olvera-García G, Aguilar-García T, Gutiérrez-Jasso F, Imaz-Rosshandler I, Rangel-Escareño C, Orozco L, Aguilar-Delfín I, Vázquez-Pérez JA, Zúñiga J, Pérez-Patrigeon S, Espinosa E. A transcriptome-based model of central memory CD4 T cell death in HIV infection. BMC Genomics 2016; 17:956. [PMID: 27875993 PMCID: PMC5120471 DOI: 10.1186/s12864-016-3308-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/17/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Human central memory CD4 T cells are characterized by their capacity of proliferation and differentiation into effector memory CD4 T cells. Homeostasis of central memory CD4 T cells is considered a key factor sustaining the asymptomatic stage of Human Immunodeficiency Virus type 1 (HIV-1) infection, while progression to acquired immunodeficiency syndrome is imputed to central memory CD4 T cells homeostatic failure. We investigated if central memory CD4 T cells from patients with HIV-1 infection have a gene expression profile impeding proliferation and survival, despite their activated state. METHODS Using gene expression microarrays, we analyzed mRNA expression patterns in naive, central memory, and effector memory CD4 T cells from healthy controls, and naive and central memory CD4 T cells from patients with HIV-1 infection. Differentially expressed genes, defined by Log2 Fold Change (FC) ≥ |0.5| and Log (odds) > 0, were used in pathway enrichment analyses. RESULTS Central memory CD4 T cells from patients and controls showed comparable expression of differentiation-related genes, ruling out an effector-like differentiation of central memory CD4 T cells in HIV infection. However, 210 genes were differentially expressed in central memory CD4 T cells from patients compared with those from controls. Expression of 75 of these genes was validated by semi quantitative RT-PCR, and independently reproduced enrichment results from this gene expression signature. The results of functional enrichment analysis indicated movement to cell cycle phases G1 and S (increased CCNE1, MKI67, IL12RB2, ADAM9, decreased FGF9, etc.), but also arrest in G2/M (increased CHK1, RBBP8, KIF11, etc.). Unexpectedly, the results also suggested decreased apoptosis (increased CSTA, NFKBIA, decreased RNASEL, etc.). Results also suggested increased IL-1β, IFN-γ, TNF, and RANTES (CCR5) activity upstream of the central memory CD4 T cells signature, consistent with the demonstrated milieu in HIV infection. CONCLUSIONS Our findings support a model where progressive loss of central memory CD4 T cells in chronic HIV-1 infection is driven by increased cell cycle entry followed by mitotic arrest, leading to a non-apoptotic death pathway without actual proliferation, possibly contributing to increased turnover.
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Affiliation(s)
- Gustavo Olvera-García
- Department of Research in Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Tania Aguilar-García
- Department of Research in Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Fany Gutiérrez-Jasso
- Department of Research in Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Iván Imaz-Rosshandler
- Computational Genomics Department, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Mexico City, Mexico
| | - Claudia Rangel-Escareño
- Computational Genomics Department, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Mexico City, Mexico
| | - Lorena Orozco
- Laboratory of Immunogenomics and Metabolic Diseases, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Mexico City, Mexico
| | - Irma Aguilar-Delfín
- Laboratory of Immunogenomics and Metabolic Diseases, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Mexico City, Mexico
| | - Joel A Vázquez-Pérez
- Department of Virology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Joaquín Zúñiga
- Department of Research in Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Santiago Pérez-Patrigeon
- Infectious Immunopathogenesis Laboratory, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga 15, Mexico City, Mexico
| | - Enrique Espinosa
- Department of Research in Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Mexico City, Mexico.
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93
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McGinley C, Bishop DJ. Distinct protein and mRNA kinetics of skeletal muscle proton transporters following exercise can influence interpretation of adaptations to training. Exp Physiol 2016; 101:1565-1580. [DOI: 10.1113/ep085921] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/27/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Cian McGinley
- College of Sport and Exercise Science; Victoria University; Melbourne Victoria Australia
| | - David J. Bishop
- College of Sport and Exercise Science; Victoria University; Melbourne Victoria Australia
- Institute of Sport; Exercise and Active Living (ISEAL); Victoria University; Melbourne Victoria Australia
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94
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Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJC, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction. Mol Cell Proteomics 2016; 16:121-134. [PMID: 27836980 PMCID: PMC5217778 DOI: 10.1074/mcp.m116.060301] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 11/07/2016] [Indexed: 01/05/2023] Open
Abstract
Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies.
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Affiliation(s)
- Jing Wang
- From the ‡Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232.,§Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,¶Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Zihao Ma
- From the ‡Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Steven A Carr
- ‖Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Philipp Mertins
- ‖Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Hui Zhang
- **Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21205
| | - Zhen Zhang
- **Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21205
| | - Daniel W Chan
- **Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21205
| | - Matthew J C Ellis
- §Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‡‡Department of Medicine, Baylor College of Medicine, Houston, Texas 77030
| | - R Reid Townsend
- §§Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Richard D Smith
- ¶¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Jason E McDermott
- ¶¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Xian Chen
- ‖‖University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, North Carolina 27599
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Eastlake Avenue East, Seattle, Washington 98109
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Karin D Rodland
- ¶¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232.,Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Bing Zhang
- From the ‡Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232; .,§Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,¶Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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95
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Perner J, Provazník J, Schrenková J, Urbanová V, Ribeiro JMC, Kopáček P. RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks. Sci Rep 2016; 6:36695. [PMID: 27824139 PMCID: PMC5099782 DOI: 10.1038/srep36695] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/17/2016] [Indexed: 12/22/2022] Open
Abstract
Adult females of the genus Ixodes imbibe blood meals exceeding about 100 times their own weight within 7‒9 days. During this period, ticks internalise components of host blood by endocytic digest cells that line the tick midgut epithelium. Using RNA-seq, we aimed to characterise the midgut transcriptome composition in adult Ixodes ricinus females during early and late phase of engorgement. To address specific adaptations to the haemoglobin-rich diet, we compared the midgut transcriptomes of genetically homogenous female siblings fed either bovine blood or haemoglobin-depleted serum. We noted that tick gut transcriptomes are subject to substantial temporal-dependent expression changes between day 3 and day 8 of feeding. In contrast, the number of transcripts significantly affected by the presence or absence of host red blood cells was low. Transcripts relevant to the processes associated with blood-meal digestion were analysed and involvement of selected encoded proteins in the tick midgut physiology discussed. A total of 7215 novel sequences from I. ricinus were deposited in public databases as an additional outcome of this study. Our results broaden the current knowledge of tick digestive system and may lead to the discovery of potential molecular targets for efficient tick control.
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Affiliation(s)
- Jan Perner
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jan Provazník
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jana Schrenková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Veronika Urbanová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - José M. C. Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Petr Kopáček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
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96
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Almeida Silva LF, Engel T, Reschke CR, Conroy RM, Langa E, Henshall DC. Distinct behavioral and epileptic phenotype differences in 129/P mice compared to C57BL/6 mice subject to intraamygdala kainic acid-induced status epilepticus. Epilepsy Behav 2016; 64:186-194. [PMID: 27744244 DOI: 10.1016/j.yebeh.2016.09.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/12/2016] [Accepted: 09/16/2016] [Indexed: 12/31/2022]
Abstract
Animal models of status epilepticus are important tools to understand the pathogenesis of epileptic brain injury and evaluate potential seizure-suppressive, neuroprotective, and antiepileptogenic treatments. Focal elicitation of status epilepticus by intraamygdala kainic acid in mice produces unilateral hippocampal damage and the emergence of spontaneous recurrent seizures after a short latent period. The model has been characterized in C57BL/6, BALB/c, and SJL mice where strain-specific differences were found in the extent of hippocampal damage. 129/P mice are a common background strain for genetic models and may display unique characteristics in this model. We therefore compared responses to intraamygdala kainic acid between 129/P and C57BL/6 mice. Racine scale-scored convulsive behavior during status epilepticus was substantially lower in 129/P mice compared with that in C57BL/6 mice. Analysis of surface-recorded electroencephalogram (EEG) showed differences between strains in several frequency bands; EEG total power was greater during ictal episodes while duration of seizures was slightly shorter in 129/P mice. Histological analysis revealed similar hippocampal injury between strains, with neuronal death mainly confined to the ipsilateral CA3 subfield. Expression of genes associated with gliosis and neuroinflammatory responses was also similar between strains after seizures. Video-EEG telemetry recordings showed that 129/P mice first display spontaneous seizures within a few days of status epilepticus similar to C57BL/6 mice. However, high mortality in 129/P mice prevented a quantitative comparison of the epileptic seizure phenotypes between strains. This study defined behavioral, EEG, and histopathologic features of this mouse strain in a model increasingly useful for the study of the genetic contribution to acquired epilepsy. Intraamygdala kainic acid in 129/P mice could serve as a model of nonconvulsive status epilepticus, but long-term assessments will require model adjustment to mitigate the severity of the emergent epileptic phenotype.
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Affiliation(s)
- Luiz Fernando Almeida Silva
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, 2, Ireland
| | - Tobias Engel
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, 2, Ireland
| | - Cristina R Reschke
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, 2, Ireland
| | - Ronan M Conroy
- Division of Population Health Sciences, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, 2, Ireland
| | - Elena Langa
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, 2, Ireland
| | - David C Henshall
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, 2, Ireland.
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97
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Abstract
A recent study visualizes nascent RNAs in live Drosophila embryos to establish a connection between enhancer strength and the frequency of transcriptional bursts. Interestingly, one enhancer can simultaneously activate two core promoters, challenging models of enhancer-core-promoter communication via direct protein-protein contacts.
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Affiliation(s)
- Felix Muerdter
- Research Institute of Molecular Pathology, Vienna Biocenter, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology, Vienna Biocenter, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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98
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Bergamaschi G, Di Sabatino A, Pasini A, Ubezio C, Costanzo F, Grataroli D, Masotti M, Alvisi C, Corazza GR. Intestinal expression of genes implicated in iron absorption and their regulation by hepcidin. Clin Nutr 2016; 36:1427-1433. [PMID: 27729173 DOI: 10.1016/j.clnu.2016.09.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 06/16/2016] [Accepted: 09/23/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Through inhibition of iron absorption and iron mobilization from tissue stores, hepcidin exerts a negative control on iron homeostasis. Hepcidin, in fact, promotes the degradation of ferroportin (Fpn1), the iron exporter molecule expressed on the membrane of hepatocytes and macrophages, thus preventing iron release from cells to plasma. Hepcidin effects on enterocytes, however, are less clear. Aim of the present study was to further investigate the regulation of iron absorption by hepcidin. METHODS The transcriptional response of human duodenal mucosa to hepcidin was investigated using organ cultures of duodenal biopsies perendoscopically collected from healthy controls. Biopsies were cultured for 4 h with or without hepcidin-25 and were then assayed for the expression of iron-related genes. RESULTS In samples that had not been exposed to hepcidin, correlations were found between the expression of genes involved in iron absorption: DMT1, Fpn1, Dcytb and HCP1. In ex vivo experiments hepcidin down-regulated mRNA levels of the iron transporters Fpn1, and DMT1, of the ferric reductase Dcytb, of the ferroxidase hephaestin, and of the putative heme carrier protein HCP1. CONCLUSIONS Through the reported transcriptional changes hepcidin can modulate several steps of the iron absorption process, including the reduction of dietary iron by Dcytb, its uptake by enterocytes through DMT1, the mucosal uptake of heme iron by HCP1, and enterocyte iron release to plasma by Fpn1 in conjunction with hephaestin.
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Affiliation(s)
- Gaetano Bergamaschi
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Antonio Di Sabatino
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Alessandra Pasini
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Cristina Ubezio
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Filippo Costanzo
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Davide Grataroli
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Michela Masotti
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Costanza Alvisi
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Gino R Corazza
- Department of Internal Medicine, University of Pavia Medical School, and Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
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99
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Monte E, Rosa-Garrido M, Vondriska TM, Wang J. Undiscovered Physiology of Transcript and Protein Networks. Compr Physiol 2016; 6:1851-1872. [PMID: 27783861 PMCID: PMC10751805 DOI: 10.1002/cphy.c160003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The past two decades have witnessed a rapid evolution in our ability to measure RNA and protein from biological systems. As a result, new principles have arisen regarding how information is processed in cells, how decisions are made, and the role of networks in biology. This essay examines this technological evolution, reviewing (and critiquing) the conceptual framework that has emerged to explain how RNA and protein networks control cellular function. We identify how future investigations into transcriptomes, proteomes, and other cellular networks will enable development of more robust, quantitative models of cellular behavior whilst also providing new avenues to use knowledge of biological networks to improve human health. © 2016 American Physiological Society. Compr Physiol 6:1851-1872, 2016.
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Affiliation(s)
- Emma Monte
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Manuel Rosa-Garrido
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Thomas M. Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Jessica Wang
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
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100
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Wang X, Hou J, Quedenau C, Chen W. Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals. Mol Syst Biol 2016; 12:875. [PMID: 27430939 PMCID: PMC4965872 DOI: 10.15252/msb.20166941] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/02/2022] Open
Abstract
Transcription initiated at alternative sites can produce mRNA isoforms with different 5'UTRs, which are potentially subjected to differential translational regulation. However, the prevalence of such isoform-specific translational control across mammalian genomes is currently unknown. By combining polysome profiling with high-throughput mRNA 5' end sequencing, we directly measured the translational status of mRNA isoforms with distinct start sites. Among 9,951 genes expressed in mouse fibroblasts, we identified 4,153 showed significant initiation at multiple sites, of which 745 genes exhibited significant isoform-divergent translation. Systematic analyses of the isoform-specific translation revealed that isoforms with longer 5'UTRs tended to translate less efficiently. Further investigation of cis-elements within 5'UTRs not only provided novel insights into the regulation by known sequence features, but also led to the discovery of novel regulatory sequence motifs. Quantitative models integrating all these features explained over half of the variance in the observed isoform-divergent translation. Overall, our study demonstrated the extensive translational regulation by usage of alternative transcription start sites and offered comprehensive understanding of translational regulation by diverse sequence features embedded in 5'UTRs.
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Affiliation(s)
- Xi Wang
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Jingyi Hou
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Claudia Quedenau
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Wei Chen
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
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