1 / 28

WP6.2 Genomics and microbiology

WP6.2 Genomics and microbiology. Overall Objective: To demonstrate how the integration of pathway biology and host/ pathogen genomics and post-genomics can contribute to clinical diagnosis and treatment of infected patients. Gothenburg, 13 th – 14 th June, 2005.

orinda
Download Presentation

WP6.2 Genomics and microbiology

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. WP6.2 Genomics and microbiology Overall Objective: To demonstrate how the integration of pathway biology and host/ pathogen genomics and post-genomics can contribute to clinical diagnosis and treatment of infected patients Gothenburg, 13th – 14th June, 2005

  2. WP6.2 Genomics and microbiology Host pathway: Interferon Signalling > A family of related proteins > Bind to specific receptors Activation of Interferon signalling pathways results in a defined gene expression and: Increased antigen presentation Inhibition of cellular proliferation Development of an inflammatory response An anti-infective state Gothenburg, 13th – 14th June, 2005

  3. WP6.2 Genomics and microbiology Interferon is a key Inflammatory mediator with a number of notable therapeutic applications Gothenburg, 13th – 14th June, 2005

  4. WP6.2 Genomics and microbiology Medical Informatics Bioinformatics Viral Immuno- modulatory Interactions Clinical Host/ Viral Interactions Outcomes: Secretome 1. Further insight into the virus-host interaction 2. Identification of biomarkers for validation and potential therapeutic exploitation 3. Methods for storage, manipulationand exchange of phenotype data Protein Interaction Network microRNA Phenotype DB Microarray/ Proteomic Profiling Gothenburg, 13th – 14th June, 2005

  5. WP6.2 Genomics and microbiology Objective 1: Initiation of the Study Identification and distribution of a core set of interferon Gamma-related genes/ proteins around which initial studies of WP6.2 will focus Mar Alba Host/ Pathogen Mapping UEDIN/INFORMA Core Information Host 263 Interferon gamma response genes identified Storage, Integration & Dissemination Baldo Oliva Protein Interaction Prediction Literature Review Ingenuity Pathway Assist Validation & assessment of utility Biomarker Prediction Pathogen HCMV, MCMV,HIV Martin Reczko miRNA prediction and mapping Actual number of genes involved in interferon response likely to be >1000 UEDIN ‘novel’ genes (300 – 400) identified by microarray study Published ‘novel’ genes identified by microarray study Gothenburg, 13th – 14th June, 2005

  6. WP6.2 Genomics and microbiology Objective 1: Initiation of the Study Identification and distribution of a core set of interferon Gamma-related genes/ proteins around which initial studies of WP6.2 will focus Mar Alba Host/ Pathogen Mapping UEDIN/INFORMA Core Information Host 263 Interferon gamma response genes identified Storage, Integration & Dissemination Baldo Oliva Protein Interaction Prediction Literature Review Ingenuity Pathway Assist Validation & assessment of utility Biomarker Prediction Pathogen HCMV, MCMV,HIV Martin Reczko miRNA prediction and mapping Actual number of genes involved in interferon response likely to be >1000 UEDIN ‘novel’ genes (300 – 400) identified by microarray study Published ‘novel’ genes identified by microarray study Gothenburg, 13th – 14th June, 2005

  7. WP6.2 Genomics and microbiology WP6.2 – Partner Activity Mar Alba Host/ Pathogen Mapping UEDIN/INFORMA Core Information Host 263 Interferon gamma response genes identified Storage, Integration & Dissemination Baldo Oliva Protein Interaction Prediction Literature Review Ingenuity Pathway Assist Validation & assessment of utility Biomarker Prediction Pathogen HCMV, MCMV,HIV Martin Reczko miRNA prediction and mapping Gothenburg, 13th – 14th June, 2005

  8. WP6.2 Genomics and microbiology Host/ Pathogen Mapping: Mar Alba Objective: To investigate and characterise Host and Virus protein homologies Outputs: Provides insight into methods pathogen uses to survive and modulate host responses Provides potential targets for clinical intervention Gothenburg, 13th – 14th June, 2005

  9. WP6.2 Genomics and microbiology Process: Output Input Human Protein sequences for core interferon genes (FASTA) HLA-A, HLA-B, HLA-C HHV5 UL18 Known interaction: UL18 is a natural killer cell decoy gene BLASTP sequence similarity comparison 980 HHV5 protein sequences obtained from VIDA database TNFRSF1 HHV5 UL144 Known interaction: Immune evasion viroceptor 1 Gothenburg, 13th – 14th June, 2005

  10. WP6.2 Genomics and microbiology Further steps: • Herpesviruses are a well studied group of pathogens > Sequence comparisons carried out previously: Immune related proteins popular targets for research. > Can we identify homologies in less well characterised gene products identifed by microarray. > What protein homologies are identified when all virus proteins are compared with all readily available protein sequences. • For HCMV/ MCMV • > Protein to Protein & miRNA screening may be more novel and revealing • Can approach be applied productively to HIV, GB virus C, Hepatitis C? Gothenburg, 13th – 14th June, 2005

  11. WP6.2 Genomics and microbiology WP6.2 – Partner Activity Mar Alba Host/ Pathogen Mapping UEDIN/INFORMA Core Information Host 263 Interferon gamma response genes identified Storage, Integration & Dissemination Baldo Oliva Protein Interaction Prediction Literature Review Ingenuity Pathway Assist Validation & assessment of utility Biomarker Prediction Pathogen HCMV, MCMV,HIV Martin Reczko miRNA prediction and mapping Gothenburg, 13th – 14th June, 2005

  12. WP6.2 Genomics and microbiology Viral Immunomodulatory Interactions (IMIM/ UEDIN) Objectives: To characterise protein-protein interactions: 1. Within host interferon signalling pathway 2. Between virus and host proteins Objective 1. Application of PIANA to identification of virus/ host protein interaction PIANA Yeast interactions experimentally defined by yeast 2 hybrid approach Gene COG code x 1 2 3 x y z x 7 predicted CMV-Human protein interactions e.g. KPNA4 x x 2. Interacting pairs in yeast defined which have at least 1 COG code in common with CMV proteins 1. COG codes assigned to Human CMV proteins 3. Orthologous human partner identified Gothenburg, 13th – 14th June, 2005

  13. WP6.2 Genomics and microbiology Viral Immunomodulatory Interactions (IMIM/ UEDIN) From Virus/ Host perspective (M. Alba, B. Oliva) HCMV protein Human Proteins Cyclin-dependent kinases regulatory subunit 1 (CKS-1) – Cell Cycle Cyclin-dependent kinases regulatory subunit 2 (CKS-2) – Cell Cycle Nucleoprotein interactor 1; NPI-1 [Homo sapiens] – Cell Cycle Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) (dUTP pyrophosphatase) Importin alpha-2 subunit (KPNA2) (SRP1-alpha) (RAG cohort protein 1) - Nuclear Localisation signal binding Importin alpha-4 subunit (KPNA4) (Qip1 protein) – As above Importin alpha-7 subunit (Karyopherin alpha-6) - As above Sperm associated antigen 6 (SPAG6) [Homo sapiens] – Flagellar movement Gothenburg, 13th – 14th June, 2005

  14. WP6.2 Genomics and microbiology Viral Immunomodulatory Interactions (IMIM/ UEDIN) CMV Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) > Early, nonstructural protein, hydrolyses dUTP to dUMP and pyrophosphate (PPi) > Maintains a low dUTP:dTTP ratio to minimize the misincorporation of uracil into DNA > Uracil misincorporation into DNA could influence DNA conformation and sequence-specific protein binding leading to and inability to replicate > Does not contain a nuclear localisation signal by ‘SignalP’* * Center for Biological Sequence Analysis – Technical University of Denmark - http://www.cbs.dtu.dk/index.shtml Gothenburg, 13th – 14th June, 2005

  15. WP6.2 Genomics and microbiology Viral Immunomodulatory Interactions (IMIM/ UEDIN) EBV dUTPase In vitro: Purified dUTPase - Inhibits replication of Human PBMC - Upregulates TNF-, IL-1, IL-6, IL-8 and IL-10 - Enhances NK cell lysis of targets - Inhibits synthesis of Interferon  - Primary cell type affected is macrophage In vivo: Mice injected with purified EBV dUTPase - Inhibits replication of mitogen-stimulated lymphocytes ex vivo. - Inhibits interferon-gamma after re-stimulation ex vivo. - Loss of body mass, elevated body temperature, displayed diminished locomotor activity. Gothenburg, 13th – 14th June, 2005

  16. WP6.2 Genomics and microbiology Viral Immunomodulatory Interactions (IMIM/ UEDIN) KPNA4 (importin alpha 3) Functions in import of IRF3 into nucleus from cytoplasm Kumar KP, McBride KM, Weaver BK, Dingwall C, Reich NC.Regulated nuclear-cytoplasmic localization of interferon regulatory factor 3, a subunit of double-stranded RNA-activated factor 1 Mol Cell Biol 2000 Jun 1;20(11):4159-68. Gothenburg, 13th – 14th June, 2005

  17. WP6.2 Genomics and microbiology Viral Immunomodulatory Interactions (IMIM/ UEDIN) Simplified scheme for nuclear import. • Upon synthesis of nuclear proteins in the cytoplasm, e.g. the family of importins or transportins bind to the NLS. • 2 importin/NLS-protein (or transportin/protein) complex is then actively transported into the nucleus through nuclear pores involving the Ran GTPase cycle. Gothenburg, 13th – 14th June, 2005

  18. WP6.2 Genomics and microbiology Sub-cellular Logic Interaction map of interferon signalling pathway submodule CMV dUTPase Gothenburg, 13th – 14th June, 2005

  19. WP6.2 Genomics and microbiology Objective 1: Initiation of the Study Identification and distribution of a core set of interferon Gamma-related genes/ proteins around which initial studies of WP6.2 will focus Mar Alba Host/ Pathogen Mapping UEDIN/INFORMA Core Information Host 263 Interferon gamma response genes identified Storage, Integration & Dissemination Baldo Oliva Protein Interaction Prediction Literature Review Ingenuity Pathway Assist Validation & assessment of utility Biomarker Prediction Pathogen HCMV, MCMV,HIV Martin Reczko miRNA prediction and mapping Actual number of genes involved in interferon response likely to be >1000 UEDIN ‘novel’ genes (300 – 400) identified by microarray study Published ‘novel’ genes identified by microarray study Gothenburg, 13th – 14th June, 2005

  20. WP6.2 Genomics and microbiology Objective 1: Initiation of the Study Identification and distribution of a core set of interferon Gamma-related genes/ proteins around which initial studies of WP6.2 will focus Mar Alba Host/ Pathogen Mapping UEDIN/INFORMA Core Information Host 263 Interferon gamma response genes identified Storage, Integration & Dissemination Baldo Oliva Protein Interaction Prediction Literature Review Ingenuity Pathway Assist Validation & assessment of utility Biomarker Prediction Pathogen HCMV, MCMV,HIV Martin Reczko miRNA prediction and mapping Actual number of genes involved in interferon response likely to be >1000 UEDIN ‘novel’ genes (300 – 400) identified by microarray study Published ‘novel’ genes identified by microarray study Gothenburg, 13th – 14th June, 2005

  21. WP6.2 Genomics and microbiology Storage, integration and dissemination of pathway/ biomarker information Gothenburg, 13th – 14th June, 2005

  22. WP6.2 Genomics and microbiology Storage, integration and dissemination of pathway/ biomarker information: Potential solution Stores information on proteins, genes, compounds, interactions Cognia Molecular www.cognia.com Web-based curation & query tools Public or Restricted Interface API available for development Integration purposes Visualisation Pathway Editor# Curation of 263 core pathway elements complete #http://mpe.empproject.com Gothenburg, 13th – 14th June, 2005

  23. WP6.2 Genomics and microbiology • Previous Year 1 aims for knowledgebase development: • 1) Web accessible repository of interferon signalling-related information • Further aims for knowledgebase environment • Curate current core information and then incorporate • further signalling pathway information (type 1 interferon, • TLR, TNF-alpha) selected via objective criteria. • 2) Curate data generated in course of Infobiomed project  Gothenburg, 13th – 14th June, 2005

  24. WP6.2 Genomics and microbiology Explore methods for development of an integrated ‘biomarker’ prediction tool Gothenburg, 13th – 14th June, 2005

  25. WP6.2 Genomics and microbiology ‘Biomarker’ prediction tool – Motivation > WP6-2 partners have/use a variety of valuable resources: currently being harnessed independently ARCA HIV genotype/ clinical HAART database BLASTP Protein sequence comparison GPX Microarray database IFN pathway DB Interferon knowledgebase miRNA prediction tool DNA sequence analysis and prediction PIANA Protein-Protein Interaction prediction VIDA Database of virus information Can we combine these genomic and post-genomic resources to provide the clinical or scientific researcher with a single intuitive method for identifying ‘biomarkers’? i.e. genes or gene products which play a key role in host-pathogen interaction and may be exploited scientifically and/ or clinically Gothenburg, 13th – 14th June, 2005

  26. WP6.2 Genomics and microbiology ‘Biomarker’ prediction tool – How might this be used? Example 1 : From a pathogen to Host Researcher Pathogen e.g. HCMV VIDA HCMV Protein Sequences HCMV DNA Sequence All or subset of human protein sequences Predicted P to P interactions Predicted miRNA precursors Predicted miRNA Binding sites ‘Biomarker’ Experimental Validation: Gene Expression analysis, siRNA Knowledgebase Annotation: System specific info, Literature Sequence Analysis e.g. NLS, Cellular Location Practical Applications Gothenburg, 13th – 14th June, 2005

  27. WP6.2 Genomics and microbiology ‘Biomarker’ prediction tool – How might this be used? Example 2 : From a Host to Pathogen Researcher Host System of interest e.g. Interferon related genes/ gene products Knowledgebase Annotational Information incl. Sequence, Clinical Readouts etc for host system Pathogen(s) selected (e.g. HIV, Hepatitis, GB virus ) Protein based prediction Sequence based prediction Host/ Pathogen Biomarkers Gothenburg, 13th – 14th June, 2005

  28. WP6.2 Genomics and microbiology Milestones and Objectives Year 2 Year 3 Year 1 Gothenburg Project definition (UEDIN, IMIM, LEIC, FORTH, INFORMA) Biomarker definition Data acquisition and curation Protein to protein interactions defined miRNA stem loop identification Novel genes experimentally identified Genotyping/ infection status Data Interpretation Pathway Biomarker Validation POC study on benefit from integrating clinical and bio- informatics WP6-2 Meeting Define realistic Specification Requirements capture for prediction tool Development Project Plan Prep Publications Gothenburg, 13th – 14th June, 2005

More Related