Achievements report for Graduate Student Researcher Development Grant by Taikichiro Mori Memorial Research Fund for the academic year 2008

Student name: Mohamed Helmy Mahmoud Attia Shehata

Student number: 80725860

Student grade: Masters, 2nd grade.

Affiliation: Gradute School for Media and Governance

Research project: Systems Biology (Proteomics)



Using the Graduate Student Researcher Development Grant by Taikichiro Mori Memorial Research Fund, I was able to improve my research environment and therefore, achieve significant results in my current research. This resulted in two publications, two international conferences contributions and starting a new research project. The details of the achievements are mentioned below. Basically, the research grant helped me to upgrade my workstation by adding recent hardware e.g. monitor and memory. Add new mobile workstation by purchasing new powerful laptop and some peripheral such as additional long time battery. Moreover, I used the grant to cover some of the traveling expenses while traveling for the conference. 




1 Signaling Flux Redistribution at Toll-like Recepter Pathway Junctions.

Selvarajoo, K., Takabe, Y., Gohda, J., Helmy, M., Akira, S., Tomita, M., Tsuchiya, M., Inoue, J. and Matsuo, K. Signaling Flux Redistribution at Toll-like Recepter Pathway Junctions. , PLoS ONE , 3(10) , e3430. 


Various receptors on cell surface recognize specific extracellular molecules and trigger signal transduction altering gene expression in the nucleus. Gain or loss-of-function mutations of one molecule have shown to affect alternative signaling pathways with a poorly understood mechanism. In Toll-like receptor (TLR) 4 signaling, which branches into MyD88- and TRAM-dependent pathways upon lipopolysaccharide (LPS) stimulation, we investigated the gain or loss-of-function mutations of MyD88. We predict, using a computational model built on the perturbation-response approach and the law of mass conservation, that removal and addition of MyD88 in TLR4 activation, enhances and impairs, respectively, the alternative TRAM-dependent pathway through signaling flux redistribution (SFR) at pathway branches. To verify SFR, we treated MyD88-deficient macrophages with LPS and observed enhancement of TRAM-dependent pathway based on increased IRF3 phosphorylation and induction ofCxcl10 and Ifit2. Furthermore, increasing the amount of MyD88 in cultured cells showed decreased TRAM binding to TLR4. Investigating another TLR4 pathway junction, from TRIF to TRAF6, RIP1 and TBK1, the removal of MyD88-dependent TRAF6 increased expression of TRAM-dependent Cxcl10 andIfit2. Thus, we demonstrate that SFR is a novel mechanism for enhanced activation of alternative pathways when molecules at pathway junctions are removed. Our data suggest that SFR may enlighten hitherto unexplainable intracellular signaling alterations in genetic diseases where gain or loss-of-function mutations are observed.

Online Link for PDF      

2 Predicting novel features of Toll-like Receptor 3 signaling in macrophages.

Helmy, M., Gohda, J., Inoue, J., Tomita, M., Tsuchiya, M. and Selvarajoo, K. Predicting novel features of Toll-like Receptor 3 signaling in macrophages, PLoS One, e4661


The Toll-like receptor (TLR) 3 plays a critical role in mammalian innate immune response against viral attacks by recognizing double-stranded RNA (dsRNA) or its synthetic analog polyinosinic-polycytidylic acid (poly (I:C)). This leads to the activation of MAP kinases and NF-{kappa}B which results in the induction of type I interferons and proinflammatory cytokines to combat the viral infection. To understand the complex interplay of the various intracellular signaling molecules in the regulation of NF-{kappa}B and MAP kinases, we developed a computational TLR3 model based upon perturbation-response approach. We curated literature and databases to determine the TLR3 signaling topology specifically for murine macrophages. For initial model creation, we used wildtype temporal activation profiles of MAP kinases and NF-{kappa}B and, for model testing, used TRAF6 KO and TRADD KO data. From dynamic simulations we predict i) the existence of missing intermediary steps between extracellular poly (I:C) stimulation and intracellular TLR3 binding, and ii) the presence of a novel pathway which is essential for JNK and p38, but not NF-{kappa}B, activation. Our work shows activation dynamics of signaling molecules can be used in conjunction with perturbation-response models to decipher novel signaling features of complicated immune pathways.

Online Link  Note: the link will be active starting from 2nd of March 2009        


Conferences Contributions

1- The 1st Egypt-Japan International Symposium on Science and Technology 2008 (EJISST2008)

Date and location: June 8th to 10th 2008, Waseda University, Tokyo.

Type of contribution: Oral Presentation. 

Title: Involvement of novel pathway in Toll-Like Receptor 3 signaling: an in silico prediction.

Presentation Abstract

Toll-Like Receptors (TLRs) are family of pattern recognition receptors, with 13 known members involved in the innate immunity. TLR3, an intracellular member of TLRs, invokes an innate immune response upon recognition of virus double-stranded RNA (dsRNA) or Poly I:C (dsRNA synthetic analog), and plays a crucial role in defending the body against viral infections. Stimulated TLR3 triggers a TRIF-dependant response leading to the activation of transcription factor (TF) NF-κB and MAP kinases through TRAF6 and RIP1 resulting in the induction of proinflammatory cytokines such as TNF-a and IL-6. Although there have been extensive studies on TLR3 pathways, the dynamic and mechanistic behavior of this signaling remains unclear. In this study, we adopted a systemic approach integrating computational simulation and time-course experimental data to study the dynamics of NF-κB and MAP kinases activation. We developed and used an in silico TLR3 model to simulate the time-course activation profiles of NF-κB and MAP kinases in wildtype (WT) and three genetic knock out (KO) conditions (TRAF6 KO, RIP1 KO and TAK1 KO). Comparison of model simulation with similar experimental results predicts the existence of a missing pathway from TRIF, activating MAP kinases in TLR3 signaling. Simulations of our model suggest this pathway is key for MAP kinases activation in TAK1 KO condition. Thus, our systemic approach may pave way for better understanding of complex signaling dynamics of innate immune system.



2- The 9th international conference on Systems Biology (ICSB2008).

Date and location: August 22nd to 28th 2008, Gothenburg, Sweden.

Type of contribution: Poster Presentation with 2 posters. 

Poster 1 Title: Dynamic simulation of Toll-like Receptor 3 signaling pathway PDF

Poster 2 Title: Systems biology approach reveals novel TNF-alpha signaling crosstalk PDF


New project

As I finished my project and end up with the publication mentioned above, I proceeded to a new project entitled Proteomics-based genome re-annotation for Oryza sativa. In this project I am trying to use Bioinformatics approach to analyze the proteome data of the rice plant and re-annotate the genome of the rice searching for new gene models. Details and results