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)
Introduction
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.
Publications
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.
Abstract
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.
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
Abstract
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
“