Reconstruction of Cellular Signaling Networks and Analysis of Their Properties

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Reconstruction of Cellular Signaling Networks and
Analysis of Their Properties
Jason A Papin, Tony Hunter, Bernhard O Palsson,
Shankar Subramaniam, Nature Reviews Molecular
Cell Biology, Volume 6 February 2005

• Zeynep Madak Erdogan
• Cell and Developmental Biology

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Signaling Network
Hannahan and Weinberg, Cell, 2000
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Can a biologist fix a radio?
Lazebnik Y, Cancer Cell September 2002 Vol 2
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Network Reconstruction

• Chemically accurate representation of all of the
  biochemical evens that are occurring within a
  defined signaling network, and incorporates the
  interconnectivity and functional relationships
  that are inferred from experimental data

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Orders of Magnitude

• A simple quantitative estimate of a parameter
• How many ligand molecules might a typical cell be
  exposed to at a given instant in time?
• What is the maximum number of receptors in a cell
  membrane?
• How many transcription factors are needed to
  control 25000 genes?

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Scale differencesOrders of Magnitude
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End point of signaling

• Quick responses
• Protein modificatins
• Changes in Ca2 concentration
• Slow responses
• Transcriptional regulation
• Cell migration
• Cell cycle control
• Cell proliferation
• Apoptosis

Maayan A et al, Annu Rev Biophys Biomol Struct
2005 34319-49
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What is known so far

• Large number of components
• Degree of interconnectivity
• Differences in spatio-temporal scales
• Complex control of signaling events

Weng G, et al, Science 1999 Vol 284
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In this review

• Estimates of order of magnitude in human cellular
  signaling networks
• Issues that are associated with reconstructing
  such networks
• Structural and dynamic analysis of signaling
  networks

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Order of magnitude

• Intracellular components
• Links and connectivity
• Signal reception
• Signal transmission

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Orders of Magnitude

• A simple quantitative estimate of a parameter
• How many ligand molecules might a typical cell be
  exposed to at a given instant in time?
• What is the maximum number of receptors in a cell
  membrane?
• How many transcription factors are needed to
  control 25000 genes?

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What is the maximum number of receptors in a cell
membrane?

• Assumptions
• Maximum of 25 of the cell surface area of the
  cells comprises receptor proteins
• Average cell radius is 10 um 1200um2 cell
  surface area
• Average protein receptor has radius of 5 nm 75
  nm2 for single average receptor
• Calculation
• Number of receptors300 um2/75 nm2 4X106

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Intracellular components
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Alternative Splicing

• 40-60 of genes
• Average of 8 exons/gene
• Eg TTID, IKB, CD44

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Hoffmann A et al, Science Vol 298 November 2002
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Intracellular components
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http//employees.csbsju.edu/hjakubowski/classes/ch
331/protstructure/olprotein-aminoacid.html
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Overall number estimates
Kinase
Phosphatase
Receptor
Transcription factor
518
150
1543
1850
Alternative Splicing
1295
375
3858
4625
Post-translational modifications
10360
3000
30864
37000
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Order of magnitude

• Intracellular components
• Links and connectivity
• Signal reception
• Signal transmission

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Orders of Magnitude

• A simple quantitative estimate of a parameter
• How many ligand molecules might a typical cell be
  exposed to at a given instant in time?
• What is the maximum number of receptors in a cell
  membrane?
• How many transcription factors are needed to
  control 25000 genes?

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Links and connectivity

• Combinatorics (synergetic or interfering)
• Homo/Heterodimerization of transcription factors
• For 224 transcription factors enough to control
  25000 gene expression
• x(x-1)(x-2)1
• Study by Lee et al
• Chip-on-chip/ 106 Yeast Trancription factors
• Observed 4000 interactions
• 0-181 Transcription factors bound to promoter
  with and average of 38
• Lee TI, et al, Science 2002, 298 799-804

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Links and connectivity

• GPCR unique expression profile for each tissue
• Lets assume that there are 15 receptors on a
  given cell and 2 states (bound and unbound) for
  each receptor 21532768 different ligand
  combinations
• In metabolic pathways add one reaction,
  increase in functional pathways several fold

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Order of magnitude

• Intracellular components
• Links and connectivity
• Signal reception
• Signal transmission

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Signal Reception

• 2 possibilities
• In highly differentiated cellsfew types of
  receptors(10-40) in high numbers (105/cell)
• Stem cells/undifferentiated cells high number of
  receptors(2000-30000) in low numbers (102/cell)
• Endosomal signaling

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Order of magnitude

• Intracellular components
• Links and connectivity
• Signal reception
• Signal transmission

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Signal transmission

• 2 constrains
• Maximum production and secretion of signaling
  protein
• Spatial constrain because of the extracellular
  matrix

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Reconstructing signaling networks

• Scope of reconstructing signaling networks-
  number of reactions and components to include
• Level of detail of in a construction
• Data collection for the network reconstruction
  process
• Integrative and iterative approaches

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Scope of constructed signaling network
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Regulatory modules/motifs

• Switching
• Information storage
• Amplification

Maayan A et al, Annu Rev Biophys Biomol Struct
2005 34319-49
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Modular descriptions of pathways

• Defined inputs and outputs
• Relative timescales should be comparable
• Spatial colocalization
• Contextual specificity is achieved

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Level of detail in a reconstruction
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Modeling gene networks at different
organizational levels - Part list
Schlitt T, Brazma A, FEBS Letters 2005 1859-1866
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Modeling gene networks at different
organizational levels Topology models
Schlitt T, Brazma A, FEBS Letters 2005 1859-1866
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Maayan A et al, Annu Rev Biophys Biomol Struct
2005 34319-49
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Modeling gene networks at different
organizational levels Control logic model
Schlitt T, Brazma A, FEBS Letters 2005 1859-1866
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Modeling gene networks at different
organizational levelsm-Dynamic Models
Schlitt T, Brazma A, FEBS Letters 2005 1859-1866
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Data collection for the network reconstruction
process

• Microarrays Gene expression
• CHIP-chip Global Transcription factor binding
  site analysis
• Yeast two-hybrid assay Protein-protein
  interaction
• Perturbation analysis - Gene expression
• RNA interferance Gene expression
• FRET Protein-protein interactions

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Yeast-Two-Hybrid Assay
Eric Phizicky, Philippe I. H. Bastiaens, Heng
Zhu, Michael Snyder and Stanley Fields Nature
422, 208-215 (13 March 2003)
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Mathematical analysis of network properties

• Structural network analysis
• Dynamic network analysis

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Structural network analysis
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Global level analysis

• 1,870 proteins as nodes
• Connected by 2,240 identified
• direct physical interactions

,
H. Jeong, S. P. Mason, A.-L. Barabási and Z. N.
OltvaiNature 411, 41-42 (3 May 2001)
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Modular Level-Clustering Analysis
Alexander W. Rives and Timothy Galitski PNAS
February 4, 2003 vol. 100 no. 3 1128-1133
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Individual protein function level-Spectral
Analysis
Nucleic Acids Research, 2003, Vol. 31, No. 9
2443-2450
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Dynamic network analysis
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Dynamic network analysis
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Conclusions

• Additional components in signaling pathways (e.g.
  microRNA)
• Integration of metabolic and signaling
  networkseventually whole cell signaling network
• Computational developments for network
  reconstruction and data mining
• Eventually bioengineering analysis of signaling
  networks

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Questions?
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