Modeling of signaling pathways in chondrocytes based on phosphoproteomic and cytokine release data.
OBJECTIVE
Chondrocyte signaling is widely identified as a key component in cartilage homeostasis. Dysregulations of the signaling processes in chondrocytes often result in degenerative diseases of the tissue. Traditionally, the literature has focused on the study of major players in chondrocyte signaling, but without considering the cross-talks between them. In this paper, we systematically interrogate the signal transduction pathways in chondrocytes, on both the phosphoproteomic and cytokine release levels.


METHODS
The signaling pathways downstream 78 receptors of interest are interrogated. On the phosphoproteomic level, 17 key phosphoproteins are measured upon stimulation with single treatments of 78 ligands. On the cytokine release level, 55 cytokines are measured in the supernatant upon stimulation with the same treatments. Using an Integer Linear Programming (ILP) formulation, the proteomic data is combined with a priori knowledge of proteins' connectivity to construct a mechanistic model, predictive of signal transduction in chondrocytes.


RESULTS
We were able to validate previous findings regarding major players of cartilage homeostasis and inflammation (e.g., IL1B, TNF, EGF, TGFA, INS, IGF1 and IL6). Moreover, we studied pro-inflammatory mediators (IL1B and TNF) together with pro-growth signals for investigating their role in chondrocytes hypertrophy and highlighted the role of underreported players such as Inhibin beta A (INHBA), Defensin beta 1 (DEFB1), CXCL1 and Flagellin, and uncovered the way they cross-react in the phosphoproteomic level.


CONCLUSIONS
The analysis presented herein, leveraged high throughput proteomic data via an ILP formulation to gain new insight into chondrocytes signaling and the pathophysiology of degenerative diseases in articular cartilage.
Mechanical Engineering Department, National Technical University of Athens, Athens, Greece; Protatonce Ltd., Athens, Greece.
I N
IN
Melas
Mechanical Engineering Department, National Technical University of Athens, Athens, Greece.
A D
AD
Chairakaki
Mechanical Engineering Department, National Technical University of Athens, Athens, Greece.
E I
EI
Chatzopoulou
Mechanical Engineering Department, National Technical University of Athens, Athens, Greece; Protatonce Ltd., Athens, Greece.
D E
DE
Messinis
Mechanical Engineering Department, National Technical University of Athens, Athens, Greece.
T
T
Katopodi
Protatonce Ltd., Athens, Greece.
V
V
Pliaka
Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
S
S
Samara
AVT Process Systems Engineering (SVT), RWTH Aachen University, Aachen, Germany.
A
A
Mitsos
Department of Orthopaedic Surgery, University of Thessalia, Larissa, Greece.
Z
Z
Dailiana
Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
P
P
Kollia
Mechanical Engineering Department, National Technical University of Athens, Athens, Greece. Electronic address: leo@mail.ntua.gr.
L G
LG
Alexopoulos
D019902:Chondrocytes / Q000737:chemistry*; D016207:Cytokines / Q000032:analysis*; D006801:Humans; D008024:Ligands; D008954:Models, Biological; D020543:Proteome / Q000032:analysis*; D015398:Signal Transduction
D016207:Cytokines; D008024:Ligands; D020543:Proteome
Modeling signaling pathways; Pathway optimization; Phosphoproteomic signaling; Signaling pathways in chondrocytes