TY - JOUR
T1 - Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model
AU - Zhang, Le
AU - Liu, Guangdi
AU - Kong, Meijing
AU - Li, Tingting
AU - Wu, Dan
AU - Zhou, Xiaobo
AU - Yang, Chuanwei
AU - Xia, Lei
AU - Yang, Zhenzhou
AU - Chen, Luonan
N1 - Publisher Copyright: © The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
PY - 2021/7/12
Y1 - 2021/7/12
N2 - MOTIVATION: The growth and survival of myeloma cells are greatly affected by their surrounding microenvironment. To understand the molecular mechanism and the impact of stiffness on the fate of myeloma-initiating cells (MICs), we develop a systems biological model to reveal the dynamic regulations by integrating reverse-phase protein array data and the stiffness-associated pathway. RESULTS: We not only develop a stiffness-associated signaling pathway to describe the dynamic regulations of the MICs, but also clearly identify three critical proteins governing the MIC proliferation and death, including FAK, mTORC1 and NFκB, which are validated to be related with multiple myeloma by our immunohistochemistry experiment, computation and manually reviewed evidences. Moreover, we demonstrate that the systematic model performs better than widely used parameter estimation algorithms for the complicated signaling pathway. AVAILABILITY AND IMPLEMENTATION: We can not only use the systems biological model to infer the stiffness-associated genetic signaling pathway and locate the critical proteins, but also investigate the important pathways, proteins or genes for other type of the cancer. Thus, it holds universal scientific significance. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
AB - MOTIVATION: The growth and survival of myeloma cells are greatly affected by their surrounding microenvironment. To understand the molecular mechanism and the impact of stiffness on the fate of myeloma-initiating cells (MICs), we develop a systems biological model to reveal the dynamic regulations by integrating reverse-phase protein array data and the stiffness-associated pathway. RESULTS: We not only develop a stiffness-associated signaling pathway to describe the dynamic regulations of the MICs, but also clearly identify three critical proteins governing the MIC proliferation and death, including FAK, mTORC1 and NFκB, which are validated to be related with multiple myeloma by our immunohistochemistry experiment, computation and manually reviewed evidences. Moreover, we demonstrate that the systematic model performs better than widely used parameter estimation algorithms for the complicated signaling pathway. AVAILABILITY AND IMPLEMENTATION: We can not only use the systems biological model to infer the stiffness-associated genetic signaling pathway and locate the critical proteins, but also investigate the important pathways, proteins or genes for other type of the cancer. Thus, it holds universal scientific significance. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UR - http://www.scopus.com/inward/record.url?scp=85112123922&partnerID=8YFLogxK
U2 - https://doi.org/10.1093/bioinformatics/btz542
DO - https://doi.org/10.1093/bioinformatics/btz542
M3 - Article
C2 - 31350562
SN - 1367-4803
VL - 37
SP - 1554
EP - 1561
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
IS - 11
ER -