Abstract B1-19: Computable cancer hallmarks - The construction of novel computable biological network models reflecting causal mechanisms of cancer hallmarks
Authors: Luettich Karsta , Talikka Marja , Iskandar Anita , Szostak Justyna , Kogel Ulrike , Schlage Walter , Xiang Yang , Ben-Yair Vered Katz , Rotkopf Shay , Fields Brett , Park Jennifer , Hoeng Julia , Peitsch Manuel 
Published: May 2016

Abstract
Over the past few years, we constructed a number of biological network models representing comprehensive connectivity maps of fundamental molecular mechanisms regulating cell proliferation, cellular stress, and cell fate in the healthy and inflamed lung and cardiovascular system [1, 2, 3, 4]. These network models are based on causal and correlative biological relationships expressed in Biological Expression Language (BEL). We further developed a method that quantifies network response as a whole in an interpretable manner by integrating these causal networks with systems biology data (e.g. transcriptomics) and could show that quantitative network perturbation was in agreement with experimental endpoint data for many of the mechanistic effects of interest [5].
Recently, we extended our efforts in an attempt to build a comprehensive set of computational models reflecting the biology of cancer hallmarks as described by Hanahan and Weinberg [6] with specific attention to mechanisms occurring in the early stages of non-small cell lung cancer (NSCLC) development and progression. Using a dual approach of curating relevant literature and supplementing this information with experimental data sets from a variety of NSCLC microarray studies, we thus far completed the construction of a “Sustaining Proliferative Signaling/Evading Growth Suppressors” hallmark model that describes multiple autocrine and paracrine signaling pathways responsible for driving continuous growth of tumor cells (e.g. growth factor/growth factor receptor, MAPK, JAK/STAT signaling etc.) and deregulating cell cycle check points, as well as a “Resisting Cell Death” hallmark model combining biological mechanisms indicative of intrinsic and extrinsic apoptosis pathways, necroptosis and autophagy that ensure (lung) tumor maintenance and survival. Processes related to VEGF- and other growth factor-driven angiogenesis, vascular sprouting and tubulogenesis, HIF1A signaling and endothelial cell activation were included in an “Inducing Angiogenesis” hallmark model. The latter is closely connected to the hallmark model “Activating Invasion and Metastasis” which also considers the mechanisms associated with the acquisition of invasive capabilities by e.g. epithelial-mesenchymal transition, the degradation of extracellular matrix, and epithelial and endothelial permeability permitting tumor cell dissemination. We further built a “Deregulating Cellular Energetics” hallmark model reflecting the metabolic switch in tumor cells to aerobic glycolysis including various aspects of hypoxia and autophagy.
Our focus at the current time is to address the features associated with tumor immune surveillance as exemplified by the complex interplay between tumor cells and tumor-infiltrating lymphocytes, macrophages, dendritic cells and natural killer cells which could be reflected in an “Avoiding Immune Destruction” hallmark model. As a next step we wish to integrate specific mechanisms that contribute to persistent pro-inflammatory signaling into a “Tumor-promoting Inflammation” hallmark network model. This will be followed by a comprehensive review of the newly constructed models and, if necessary, further augmentation by literature and validation with molecular data. Ultimately, we will employ our previously developed network quantification approach together with a number of publicly available lung cancer data sets to objectively evaluate the predictability of disease mechanisms in silico using transcriptomics data, and we hope that, if successful in this endeavor, various applications from drug development to environmental impact analysis could benefit from employing this portfolio of network models in unraveling disease-specific mechanisms and identifying new therapeutic targets.
[1] Westra JW, Schlage WK, Frushour BP et al. (2011). Construction of a computable cell proliferation network focused on non-diseased lung cells. BMC Syst Biol. 5, 105.
[2] Gebel S, Lichtner RB, Frushour B et al. (2013). Construction of a computable network model for DNA damage, autophagy, cell death, and senescence. Bioinform Biol Insights 7, 97-117.
[3] Westra JW, Schlage WK, Hengstermann A et al. (2013). A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue. Bioinform Biol Insights 7, 167-192.
[4] De León H, Boué S, Schlage WK et al. (2014). A vascular biology network model focused on inflammatory processes to investigate atherogenesis and plaque instability. J Transl Med. 12, 185.
[5] Thomson TM, Sewer A, Martin F et al. (2013). Quantitative assessment of biological impact using transcriptomic data and mechanistic network models. Toxicol Appl Pharmacol. 272(3), 863-878.
[6] Hanahan D & Weinberg RA (2011). Hallmarks of Cancer: The Next Generation. Cell 144(5), 646–674.
Citation Format: Karsta Luettich, Marja Talikka, Anita Iskandar, Justyna Szostak, Ulrike Kogel, Walter Schlage, Yang Xiang, Vered Katz Ben-Yair, Shay Rotkopf, Brett Fields, Jennifer Park, Julia Hoeng, Manuel Peitsch. Computable cancer hallmarks - The construction of novel computable biological network models reflecting causal mechanisms of cancer hallmarks. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-19.