STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification

Extrinsic apoptosis is a programmed cell death triggered by external ligands, such as the TNF-related apoptosis inducing ligand (TRAIL). Depending on the cell line, the specific molecular mechanisms leading to cell death may significantly differ. Precise characterization of these differences is crucial for understanding and exploiting extrinsic apoptosis. Cells show distinct behaviors on several aspects of apoptosis, including (i) the relative order of caspases activation, (ii) the necessity of mitochondria outer membrane permeabilization (MOMP) for effector caspase activation, and (iii) the survival of cell lines overexpressing Bcl2. These differences are attributed to the activation of one of two pathways, leading to classification of cell lines into two groups: type I and type II. In this work we challenge this type I/type II cell line classification. We encode the three aforementioned distinguishing behaviors in a formal language, called signal temporal logic (STL), and use it to extensively test the validity of a previously-proposed model of TRAIL-induced apoptosis with respect to experimental observations made on different cell lines. After having solved a few inconsistencies using STL-guided parameter search, we show that these three criteria do not define consistent cell line classifications in type I or type II, and suggest mutants that are predicted to exhibit ambivalent behaviors. In particular, this finding sheds light on the role of a feedback loop between caspases, and reconciliates two apparently-conflicting views regarding the importance of either upstream or downstream processes for cell-type determination. More generally, our work suggests that these three distinguishing behaviors should be merely considered as type I/II features rather than cell-type defining criteria. On the methodological side, this work illustrates the biological relevance of STL-diagrams, STL population data, and STL-guided parameter search implemented in the tool Breach. Such tools are well-adapted to the ever-increasing availability of heterogeneous knowledge on complex signal transduction pathways.Author Summary: Apoptosis, a major form of programmed cell death, plays a crucial role in shaping organs during development and controls homeostasis and tissue integrity throughout life. Defective apoptosis is often involved in cancer development and progression. Current understanding of externally triggered apoptosis is that death results from the activation of one out of two parallel signal transduction pathways. This leads to a classification of cell lines in two main types: type I and II. In the context of chemotherapy, understanding the cell-line-specific molecular mechanisms of apoptosis is important since this could guide drug usage. Biologists investigate the details of signal transduction pathways often at the single cell level and construct models to assess their current understanding. However, no systematic approach is employed to check the consistency of model predictions and experimental observations on various cell lines. Here we propose to use a formal specification language to encode the observed properties and a systematic approach to test whether model predictions are consistent with expected properties. Such property-guided model development and model revision approaches should guarantee an optimal use of the often heterogeneous experimental data.