Abstract PHB04: Predictive modeling, applied to genetically engineered mouse models of breast or lung cancer, provides insights into major oncogenic pathways

The H2020 project CanPathPro is building and validating a computational predictive modelling platform applied to cancer. To this end, we develop and refine bioinformatic and experimental tools, utilized in generation and evaluation of systems biology modeling predictions. The presented work employs the following technologies and methodologies: biologic systems representing 3 levels of biologic complexity (genetically engineered mouse models—GEMMs—of breast or lung cancer, organoids and cell lines derived thereof); next-generation sequencing and SWATH-based phospho/proteomics; and two large-scale computational mechanistic models. The highly defined biologic systems are used (i) to activate selected oncogenic stimuli that modulate pathway components in a systematic manner; (ii) to characterize the signaling changes occurring during cancer development—thus generating temporally resolved datasets for model training; and (iii) to validate, in vitro and in vivo, the modeling predictions. The mechanistic models, based on ordinary differential equations, enable prediction of phenotypes and drug response in mouse or human. Model parameters are defined using project-derived experimental data, either via parameter estimation strategies or via selection of parameter distributions by a Monte Carlo approach. For simulations, the models are initialized with transcriptome data, either from GEMM-derived cell lines grown under variable conditions or from GEMM-derived neoplastic and tumor tissue, representing lesion progression. The models also integrate the relevant mutations. Results, obtained by iterative rounds of in silico predictions and in vitro validation, include in silico identification (i) of the activation status of oncogenic pathways in GEMMs, organoids, and cell lines; (ii) of the signaling changes induced by the in vitro growth conditions (e.g., growth factor modulation, drug treatments) and by the mutational profile of cell lines/organoids, or by the mutational profile and lesion stage of each GEMM; and (iii) of the drug response of cell lines and GEMMs. In conclusion, this work encompasses a highly integrative systems biology approach generating and validating new hypotheses on cancer pathways signaling and crosstalk, identifying new signal flow, and suggests new ways to interfere with tumor growth.

This abstract is also being presented as Poster B49.

Citation Format: Julio Banga, Lucien Frappart, Jan Hasenauer, Yann Herault, Jos Jonkers, David Koubi, Bodo Lange, Glenn Terje Lines, Aspasia Plouidou, Oliver Rinner. Predictive modeling, applied to genetically engineered mouse models of breast or lung cancer, provides insights into major oncogenic pathways [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PHB04.

Blood CD9+ B cell, a biomarker of bronchiolitis obliterans syndrome after lung transplantation

Bronchiolitis obliterans syndrome is the main limitation for long-term survival after lung transplantation. Some specific B cell populations are associated with long-term graft acceptance. We aimed to monitor the B cell profile during early development of bronchiolitis obliterans syndrome after lung transplantation. The B cell longitudinal profile was analyzed in peripheral blood mononuclear cells from patients with bronchiolitis obliterans syndrome and patients who remained stable over 3 years of follow-up. CD24^hi CD38^hi transitional B cells were increased in stable patients only, and reached a peak 24 months after transplantation, whereas they remained unchanged in patients who developed a bronchiolitis obliterans syndrome. These CD24^hi CD38^hi transitional B cells specifically secrete IL-10 and express CD9. Thus, patients with a total CD9⁺ B cell frequency below 6.6% displayed significantly higher incidence of bronchiolitis obliterans syndrome (AUC = 0.836, PPV = 0.75, NPV = 1). These data are the first to associate IL-10-secreting CD24^hi CD38^hi transitional B cells expressing CD9 with better allograft outcome in lung transplant recipients. CD9-expressing B cells appear as a contributor to a favorable environment essential for the maintenance of long-term stable graft function and as a new predictive biomarker of bronchiolitis obliterans syndrome-free survival.

Abstract 1296: CanPathPro—development of a platform for predictive pathway modelling using genetically engineered mouse models

Omics technologies are generating complex molecular datasets that are exponentially increasing the cancer knowledge base and opening up new therapeutic possibilities. However, current approaches to analysing such data are often confined to statistical and pattern recognition techniques, or at best modelling of a single cellular signalling pathway, rather than the complex cross-talks of pathways that determine cancer onset and progression and response to therapy. New solutions to optimally exploit this wealth of data for basic research, better treatment and stratification of patients, as well as more efficient targeted drug development are required. CanPathPro (www.canpathpro.eu), an EU Horizon 2020 project, is addressing the challenge of predictive modelling of biological data by developing and refining bioinformatic and experimental tools for the evaluation and control of systems biology modelling predictions. Components comprise highly defined mouse and organotypic experimental systems, next-generation sequencing, SWATH-based proteomics and a systems biology computational model for data integration, visualisation and predictive modelling. Within CanPathPro, genetically engineered mouse models are used to follow the temporal changes occurring during cancer development, including the histology of the tumour, the genome and transcriptome using next-generation sequencing and the (phospho-)proteome using SWATH technology. The systems biology computational model is optimised in an iterative fashion through perturbation experiments of tumor-tissue-derived cell lines and organoids, permitting the validation of pathway and parameter information. In this way, CanPathPro takes a unique approach combining classic cancer research with omics data and systems biology tools, to develop and validate a new biotechnological application: a combined systems and experimental biology platform for generating and testing cancer signalling hypotheses in biomedical research. The CanPathPro-generated platform will enable in silico identification of cancer signalling networks critical for tumour development and will allow users to predict activation status of individual pathways, following integration of user (or public) data sets in the pathway models. The innovative approach taken by CanPathPro is set to have broad and significant impact on diverse areas, from cancer research and personalised medicine to drug discovery and development, and ultimately improving outcomes for cancer patients.

Citation Format: Christoph Wierling, Yann Herault, Jos Jonkers, Aspasia Ploubidou, Lucien Frappart, Jan Hasenauer, Julio Banga, Oliver Rinner, Valeriya Naumova, David Koubi, Bodo Lange. CanPathPro—development of a platform for predictive pathway modelling using genetically engineered mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1296.

Nerve Growth Factor Signaling from Membrane Microdomains to the Nucleus: Differential Regulation by Caveolins

Membrane microdomains or "lipid rafts" have emerged as essential functional modules of the cell, critical for the regulation of growth factor receptor-mediated responses. Herein we describe the dichotomy between caveolin-1 and caveolin-2, structural and regulatory components of microdomains, in modulating proliferation and differentiation. Caveolin-2 potentiates while caveolin-1 inhibits nerve growth factor (NGF) signaling and subsequent cell differentiation. Caveolin-2 does not appear to impair NGF receptor trafficking but elicits prolonged and stronger activation of MAPK (mitogen-activated protein kinase), Rsk2 (ribosomal protein S6 kinase 2), and CREB (cAMP response element binding protein). In contrast, caveolin-1 does not alter initiation of the NGF signaling pathway activation; rather, it acts, at least in part, by sequestering the cognate receptors, TrkA and p75NTR, at the plasma membrane, together with the phosphorylated form of the downstream effector Rsk2, which ultimately prevents CREB phosphorylation. The non-phosphorylatable caveolin-1 serine 80 mutant (S80V), no longer inhibits TrkA trafficking or subsequent CREB phosphorylation. MC192, a monoclonal antibody towards p75NTR that does not block NGF binding, prevents exit of both NGF receptors (TrkA and p75NTR) from lipid rafts. The results presented herein underline the role of caveolin and receptor signaling complex interplay in the context of neuronal development and tumorigenesis.

RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research

Research into rare diseases is typically fragmented by data type and disease. Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype, genomic data, biomaterial availability, and research/trial data sets. Such data must be linked at both an individual-patient and whole-cohort level to enable researchers to gain a complete view of their disease and patient population of interest. Data access and authorization procedures are required to allow researchers in multiple institutions to securely compare results and gain new insights. Funded by the European Union's Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseases.

Resveratrol-induced apoptotic death in human U251 glioma cells

Resveratrol (trans-3,4',5-trihydroxystilbene) is a naturally occurring polyphenolic compound highly enriched in grapes, peanuts, red wine, and a variety of food sources. Resveratrol has antiinflammatory and antioxidant properties, and also has potent anticancer properties. Human glioma U251 cells were used to understand the molecular mechanisms by which resveratrol acts as an anticancer agent, since glioma is a particularly difficult cancer to treat and eradicate. Our data show that resveratrol induces dose- and time-dependent death of U251 cells, as measured by lactate dehydrogenase release and internucleosomal DNA fragmentation assays. Resveratrol induces activation of caspase-3 and increases the cleavage of the downstream caspase substrate, poly(ADP-ribose) polymerase. Resveratrol-induced DNA fragmentation can be completely blocked by either a general caspase inhibitor (Z-VAD-FMK) or a selective caspase-3 inhibitor (Z-DEVD-FMK), but not by a selective caspase-1 inhibitor. Resveratrol induces cytochrome c release from mitochondria to the cytoplasm and activation of caspase-9. Resveratrol also increases expression of proapoptotic Bax and its translocation to the mitochondria. Resveratrol inhibits U251 proliferation, as measured by MTS assay [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt], and induces G0/G1 growth arrest, as determined by flow cytometry. The cyclin-dependent kinase inhibitor, olomoucine, prevents cell cycle progression and resveratrol-induced apoptosis. These results suggest that multiple signaling pathways may underlie the apoptotic death of U251 glioma induced by resveratrol, which warrants further exploration as an anticancer agent in human glioma.

Critical role for Kalirin in nerve growth factor signaling through TrkA

Kalirin is a multidomain guanine nucleotide exchange factor (GEF) that activates Rho proteins, inducing cytoskeletal rearrangement in neurons. Although much is known about the effects of Kalirin on Rho GTPases and neuronal morphology, little is known about the association of Kalirin with the receptor/signaling systems that affect neuronal morphology. Our experiments demonstrate that Kalirin binds to and colocalizes with the TrkA neurotrophin receptor in neurons. In PC12 cells, inhibition of Kalirin expression using antisense RNA decreased nerve growth factor (NGF)-induced TrkA autophosphorylation and process extension. Kalirin overexpression potentiated neurotrophin-stimulated TrkA autophosphorylation and neurite outgrowth in PC12 cells at a low concentration of NGF. Furthermore, elevated Kalirin expression resulted in catalytic activation of TrkA, as demonstrated by in vitro kinase assays and increased NGF-stimulated cellular activation of Rac, Mek, and CREB. Domain mapping demonstrated that the N-terminal Kalirin pleckstrin homology domain mediates the interaction with TrkA. The effects of Kalirin on TrkA provide a molecular basis for the requirement of Kalirin in process extension from PC12 cells and for previously observed effects on axonal extension and dendritic maintenance. The interaction of TrkA with the pleckstrin homology domain of Kalirin may be one example of a general mechanism whereby receptor/Rho GEF pairings play an important role in receptor tyrosine kinase activation and signal transduction.

Inhibitors of iNOS protects PC12 cells against the apoptosis induced by oxygen and glucose deprivation

It has been shown that deletion of the gene encoding the inducible form of nitric oxide synthase (iNOS) results in a reduction of ischemia-induced apoptotic cell death, suggesting the detrimental role of iNOS. The signaling pathways by which iNOS mediates apoptotic cell death under ischemic conditions remain unclear. Understanding the molecular mechanisms of iNOS-mediated apoptotic cell death in ischemia may offer opportunities for potential therapeutic intervention. In the current study, undifferentiated rat pheochromocytoma PC12 cells, exposed to oxygen and glucose deprivation (OGD) followed by reperfusion (adding back oxygen and glucose, OGD-R), were used as an in vitro model of ischemia. The iNOS expression and activity were increased during OGD-R. OGD-R-induced apoptosis was demonstrated by the increase of LDH release, cytosolic release of cytochrome C and caspase-3 activity. Inhibition of iNOS activity by selective iNOS inhibitors, aminoguanidine and 1400W, reduces OGD-R-induced apoptotic cell death, as demonstrated by the decrease of LDH release, cytochrome C release, and caspase-3 activity. These results suggest the critical role of iNOS in mediating apoptosis under ischemic conditions, likely through the induction of caspase-3 activity.

Roles of Ras-Erk in Apoptosis of PC12 Cells Induced by Trophic Factor Withdrawal or Oxidative Stress

To understand the role of Ras-MAPK (mitogen-activated protein kinase) in trophic factor withdrawal- and oxidative stress-induced apoptotic cell death processes, undifferentiated rat pheochromocytoma PC12 cells and a PC12 variant cell line stably expressing the Ras dominant-negative mutant (M-M17-26) were subjected to serum withdrawal in the absence or presence of H2O2 treatment. The extent of cell death was analyzed by lactate dehydrogenase release, internucleosomal DNA fragmentation, and caspase-3 assays. Both serum withdrawal and H2O2 treatment induced apoptotic cell death in PC12 cells, and the extent of cell death was greatly enhanced in M-M17-26 cells. DNA fragmentation induced by serum withdrawal or H2O2 treatment was blocked completely by a general caspase inhibitor, Z-VAD-FMK. A selective MAPK kinase inhibitor, U0126, blocked the H2O2-induced phosphorylation of Erk1/2 (extracellular signal-regulated kinase) in PC12 cells and increased the levels of active caspase-3 in M-M17-26 under serum withdrawal or H2O2 treatment. In addition, the short-term H2O2 treatment (5-30 min) was sufficient to cause DNA fragmentation in M-M17-26 cells even though H2O2 was removed and cells were incubated in regular growth medium with complete serum for 24 h. However, similar, short-term H2O2 treatment of PC12 cells did not induce DNA fragmentation 24 h later. These results suggest that the Ras-Erk pathway is critical in mediating protection against apoptotic cell death induced by either trophic factor withdrawal or increased oxidative stress.

Role of Bcl-2 family of proteins in mediating apoptotic death of PC12 cells exposed to oxygen and glucose deprivation

Apoptotic cell death has been observed in many in vivo and in vitro models of ischemia. However, the molecular pathways involved in ischemia-induced apoptosis remain unclear. We have examined the role of Bcl-2 family of proteins in mediating apoptosis of PC12 cells exposed to the conditions of oxygen and glucose deprivation (OGD) or OGD followed by restoration of oxygen and glucose (OGD-restoration, OGD-R). OGD decreased mitochondrial membrane potential and induced necrosis of PC12 cells, which were both prevented by the overexpression of Bcl-2 proteins. OGD-R caused apoptotic cell death, induced cytochrome C release from mitochondria and caspase-3 activation, decreased mitochondrial membrane potential, and increased levels of pro-apoptotic Bax translocated to the mitochondrial membrane, all of which were reversed by overexpression of Bcl-2. These results demonstrate that the cell death induced by OGD and OGD-R in PC12 cells is potentially mediated through the regulation of mitochondrial membrane potential by the Bcl-2 family of proteins. It also reveals the importance of developing therapeutic strategies for maintaining the mitochondrial membrane potential as a possible way of reducing necrotic and apoptotic cell death that occurs following an ischemic insult.

Nitric oxide synthase inhibition during development: effect on apoptotic death of dopamine neurons

Naturally occurring cell death via apoptosis occurs in the substantia nigra pars compacta (SNc) during rat development, culminating during the perinatal period. We previously showed that lipid peroxidation-mediated oxidative stress is not involved in this cell death process. Nitric oxide (NO) has been proposed to be critical for many developmental processes in brain and has been shown to mediate cell death in neurotoxin models of neurodegenerative disorders. Here, we reported that in vivo pre- and postnatal treatment with the non-specific NO synthase (NOS) inhibitor, L-NAME (60 mg/kg), or with the neuronal NOS inhibitor, 7-NI (30 mg/kg), dramatically decreased the NOS activity as well as the NADPH-diaphorase staining in brain. However, those treatments did not rescue dopamine neurons from developmental death, suggesting that NO is not involved in vivo in developmental death of these neurons or in the overall development of the SNc.

Regulation of expression and enzymatic activities of tyrosine and tryptophan hydroxylases in rat brain after acute electroconvulsive shock

Acute electroconvulsive shock (ECS) causes a significant increase of protein synthesis in depressive patients and such an increase raises the possibility that the regulation of specific proteins and enzymatic activities in the brain might be one of the mechanisms required for the induction of long-term adaptive neurochemical changes after electroconvulsive therapy. In current studies, we investigated and compared simultaneously the short- and long-term effects of an acute ECS on the expression and enzymatic activities of both tyrosine and tryptophan hydroxylases (TH and TpOH, respectively) in different rat brain areas. Our results demonstrated that an acute ECS produced: (1) a long-lasting decrease in TH and TpOH protein levels in locus ceruleus (LC), ventral tegmental area (VTA) and in TpOH protein level in the raphe centralis (RC), maximal at 72 h, with concomitant changes in mRNA levels and enzymatic activities in the LC only; (2) large increase of TpOH protein levels in the frontal cortex (Cxf) (+145%) and increase of TH protein levels in the hippocampus (Hip) (+207%), maximal at 72 h and 7 days which was not accompanied by corresponding increase of in vivo enzymatic activities. Furthermore, a second ECS increased in vivo TpOH activity in the Cxf (+19%) while decreasing K(m) value (-50%) for tetrahydrobiopterin cofactor. A stability of the observed findings on TpOH activity in the Cxf after repeated ECS might be one of the mechanisms for the antidepressant effects of electroconvulsive therapy.

Early and prolonged widespread increase in brain protein synthesis following a single electroconvulsive shock in free-moving rats

The autoradiographic method with l-[35S] methionine ([35S]Met) was used to determine the effect of a single electroconvulsive shock (ECS) on local rates of protein synthesis in the adult rat brain in free-moving conditions. We have estimated the relative contribution of methionine derived from protein breakdown to the intracellular precursor amino acid pool (tRNA pool) for protein synthesis. In steady-state conditions, we showed a large contribution (around 60%) of Met recycling into the precursor pool (lambda=0.37+/-0.11), after a single ECS. In all the 36 brain regions examined, apparent rates of protein synthesis were greatly increased (21-50%) 3 h after a single ECS indicating a generalized effect in rat brain. This ECS-induced activation of the overall rate of brain protein synthesis persisted for at least 24 h after cessation of ECS. This is consistent with the hypothesis that electroconvulsive therapy is associated with long-term molecular changes in neuronal activity.