Mathematical modelling of stress signalling and cell fate during genotoxic stress

Apoptosis is an intracellular signalling pathway that initiates cell suicide upon diverse stress signals, such as genotoxic stress caused by DNA damaging agents. Its deregulation is often associated with carcinogenesis and failure of chemotherapy. In human cells, mitochondrial outer membrane permeabilisation (MOMP) is a key event in linking intrinsic stress signals to the induction of apoptosis, and hence a major decision point that determines the cell’s fate. MOMP is caused and regulated by pro- and anti-apoptotic proteins of the BCL-2 family. Besides their various compositions and concentrations among different tissues, these proteins exhibit a high diversity in their molecular interactions. This diversity and the different binding affinities between proteins of this group aggravate reliable predictions of cell fates or patient responses to chemotherapy, based solely on protein expression levels. In this thesis, we designed a computational model that includes the topology of interaction of key members of the pro- and anti-apoptotic BCL-2 family and considered the distinct binding affinities of these proteins. Using the model, we were able to support the hypothesis of mode I and mode II inhibition of MOMP whereby the anti-apoptotic BCL-2 proteins are more effective in inhibiting the pro-apoptotic proteins BAK and BAX than the pro-apoptotic BH3-only proteins. Based on quantification of the BCL-2 proteins, we studied the concept of direct and indirect activation and found that the direct activation model successfully described cancer cell responses to the DNA damaging agents 5-fluorouracil and oxaliplatin. Applied to colorectal cancer patients, the designed model predicted patients’ clinical outcome to adjuvant and neo-adjuvant therapy based on patient-specific protein profiles. We investigated the model’s ability to determine whether, and to which extent, cancer cells can be re-sensitised to novel therapeutic agents that inhibit anti-apoptotic BCL-2 proteins. In conclusion, we provided a predictive and prognostic tool that may help to optimise chemotherapeutic treatment of colorectal cancer patients

Systems analysis of cancer cell heterogeneity in caspase-dependent apoptosis subsequent to mitochondrial outer membrane permeabilization.

Deregulation of apoptosis is a hallmark of carcinogenesis. We here combine live cell imaging and systems modeling to investigate caspase-dependent apoptosis execution subsequent to mitochondrial outer membrane permeabilization (MOMP) in several cancer cell lines. We demonstrate that, although most cell lines that underwent MOMP also showed robust and fast activation of executioner caspases and apoptosis, the colorectal cancer cell lines LoVo and HCT-116 Smac(-/-), similar to X-linked inhibitor of apoptosis protein (XIAP)-overexpressing HeLa (HeLa XIAP(Adv)) cells, only showed delayed and often no caspase activation, suggesting apoptosis impairment subsequent to MOMP. Employing APOPTO-CELL, a recently established model of apoptosis subsequent to MOMP, this impairment could be understood by studying the systemic interaction of five proteins that are present in the apoptosis pathway subsequent to MOMP. Using APOPTO-CELL as a tool to study detailed molecular mechanisms during apoptosis execution in individual cell lines, we demonstrate that caspase-9 was the most important regulator in DLD-1, HCT-116, and HeLa cells and identified additional cell line-specific co-regulators. Developing and applying a computational workflow for parameter screening, systems modeling identified that apoptosis execution kinetics are more robust against changes in reaction kinetics in HCT-116 and HeLa than in DLD-1 cells. Our systems modeling study is the first to draw attention to the variability in cell specific protein levels and reaction rates and to the emergent effects of such variability on the efficiency of apoptosis execution and on apoptosis impairment subsequent to MOMP

Higher Dimensional Operators in Top Condensation from a Renormalization Group Point of View

The predictive power of top-condensation models strongly depends on the behaviour of higher dimensional operators. These are analyzed in this paper by an extension of the standard renormalization group (RG) arguments which turns out to be a surprisingly powerful tool. Top-condensation models intermediated by underlying scalar exchange can be shown to be mere reparametrizations of the standard model. Further on, RG-arguments show that dynamical vector states cannot be lowered in top-condensation models. Finally we give a general argument concerning the size of higher dimensional operators of heavy vector exchange.Comment: 21 pages, latex2e, axodraw.sty, epsfig.sty, 4 postscript figures. Some of the discussions extended and clarifie

Calnexin, an ER-induced protein, is a prognostic marker and potential therapeutic target in colorectal cancer.

BACKGROUND: Colorectal cancer (CRC) is a leading cause of cancer mortality in the Western world and commonly treated with genotoxic chemotherapy. Stress in the endoplasmic reticulum (ER) was implicated to contribute to chemotherapeutic resistance. Hence, ER stress related protein may be of prognostic or therapeutic significance. METHODS: The expression levels of ER stress proteins calnexin, calreticulin, GRP78 and GRP94 were determined in n = 23 Stage II and III colon cancer fresh frozen tumour and matched normal tissue samples. Data were validated in a cohort of n = 11 rectal cancer patients treated with radiochemotherapy in the neoadjuvant setting. The calnexin gene was silenced using siRNA in HCT116 cells. RESULTS: There were no increased levels of ER stress proteins in tumour compared to matched normal tissue samples in Stage II or III CRC. However, increased calnexin protein levels were predictive of poor clinical outcome in the patient cohort. Data were validated in the rectal cancer cohort treated in the neoadjuvant setting. Calnexin gene-silencing significantly reduced cell survival and increased cancer cell susceptibility to 5FU chemotherapy. CONCLUSION: Increased tumour protein levels of calnexin may be of prognostic significance in CRC, and calnexin may represent a potential target for future therapies

Assessment of synaptic loss in mouse models of β-amyloid and tau pathology using [18F]UCB-H PET imaging

Objective: In preclinical research, the use of [F-18]Fluorodesoxyglucose (FDG) as a biomarker for neuro-degeneration may induce bias due to enhanced glucose uptake by immune cells. In this study, we sought to investigate synaptic vesicle glycoprotein 2A (SV2A) PET with [F-18]UCB-H as an alternative preclinical biomarker for neurodegenerative processes in two mouse models representing the pathological hallmarks of Alzheimer's disease (AD). Methods: A total of 29 PS2APP, 20 P301S and 12 wild-type mice aged 4.4 to 19.8 months received a dynamic [F-18]UCB-H SV2A-PET scan (14.7 +/- 1.5 MBq) 0-60 min post injection. Quantification of tracer uptake in cortical, cerebellar and brainstem target regions was implemented by calculating relative volumes of distribution (V-T) from an image-derived-input-function (IDIF). [F-18]UCB-H binding was compared across all target regions between transgenic and wild-type mice. Additional static scans were performed in a subset of mice to compare [F-18]FDG and [F-18]GE180 (18 kDa translocator protein tracer as a surrogate for microglial activation) standardized uptake values (SUV) with [F-18]UCB-H binding at different ages. Following the final scan, a subset of mouse brains was immunohistochemically stained with synaptic markers for gold standard validation of the PET results. Results: [F-18]UCB-H binding in all target regions was significantly reduced in 8-months old P301S transgenic mice when compared to wild-type controls (temporal lobe: p = 0.014;cerebellum: p = 0.0018;brainstem: p = 0.0014). Significantly lower SV2A tracer uptake was also observed in 13-months (temporal lobe: p = 0.0080;cerebellum: p = 0.006) and 19-months old (temporal lobe: p = 0.0042;cerebellum: p = 0.011) PS2APP transgenic versus wild-type mice, whereas the brainstem revealed no significantly altered [F-18]UCB-H binding. Immunohistochemical analyses of post-mortem mouse brain tissue confirmed the SV2A PET findings. Correlational analyses of [F-18]UCB-H and [F-18]FDG using Pearson's correlation coefficient revealed a significant negative association in the PS2APP mouse model (R = -0.26, p = 0.018). Exploratory analyses further stressed microglial activation as a potential reason for this inverse relationship, since [F-18]FDG and [F-18]GE180 quantification were positively correlated in this cohort (R = 0.36, p = 0.0076). Conclusion: [F-18]UCB-H reliably depicts progressive synaptic loss in PS2APP and P301S transgenic mice, potentially qualifying as a more reliable alternative to [F-18]FDG as a biomarker for assessment of neuro-degeneration in preclinical research

Erratum to: Calnexin, an ER stress-induced protein, is a prognostic marker and potential therapeutic target in colorectal cancer

Erratum to: Calnexin, an ER stress-induced protein, is a prognostic marker and potential therapeutic target in colorectal cancer

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.Peer reviewe

Long-term effects of medical management on growth and weight in individuals with urea cycle disorders

Low protein diet and sodium or glycerol phenylbutyrate, two pillars of recommended long-term therapy of individuals with urea cycle disorders (UCDs), involve the risk of iatrogenic growth failure. Limited evidence-based studies hamper our knowledge on the long-term effects of the proposed medical management in individuals with UCDs. We studied the impact of medical management on growth and weight development in 307 individuals longitudinally followed by the Urea Cycle Disorders Consortium (UCDC) and the European registry and network for Intoxication type Metabolic Diseases (E-IMD). Intrauterine growth of all investigated UCDs and postnatal linear growth of asymptomatic individuals remained unaffected. Symptomatic individuals were at risk of progressive growth retardation independent from the underlying disease and the degree of natural protein restriction. Growth impairment was determined by disease severity and associated with reduced or borderline plasma branched-chain amino acid (BCAA) concentrations. Liver transplantation appeared to have a beneficial effect on growth. Weight development remained unaffected both in asymptomatic and symptomatic individuals. Progressive growth impairment depends on disease severity and plasma BCAA concentrations, but cannot be predicted by the amount of natural protein intake alone. Future clinical trials are necessary to evaluate whether supplementation with BCAAs might improve growth in UCDs