Abstract 4566: Triplex DNA-binding proteins in resected normal and tumor tissues from colorectal cancer patients: Biological and clinical relevance

This study is to determine if triplex DNA-binding proteins in human cells play an important role in processes that lead to cancer such as genetic instability or growth deregulation. Cytoplasmic and nuclear extracts from 60 colorectal cancer patients’ tumor (T) and normal (N) tissues were isolated and examined by gel shifts (EMSA) for triplex DNA-binding proteins. Total tumor extracts showed significantly higher triplex DNA-binding activities of the major H3 complex than normal tissue extracts (Wilcoxon test). Neither T-staging nor M-staging at diagnosis was associated with any of the factors, but N-Stage was significantly associated with the ratio of tumor/normal (T/N) for the total of cytoplasmic and nuclear extracts. This means all patients without lymph node affectation had decreased binding ratios (T/N) in both cytoplasmic and nuclear extracts. Kaplan-Meier survival analysis using a cut-off of 1.5 (rounded-up median) for the nuclear binding activity ratio (T/N) showed significantly poorer survival for those patients whose nuclear binding was greater than 1.5. This suggests that although the major triplex DNA-binding protein is present in normal tissue extracts, it is more abundant in tumor extracts, and that a specific abundance of the major triplex-binding protein (H3) in the tumor nucleus is associated with poorer patient survival. Biotinylated triplex DNA-protein complexes were isolated from the RKO colorectal cancer cell line with streptavidin-agarose and analyzed by nano-HPLC ESI-MS-MS. We identified 100 and 60 kDa proteins from nuclear extracts as PSF (polypyrimidine tract binding-associated splicing factor) and p54nrb (NonO), known to function as RNA polymerase II-associated splicing factors, bind as heterodimers, and implicated in the regulation of expression of the myc family of oncoproteins and COX2. We also identified a 75 kDa protein from cytoplasmic extracts as U2AF65 (U2 small nuclear RNA auxiliary factor 2 isoform b), also a splicing factor that can directly interact with p54 nrb and shuttle continuously between the nucleus and cytoplasm. To examine differences between tumor and normal tissues in multiple signaling proteins and proteins known to be relevant in colorectal cancer, reverse phase protein array (RPPA), Pearson correlation and cluster analysis of tumor nuclear lysates ranked from lowest to highest H3 EMSA values shows a highly significant correlation between decreased β-catenin expression in tissues that have the lowest H3 EMSA values and increased β-catenin expression in tissues that have the highest H3 EMSA values. We found this pattern in all tissue lysate types: normal-cytoplasm, normal-nucleus, tumor-cytoplasm, and tumor-nucleus. We believe these splicing factors are overexpressed in tumor tissues and could cause deregulated growth of cells by influencing other proteins associated with tumorigenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4566.

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions

Background

Modern gene perturbation techniques, like RNA interference (RNAi), enable us to study effects of targeted interventions in cells efficiently. In combination with mRNA or protein expression data this allows to gain insights into the behavior of complex biological systems.

Results

In this paper, we propose Deterministic Effects Propagation Networks (DEPNs) as a special Bayesian Network approach to reverse engineer signaling networks from a combination of protein expression and perturbation data. DEPNs allow to reconstruct protein networks based on combinatorial intervention effects, which are monitored via changes of the protein expression or activation over one or a few time points. Our implementation of DEPNs allows for latent network nodes (i.e. proteins without measurements) and has a built in mechanism to impute missing data. The robustness of our approach was tested on simulated data. We applied DEPNs to reconstruct the ERBB signaling network in de novo trastuzumab resistant human breast cancer cells, where protein expression was monitored on Reverse Phase Protein Arrays (RPPAs) after knockdown of network proteins using RNAi.

Conclusion

DEPNs offer a robust, efficient and simple approach to infer protein signaling networks from multiple interventions. The method as well as the data have been made part of the latest version of the R package "nem" available as a supplement to this paper and via the Bioconductor repository.

Neurodegeneration and prolonged immediate early gene expression throughout cortical areas of the rat brain following acute administration of dizocilpine

N-methyl-d-aspartate receptor antagonist drugs (NMDA-A), such as dizocilpine (MK801), induce long-lasting behavioral disturbances reminiscent to psychotic disorders in humans. To identify cortical structures affected by NMDA-A, we used a single dose of MK801 (10 mg/kg) that caused low and high neurodegeneration in intact and orchiectomized male rats, respectively. Degenerating somas (neuronal death) and axonal/synaptic endings (terminal degeneration) were depicted by a silver technique, and functionally affected cortical neuronal subpopulations by Egr-1, c-Fos, and FosB/DeltaFosB-immunolabeling. In intact males, MK801 triggered a c-Fos induction that remained high for more than 24 h in selected layers of the retrosplenial, somatosensory and entorhinal cortices. MK801-induced neurodegeneration reached its peak at 72 h. Degenerating somas were restricted to layer IV of the granular subdivision of the retrosplenial cortex, and were accompanied by suppression of Egr-1 immunolabeling. Terminal degeneration extended to selected layers of the retrosplenial, somatosensory and parahippocampal cortices, which are target areas of retrosplenial cortex. Induction of FosB/DeltaFosB by MK801 also extended to the same cortical layers affected by terminal degeneration, likely reflecting the damage of synaptic connectivity. In orchiectomized males, the neurodegenerative and functional effects of MK801 were exacerbated. Degenerative somas in layer IV of the retrosplenial cortex significantly increased, with a parallel enhancement of terminal degeneration and FosB/DeltaFosB-expression in the mentioned cortical structures, but no additional areas were affected. These observations reveal that synaptic dysfunction/degeneration in the retrosplenial, somatosensory and parahippocampal cortices might underlie the long-lasting impairments induced by NMDA-A.

Construction of biosensor systems for determining the pathophysiological potential of carrageenan variants

In vitro systems for monitoring safety of nutritional additives are desirable for high-throughput screenings and as a substitute for animal models. Carrageenan (CGN) is a sulfated polysaccharide widely used as a thickener and texturizer in human nutrition and is intensely discussed regarding its pathophysiological potential. Low molecular weight (lm) variants of CGN are considered to exert more profound pathophysiological effects in vivo than high molecular weight (hm) variants. We used a systematic approach to construct reporter systems allowing distinction between CGN-variants with different pathophysiological potential. Reporter systems utilizing segments of the CGN-responsive DMBT1 promoter did not display substantial activity in SW620 cells of intestinal epithelial origin. Genome-wide profiling revealed stronger qualitative and quantitative changes in global gene activities for hm-CGN than for lm-CGN (824 versus 91 genes; -6.64 to 22.33-fold for hm-CGN versus the range of -2.65 to 2.96-fold for lm-CGN). Reporter systems with segments of the IL-8 promoter showed a specific activation in response to hm-sulfated polysaccharides with lower pathophysiological potential in vivo and provided a better classification of CGN-variants than cytotoxicity assays in vitro. IL-8 reporter systems can be used for discerning between the effects of sulfated polysaccharides in vivo. Our data further provide initial insights into the molecular mechanisms that may play a role in the different effects of CGN-variants.

Living with death: the evolution of the mitochondrial pathway of apoptosis in animals

The mitochondrial pathway of cell death, in which apoptosis proceeds following mitochondrial outer membrane permeabilization, release of cytochrome c, and APAF-1 apoptosome-mediated caspase activation, represents the major pathway of physiological apoptosis in vertebrates. However, the well-characterized apoptotic pathways of the invertebrates C. elegans and D. melanogaster indicate that this apoptotic pathway is not universally conserved among animals. This review will compare the role of the mitochondria in the apoptotic programs of mammals, nematodes, and flies, and will survey our knowledge of the apoptotic pathways of other, less familiar model organisms in an effort to explore the evolutionary origins of the mitochondrial pathway of apoptosis.

Plant pathogen forensics: capabilities, needs, and recommendations

A biological attack on U.S. crops, rangelands, or forests could reduce yield and quality, erode consumer confidence, affect economic health and the environment, and possibly impact human nutrition and international relations. Preparedness for a crop bioterror event requires a strong national security plan that includes steps for microbial forensics and criminal attribution. However, U.S. crop producers, consultants, and agricultural scientists have traditionally focused primarily on strategies for prevention and management of diseases introduced naturally or unintentionally rather than on responding appropriately to an intentional pathogen introduction. We assess currently available information, technologies, and resources that were developed originally to ensure plant health but also could be utilized for postintroduction plant pathogen forensics. Recommendations for prioritization of efforts and resource expenditures needed to enhance our plant pathogen forensics capabilities are presented.