Parascolymia (Scleractinia: Lobophylliidae) in the Central Paratethys Sea (Vienna Basin, Austria) and its possible biogeographic implications

Palaeobiogeographical and palaeodiversity patterns of scleractinian reef corals are generally biased due to uncertain taxonomy and a loss of taxonomic characters through dissolution and recrystallization of the skeletal aragonite in shallow marine limestones. Herein, we describe a fossil lobophylliid coral in mouldic preservation from the early middle Miocene Leitha Limestone of the Central Paratethys Sea (Vienna Basin, Austria). By using grey-scale image inversion and silicone rubber casts for the visualization of the original skeletal anatomy and the detection of distinct micromorphological characters (i.e. shape of septal teeth, granulation of septocostae) Parascolymia bracherti has been identified as a new species in spite of the dissolved skeleton. In the recent era, Parascolymia like all Lobophylliidae is restricted to the Indo-Pacific region, where it is represented by a single species. The new species proves the genus also in the Miocene Mediterranean reef coral province. A review of the spatio-temporal relationships of fossil corals related to Parascolymia indicates that the genus was probably rooted in the Eastern Atlantic‒Western Tethys region during the Paleocene to Eocene and reached the Indo-Pacific region not before the Oligocene. The revealed palaeobiogeographical pattern shows an obvious congruence with that of Acropora and tridacnine bivalves reflecting a gradual equatorwards retreat of the marine biodiversity center parallel to the Cenozoic climate deterioration.

Lung neuroendocrine tumors: correlation of ubiquitinylation and sumoylation with nucleo-cytosolic partitioning of PTEN

Background

The tumor suppressor phosphatase and tensin homolog (PTEN) is a pleiotropic enzyme, inhibiting phosphatidyl-inositol-3 kinase (PI3K) signaling in the cytosol and stabilizing the genome in the nucleus. Nucleo-cytosolic partitioning is dependent on the post-translational modifications ubiquitinylation and sumoylation. This cellular compartmentalization of PTEN was investigated in lung neuroendocrine tumors (lung NET).

Methods

Tumor tissues from 192 lung NET patients (surgical specimens = 183, autopsies = 9) were investigated on tissue microarrays. PTEN was H-scored by two investigators in nucleus and cytosol using the monoclonal antibody 6H2.1. Results were correlated with immunoreactivity for USP7 (herpes virus-associated ubiquitin-specific protease 7) and SUMO2/3 (small ubiquitin-related modifier protein 2/3) as well as PTEN and p53 FISH gene status. Clinico-pathologic data including overall survival, proliferation rate and diagnostic markers (synaptophysin, chromogranin A, Mib-1, TTF-1) were recorded.

Results

The multicentre cohort included 58 typical carcinoids (TC), 42 atypical carcinoids (AC), 32 large cell neuroendocrine carcinomas (LCNEC) and 60 small cell lung carcinomas (SCLC). Carcinoids were smaller in size and had higher synaptophysin and chromogranin A, but lower TTF-1 expressions. Patients with carcinoids were predominantly female and 10 years younger than patients with LCNEC/SCLC. In comparison to the carcinoids, LCNEC/SCLC tumors presented a stronger loss of nuclear and cytosolic PTEN associated with a loss of PTEN and p53. Concomitantly, a loss of nuclear USP7 but increase of nuclear and cytosolic SUMO2/3 was found. Loss of nuclear and cytosolic PTEN, loss of nuclear USP7 and increase of cytosolic SUMO2/3 thus correlated with poor survival. Among carcinoids, loss of cytosolic PTEN was predominantly found in TTF1-negative larger tumors of male patients. Among SCLC, loss of both cytosolic and nuclear PTEN but not proliferation rate or tumor size delineated a subgroup with poorer survival (all p-values <0.05).

Conclusions

Cellular ubiquitinylation and sumoylation likely influence the functional PTEN loss in high grade lung NET. Both nuclear and cytosolic PTEN immunoreactivity should be considered for correlation with clinico-pathologic parameters.

Abstract 4794: Kras mutation is associated with elevated myeloblastin activity in human lung adenocarcinoma

Background Lung cancer is the leading cause of all cancer deaths worldwide with suboptimal prognosis and treatment options. Therefore we aimed to identify molecular characteristics with a predictive clinical utility that at the same time might represent novel therapeutic targets for human lung adenocarcinoma. Within this study we investigated KRAS mutations, a gene frequently mutated in lung adenocarcinoma and their association with enzymatic activities of members of the serine hydrolase superfamily, a large class of enzymes that have previously been linked to cancer. Methods Participating individuals underwent surgery for lung adenocarcinoma at the University Hospital Zurich between 2003 and 2006. Formalin fixed, paraffin embedded as well as snap-frozen lung adenocarcinoma samples were histologically reviewed by a pathologist. Mutation detection was performed via a custom service by Sequenom. Cell extracts derived from human snap-frozen biopsies were processed prior to mass spectrometric analysis as previously described to analyze serine hydrolase activities. Results Mutation analysis of 40 human lung adenocarcinoma specimens identified 4 patients (10%) harbouring a cysteine for glycine substitution at position 12 (G12C) in the KRAS gene. By employing two-sided unpaired t-test we found a statistical significant (p = 0.01) activity difference of the enzyme myeloblastin between patients harbouring a G12C mutation in the KRAS gene and patients harbouring no KRAS mutation. Conclusions The results of this study revealed that the activity of myeloblastin is significantly altered in lung adenocarcinoma biopsies harboring a KRAS gene mutation. Based on the results of this study we conclude that the combination of activity-based proteomics with mutational analysis is a valid approach for the discovery of novel biomarkers for human lung adenocarcinoma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4794. doi:1538-7445.AM2012-4794

KRAS mutation is associated with elevated myeloblastin activity in human lung adenocarcinoma

Lung cancer is the leading cause of all cancer deaths worldwide with suboptimal prognosis and treatment options. Therefore this study aimed to identify molecular characteristics with a predictive clinical utility which at the same time might represent novel therapeutic targets for human lung adenocarcinoma. Within this study mutations of v-Ki-RAS2 Kirsten rat sarcoma viral oncogene homolog (KRAS), a gene frequently mutated in lung adenocarcinoma, and their association with enzymatic activities, as assessed by activity-based proteomics, of members of the serine hydrolase (SH) superfamily, a large class of enzymes that have previously been linked to cancer was investigated. The results revealed that the activity of myeloblastin was significantly altered in the lung adenocarcinoma biopsies harboring a KRAS gene mutation. In conclusion myeloblastin is a potential therapeutic target for human lung adenocarcinoma, indicating that the combination of activity-based proteomics with mutational analysis is a valid approach for the discovery of novel biomarkers.

Additive genetic variance of quantitative traits in natural and pond-bred populations of the Lake Tanganyika cichlid Tropheus moorii

Quantitative genetic studies in natural populations are of growing interest to speciation research since divergence is often believed to arise through micro-evolutionary change, caused by natural selection on functional morphological traits. The species flock of cichlid fishes in Africa's oldest lake, Lake Tanganyika, offers a rare opportunity to study this process. Using the cichlid species Tropheus moorii, we assessed the potential for microevolution in a set of morphological traits by estimating their quantitative genetic basis of variation. Two approaches were employed: (1) estimation of trait heritabilities (h²) in situ from a sample of wild caught fish, and (2) estimation of h² from first generation offspring produced in a semi-natural breeding experiment. In both cases, microsatellite data were used to infer pedigree structure among the sampled individuals and estimates of h² were made using an animal model approach. Although power was limited by the pedigree structures estimated (particularly in the wild caught sample), we nonetheless demonstrate the presence of significant additive genetic variance for aspects of morphology that, in the cichlid species Tropheus moorii, are expected to be functionally and ecologically important, and therefore likely targets of natural selection. We hypothesize that traits showing significant additive genetic variance, such as the mouth position have most likely played a key role in the adaptive evolution of the cichlid fish Tropheus moorii.

Abstract 5576: Activity based protein profiling of human lung adenocarcinoma biopsies

Rationale

Lung cancer is the leading cause of all cancer related deaths and treatment is still suboptimal. Novel biomarkers with a reliable predictive significance which may additionally represent therapeutic targets are therefore of utmost importance. In the post genomic era most biomarker studies aim to measure abundances instead of real enzymatic activities. Therefore crucial changes in enzymatic activities during tumor progression and treatment response might not be detected. In order to circumvent these limitations a new methodology termed Activity Based Protein Profiling (ABPP), developed by Professor B. Cravatt and colleagues, may be a promising option. The methodology employs so-called Activity Based Probes (ABPs) that selectively bind to active sites of members of distinct enzyme superfamilies, thereby making an activity read-out of any given proteome possible. Using ABPs targeting serine hydrolases, a large and diverse class of enzymes that have previously been linked to lung cancer development, we introduced ABPP as a screening platform in a clinical setting.

Methods

A directed mass spectrometric approach was used for qualitative and quantitative analysis of ABP labeled proteomes. Samples were analyzed on an FTICR mass spectrometer (LTQ-FTMS, Thermo Finnigan, Bremen, Germany). Mass spectrometric data were searched against a recently updated human database (UniProt) using the Mascot search engine (version 2.2). SuperHirn v0.3 was used for label-free quantitation. Inclusion/exclusion lists were generated based on data derived from discovery-driven experiments in data-dependent acquisition mode.

Results

Approximately 30 serine hydrolases - mostly esterases and proteases - were identified per investigated proteome of the human lung adenocarcinoma cell line CaLu-3. Certain enzymes like Fatty Acid Synthase (FASN) or Kallikrein-6 (KLK6) have previously been associated with lung cancer development or lung cancer diagnosis, respectively. However, other enzymes like Neutral cholesterol ester hydrolase 1 (NCEH1) have not been linked to lung cancer so far or even represent uncharacterized proteins (Abhydrolase domain-containing protein 10, ABHD10). Interestingly, several threonine proteases were identified, indicating that this class of enzymes is also susceptible to the ABP targeting serine hydrolases.

Conclusion

ABPP allows fast and semi-quantitative analysis of enzymatic activity profiles in cell lines and primary human specimen. We aim to apply the established methodology on &gt;100 pairs of fresh-frozen human lung adenocarcinoma biopsies and corresponding normal lung tissues from our tumor bank and link activity profiles of serine hydrolases to clinical follow-up data. The results of this study will ideally allow the discrimination of low-/ high-risk lung adenocarcinoma patients.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

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 5576.

Laser-capture microdissection impairs activity-based protein profiles for serine hydrolase in human lung adenocarcinoma

Laser-capture microdissection (LCM) enables the selection of a specific and pure cell population from a heterogenous tissue such as tumors. Activity-based protein profiling/profile (ABPP) is a chemical technology using enzyme-specific active site-directed probes to read out the functional state of many enzymes directly in any proteome. The aim of this work was to assess the compatibility of LCM with downstream ABPP for serine hydrolase (SH) in human lung adenocarcinoma. Fresh frozen lung adenocarcinoma tissue was stained with hematoxylin, toluidine blue, or methyl green (MG). Proteome from stained tissue was labeled further with SH-directed probes, and ABPPs were determined on a one-dimensional gel-based approach. This allowed us to assess the impact of staining procedures on their ABPPs. The effect of the LCM process on ABPPs was assessed furthermore using MG-stained lung adenocarcinoma tissue. The staining procedures led to strong changes in ABPPs. However, MG staining seemed the most compatible with downstream ABPP. MG-stained, laser-captured, microdissected tissue showed additional change in profiles as a result of the denaturing property of extraction buffer but not to the microdissection process itself. LCM staining procedures but not microdissection per se interfered with downstream ABPP and led to a strong change in ABPPs of SHs in human lung adenocarcinoma.

Characterization of mammary epithelial cell line HC11 using the NIA 15k gene array reveals potential regulators of the undifferentiated and differentiated phenotypes

Differentiation of undifferentiated mammary epithelial stem and/or progenitor cells results in the production of luminal-ductal and myoepithelial cells in the young animal and upon pregnancy, the production of luminal alveolar cells. A few key regulators of differentiation have been identified, though it is not known yet how these proteins function together to achieve their well-orchestrated products. In an effort to identify regulators of early differentiation, we screened the NIA 15k gene array of 15,247 developmentally expressed genes using mouse mammary epithelial HC11 cells as a model of differentiation. We have confirmed a number of genes preferentially expressed in the undifferentiated cells (Lgals1, Ran, Jam-A and Bmpr1a) and in those induced to undergo differentiation (Id1, Nfkbiz, Trib1, Rps21, Ier3). Using antibodies to the proteins encoded by Lgals1, and Jam-A, we confirmed that their proteins levels were higher in the undifferentiated cells. Although the amounts of bone morphogenetic protein receptor-1A (BMPR1A) protein were present at all stages, we found the activity of its downstream signal transduction pathway, as measured by the presence of phosphorylated-SMAD1, -SMAD5, and -SMAD8, is elevated in undifferentiated cells and decreases in fully differentiated cells. This evidence supports that the BMPR1A pathway functions primarily in undifferentiated mammary epithelial cells. We have identified a number of genes, of known and unknown function, that are candidates for the maintenance of the undifferentiated phenotype and for early regulators of mammary alveolar cell differentiation.