Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5) and altered Axin-1 expression during tumour progression

BACKGROUND: Splicing processes might play a major role in carcinogenesis and tumour progression. The Wnt pathway is of crucial relevance for cancer progression. Therefore we focussed on the Wnt/β-catenin signalling pathway in order to validate the expression of sequences predicted as alternatively spliced by bioinformatic methods. Splice variants of its key molecules were selected, which may be critical components for the understanding of colorectal tumour progression and may have the potential to act as biological markers. For some of the Wnt pathway genes the existence of splice variants was either proposed (e.g. β-Catenin and CTNNB1) or described only in non-colon tissues (e.g. GSK3β) or hitherto not published (e.g. LRP5). RESULTS: Both splice variants – normal and alternative form – of all selected Wnt pathway components were found to be expressed in cell lines as well as in samples derived from tumour, normal and healthy tissues. All splice positions corresponded totally with the bioinformatical prediction as shown by sequencing. Two hitherto not described alternative splice forms (CTNNB1 and LRP5) were detected. Although the underlying EST data used for the bioinformatic analysis suggested a tumour-specific expression neither a qualitative nor a significant quantitative difference between the expression in tumour and healthy tissues was detected. Axin-1 expression was reduced in later stages and in samples from carcinomas forming distant metastases. CONCLUSION: We were first to describe that splice forms of crucial genes of the Wnt-pathway are expressed in human colorectal tissue. Newly described splicefoms were found for β-Catenin, LRP5, GSK3β, Axin-1 and CtBP1. However, the predicted cancer specificity suggested by the origin of the underlying ESTs was neither qualitatively nor significant quantitatively confirmed. That let us to conclude that EST sequence data can give adequate hints for the existence of alternative splicing in tumour tissues. That no difference in the expression of these splice forms between cancerous tissues and normal mucosa was found, may indicate that the existence of different splice forms is of less significance for cancer formation as suggested by the available EST data. The currently available EST source is still insufficient to clearly deduce colon cancer specificity. More EST data from colon (tumour and healthy) is required to make reliable predictions

Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5) and altered Axin-1 expression during tumour progression

Abstract Background Splicing processes might play a major role in carcinogenesis and tumour progression. The Wnt pathway is of crucial relevance for cancer progression. Therefore we focussed on the Wnt/β-catenin signalling pathway in order to validate the expression of sequences predicted as alternatively spliced by bioinformatic methods. Splice variants of its key molecules were selected, which may be critical components for the understanding of colorectal tumour progression and may have the potential to act as biological markers. For some of the Wnt pathway genes the existence of splice variants was either proposed (e.g. β-Catenin and CTNNB1) or described only in non-colon tissues (e.g. GSK3β) or hitherto not published (e.g. LRP5). Results Both splice variants – normal and alternative form – of all selected Wnt pathway components were found to be expressed in cell lines as well as in samples derived from tumour, normal and healthy tissues. All splice positions corresponded totally with the bioinformatical prediction as shown by sequencing. Two hitherto not described alternative splice forms (CTNNB1 and LRP5) were detected. Although the underlying EST data used for the bioinformatic analysis suggested a tumour-specific expression neither a qualitative nor a significant quantitative difference between the expression in tumour and healthy tissues was detected. Axin-1 expression was reduced in later stages and in samples from carcinomas forming distant metastases. Conclusion We were first to describe that splice forms of crucial genes of the Wnt-pathway are expressed in human colorectal tissue. Newly described splicefoms were found for β-Catenin, LRP5, GSK3β, Axin-1 and CtBP1. However, the predicted cancer specificity suggested by the origin of the underlying ESTs was neither qualitatively nor significant quantitatively confirmed. That let us to conclude that EST sequence data can give adequate hints for the existence of alternative splicing in tumour tissues. That no difference in the expression of these splice forms between cancerous tissues and normal mucosa was found, may indicate that the existence of different splice forms is of less significance for cancer formation as suggested by the available EST data. The currently available EST source is still insufficient to clearly deduce colon cancer specificity. More EST data from colon (tumour and healthy) is required to make reliable predictions.</p

Foraminifera as markers of Holocene sea-level fluctuations and water depths of ancient harbours - A case study from the Bay of Elaia (W Turkey)

The absence of common sea-level indicators in the study area of Elaia, Pergamum's harbour city in Hellenistic and Roman times, forced to establish a new reliable indicator, which was found in the foraminifera associations in connection with the transgressive contact. The strength of this indicator is the exclusion of post-depositional compaction. Accompanied by a well-dated archaeological index point at a breakwater, the micropalaeontological indicator enabled the establishment of a reliable regional sea-level curve (RSL curve) for the Bay of Elaia. It is in good agreement with other curves for the Aegean region and in general agreement to the glacio-hydro-isostatic model for the region. Our sea-level curve proves, for the first time at a continental site on the Turkish Aegean coast, the today's sea-level peak. Water-depth modelling for the so-called closed harbour of Elaia reveals the capacity to fully accommodate the common ship classes of Hellenistic and early Roman times until around 150 CE, while water depth estimates for the so-called open harbour of the city verifies the usage of the adjacent ship sheds during Elaia's prime. (C) 2017 Elsevier B.V. All rights reserved

The harbour of Elaia: A palynological archive for human environmental interactions during the last 7500 years

Elaia, the harbour city for ancient Pergamon (western Turkey), was investigated using geoarchaeological methods. The rise and fall of Elaia were closely linked to the flourishing period of Pergamon, which ruled wide parts of today's western Turkey in Hellenistic times. In the framework of this research, the palynological analysis of a 9 m sediment core, Ela-70, retrieved from the enclosed harbour of the city, was carried out to reconstruct the vegetation and environmental history of the wider Gulf of Elaia region. An age-depth model, based on 11 calibrated radiocarbon ages, starting from 7.5 ka BP, provides the basis for the high resolution study of sediments from the Hellenistic period, as well as before and after. The lower part of the pollen diagram is characterised by high percentages of deciduous oaks and pines, suggesting the dominance of open forests close to the coring site. The change from oak forests to a cultural landscape, with olive, pistachio, walnut, and grape, started around 850 BC, reaching a maximum ca. 250 BC, and continuing to ca. AD 800. This period is characterised by increase of fire activity, soil erosion intensity, and pastoral farming. Such long-lasting intensive land use likely led to the climax ecosystem turnover from open deciduous oak forests to pine stands, while salt marshes developed around the coring site. The discovery of the dinoflagellate cysts of Peridinium ponticum, a Black Sea endemic species, in the harbour of Elaia evidences maritime trade between the Aegean Sea and the Black Sea; its first occurrence coincides with the time of the Mithridatic Wars (1st century BC). In conclusion, palynological data, in addition to historical and archaeological records, provide a deeper insight into human environmental interactions, as derived from the geoarchaeological archive of the harbour of Elaia. (C) 2016 Elsevier Ltd. All rights reserved

The environs of Elaia's ancient open harbour - a reconstruction based on microfaunal evidence

During Hellenistic and Roman times, Elaia, the harbour city of ancient Pergamum, was an important place of trading and traffic. Intense mercantile and military activities are documented by literary sources and archaeological evidences. Geomagnetic and geoelectric investigations detected building structures close to the ancient coastline, which are interpreted as ship sheds. The aim of this study was to reconstruct the coastal evolution, particularly with regard to harbour-related facilities. For that purpose, a 10 m long sediment core was drilled in the area of the ancient open harbour immediately in front of the supposed ship sheds. It was studied with the tools of micropalaeontology, geophysics, sedimentology and geochemistry. To improve the reconstruction of the palaeoenvironmental conditions, reference samples of modern environments of the area were analysed. As indicated by marine ostracod and foraminifer taxa, the sediment core shows (from bottom to top) that the initially fully marine conditions changed to a more restricted fauna indicative for a more sheltered bay with brackish waters. This layer dates to Hellenistic times. It can, however, be shown that the siltation process had produced a lagoon system already several hundred years BC. The Elaia embayment was first used as a natural harbour. It was equipped with breakwaters in the Hellenistic period. The progressive siltation caused the abandonment of the harbour in Late Roman Times. (C) 2014 Elsevier Ltd. All rights reserved

Taken from the sea, reclaimed by the sea: The fate of the closed harbour of Elaia, the maritime satellite city of Pergamum (Turkey)

During Hellenistic times, when the Pergamenian kingdom was prospering, Pergamum was operating an important harbour, used by merchants and military at the city of Elaia. This paper focuses on the development, utilisation and decay of the closed harbour of Elaia, which is discussed in the context of the landscape evolution of the environs of the ancient settlement. Based on geoarchaeological, archaeological and literary evidence, the construction of two harbour moles in order to provide shelter against wave action and enemies can be attributed to the early Hellenistic period. Geoelectric measurements revealed the construction profile of the moles. Coring evidence indicated that together with mole construction, a greater area of the formerly shallow marine and sublittoral terrain was consolidated, most probably to create space for harbour installations. The closed harbour basin was used intensely during Hellenistic and Roman times. Later, continued siltation hindered further usage. In combination with the decline of the city of Elaia in Late Antiquity, this was the reason why the harbour was abandoned. Scenarios for the time of the maximum transgression of the sea around 2500 BC, the early Hellenistic times around 300 BC, and Late Antiquity AD 500, are presented. (C) 2013 Elsevier Ltd and INQUA. All rights reserved