An exfoliation and enrichment strategy results in improved transcriptional profiles when compared to matched formalin fixed samples

<p>Abstract</p> <p>Background</p> <p>Identifying the influence formalin fixation has on RNA integrity and recovery from clinical tissue specimens is integral to determining the utility of using archival tissue blocks in future molecular studies. For clinical material, the current gold standard is unfixed tissue that has been snap frozen. Fixed and frozen tissue however, both require laser capture microdissection to select for a specific cell population to study. The recent development of a sampling method capable of obtaining a viable, enriched cell population represents an alternative option in procuring cells from clinical material for molecular research purposes. The expression profiles of cells obtained by using this procurement approach, in conjunction with the profiles from cells laser capture microdissected from frozen tissue sections, were compared to the expression profiles from formalin fixed cells to determine the influence fixation has on expression profiles in clinical material.</p> <p>Methods</p> <p>Triplicate samples of non-neoplastic colonic epithelial cells were recovered from a hemicolectomy specimen using three different procurement methods from the same originating site: 1) an exfoliation and enrichment strategy 2) laser capture microdissection from formalin fixed tissue and 3) laser capture microdissection from frozen tissue. Parameters currently in use to assess RNA integrity were utilized to assess the quality of recovered RNA. Additionally, an expression microarray was performed on each sample to assess the influence each procurement technique had on RNA recovery and degradation.</p> <p>Results</p> <p>The exfoliation/enrichment strategy was quantitatively and qualitatively superior to tissue that was formalin fixed. Fixation negatively influenced the expression profile of the formalin fixed group compared to both the frozen and exfoliated/enrichment groups.</p> <p>Conclusion</p> <p>The exfoliation/enrichment technique represents a superior alternative in tissue procurement and RNA recovery relative to formalin fixed tissue. None of the deleterious effects associated with formalin fixation are encountered in the exfoliated/enriched samples because of the absence of its use in this protocol. The exfoliation/enrichment technique also represents an economical alternative that will yield comparable results to cells enriched by laser capture microdissection from frozen tissue sections.</p

Multi-proxy analysis in defining sedimentary processes in very recent prodelta deposits: the Northern Phlegraean offshoreexample (Eastern Tyrrhenian Margin)

A multi-proxy analysis of Volturno River prodelta deposits in the outer shelf of Northern Phlegraean margin (Eastern Tyrrhenian Sea) has been carried out to reconstruct the sedimentary processes acting during recent times. The late Holocene sediments were characterized through Subbottom Chirp profiles coupled with sedimentological and petrophysical data. The chronostratigraphic framework was achieved by means of colorimetric parameter a* correlations with nearby dated marine sediment. A time interpretation of about 2,300 years BP is estimated for the sedimentary record collected in the cores. Seismic stratigraphic analysis shows late Holocene outer shelf deposits, characterized by fluid escape features and small-offset faults. However, the undisturbed sedimentation and the preservation of an internal geometry at decimetre scale, as detected by the sedimentological and petrophysical analysis, indicates a slow sliding without sediment reworking for this sedimentological body. So far a possible recent (\2,300 years BP) shear dominated downward displacement of high water content sediments, triggered by the occurrence of seismic activity, is inferred. Based on the depth-age conversion of the detected lithological features, a regular climatically driven change in the sediment supply of the prodelta depositional environment is suggested. The detection of spectrophotometry correlations of Holocene shelf margin sediments, several km apart, goes beyond the previous work and confirms even for continental shelf area the potential value of spectrophotometer data in high-resolution stratigraphic correlations