Flinders Medical Centre, Adelaide, Australia

Presentation Abstract

The importance of cleanliness: the use of archived FFPE tissues for research purposes

The clinical standard for preparing tissues for histopathological assessment is formalin fixation and paraffin embedding (FFPE). During this process, the tissue architecture is preserved and often excess tissue is stored in archival banks. This resource offers a vast repository of tissue material which in most cases is paired with detailed clinical data.

For researchers, access to excess FFPE tissues from diagnostic laboratories offers a valuable resource for retrospective analysis of diagnostic and prognostic biomarkers, as well as the ability to understand the molecular mechanisms of disease initiation and progression. Various studies have shown that even when stored for decades the material within the blocks does not change over time.

However, the process of FFPE induces numerous chemical changes and degradation to DNA, RNA and protein that can hamper its usefulness for research purposes. To be able to consistently generate reproducible results in the laboratory there are several important factors that need to be considered when processing samples for research use which varying depending on the downstream molecular applications. For example, if RNA is to be extracted from the FFPE blocks, the first 2-3 sections should be discarded as oxidation on the tissue block surface can rapidly degrade the RNA.

For proteomic analysis, sections need to mounted on uncoated slides as PEI coating can introduce polymer contamination into the mass spectrometer.

These factors will be further discussed along with some examples of where we have utilised FFPE samples to answer key questions in our research on chronic lymphocytic leukaemia.




Lauren completed her PhD in 2011 at Flinders University in the area of kidney disease and carried out her postdoctoral studies in B-cell autoimmunity. Her interest in B-cell biology and skills and knowledge of proteomic techniques saw her take up a position in haematology, where she began to unravel the proteome of leukaemia cells. She also developed a strong interest in the role of secreted proteins in tumour microenvironment and how these can promote survival of lymphocytes from patients with chronic lymphocytic leukaemia (CLL). More recently, her work has focused on cancer cell metabolism and understanding the fuel requirements that promote proliferation of CLL cells within the lymph nodes and bone marrow, with the view to disrupting these pathways with new therapies. She has extensive experience in identification of proteins from archived tissue samples.

She was recently awarded a 3-year early career researcher fellowship by Cancer Council SA (Beat Cancer Scheme) to continue carrying out her work investigating cancer cell bioenergetics. She currently works in Molecular Medicine and Pathology and is part of the CLL Research Team, headed by Associate Professor Bryone Kuss.