113P - Evaluation of effects of tissue preservation methods on the proteome abundance through deep proteomics of breast cancer tissue

Background

Tumor tissue preservation methods affect proteome profiles differently. To date, no studies have reported a deep proteome comparison of four tissue preservation methods and their corresponding proteome profiles. This study sought to assess the effect of different preservation methods on quantitative proteomics of human breast adjacent normal (NC) and tumor tissues (TC) preserved in Allprotect, snap-frozen by LN2, RNAlater, and formalin solution embedded in paraffin (FFPE).

Methods

Around 7 patients’ TC and NC were preserved in four different storage conditions, which include Allprotect, LN2, RNAlater, and FFPE. A comprehensive deep proteomics analysis using mass spectrometry has been performed to evaluate the effect of storage conditions on the preservation of proteins. Protein yield and coverage were compared in four storage conditions to determine the optimum storage conditions for tissue samples to perform proteomics analysis. Unique proteins obtained from each condition were further analyzed to examine the effect of storage conditions on subcellular location. Differential analysis was performed on all individual conditions to compare the unique statistically differentially expressed proteins.

Results

TC tissues showed the highest protein yield compared to NC because the fat portion was higher in NC. The FFPE condition, followed by RNAlater, was determined to have the maximum protein coverage. Unique proteins could be detected from FFPE samples, providing a hint of the modifications induced during the paraffinization. However, the differential analysis showed more unique proteins in the Allprotect storage conditions, followed by RNAlater. The proteins CNDP2 and PLIN4 showed dysregulation in the TC sample despite the different storage conditions and may be used as therapeutic markers for breast cancer. Biological pathway analysis showed spliceosome and PPAR signaling pathways were enriched in TC compared to NC tissue.

Conclusions

This study evaluated the effects of different tissue preservation methods on proteomics analysis.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

IIT Bombay.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.