Quantitative Proteomics Using Formalin-fixed, Paraffin-embedded Biopsy Tissues in Inflammatory Disease.

Area of Science:

• Proteomics
• Pathology
• Immunology

Background:

• Access to fresh-frozen tissues (FFT) for disease pathogenesis research is limited.
• Formalin-fixed, paraffin-embedded (FFPE) tissues are widely available but may introduce bias due to formalin fixation.
• This study addresses the potential of FFPE tissues for proteomic analysis in inflammatory diseases.

Purpose of the Study:

• To compare the proteomic content of FFPE and FFTs.
• To determine the utility of FFPE tissues for studying inflammatory diseases, specifically lupus nephritis.
• To assess potential biases in protein quantification between FFPE and FFTs.

Main Methods:

• Adjacent murine lupus nephritis kidney slices were processed as FFPE or FFTs.
• Proteomics workflow involved filter-aided sample preparation and dimethyl isotope labeling.
• Nano-LC MS/MS analysis was performed using an Orbitrap XL MS.

Main Results:

• Over 97% protein identification concordance was observed between adjacent FFPE and FFTs.
• Proteins in pathways like 'systemic lupus erythematosus' and 'interferon-α' were reproducibly quantified.
• Certain immune and inflammatory proteins were quantified at lower levels in FFPE compared to FFTs (12%-29% difference).
• Pilot study on human FFPE tissues identified relevant lupus nephritis pathogenesis proteins.

Conclusions:

• Archived FFPE tissues are reliable for proteomic analysis in inflammatory diseases.
• This is the first report of lupus nephritis kidney proteomics using FFPE tissue.
• Caution is advised for quantifying certain immune and inflammation-related proteins in FFPE samples due to potential underestimation compared to FFTs.