A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer

Abstract

Context: Formalin-fixed paraffin-embedded (FFPE) tissue is a standard for specimen preservation, and as such FFPE tissue banks are an untapped resource of histologically-characterized specimens for retrospective biomarker investigation for pancreatic disease.

Objectives: We use liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to compare FFPE specimens from three different diseases of the exocrine pancreas.

Design: We investigated the proteomic profile of FFPE pancreatic tissue from 9 archived specimens that were histologically classified as: autoimmune pancreatitis (n=3), chronic pancreatitis (n=3), and pancreatic cancer (n=3), using LC-MS/MS.

Setting: This is a proteomic analysis experiment of FFPE pancreatic tissue in an academic center.

Patients: FFPE tissue specimens were provided by Dana-Farber/Harvard Cancer Center (Boston, MA, USA).

Interventions: FFPE tissue specimens were collected via routine surgical resection procedures.

Main outcome measures: We compared proteins identified from chronic pancreatitis, autoimmune pancreatitis, and pancreatic cancer FFPE pancreatic tissue.

Results: We identified 386 non-redundant proteins from 9 specimens. Following our filtering criteria, 73, 29, and 53 proteins were identified exclusively in autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer specimens, respectively.

Conclusions: We report that differentially-expressed proteins can be identified among FFPE tissues specimens originating from individuals with different histological diagnoses. These proteins merit further confirmation with a greater number of specimens and orthogonal validation, such as immunohistochemistry. The mass spectrometry-based methodology used herein has the potential to enhance diagnostic biomarker and therapeutic target discovery, further advancing pancreatic research.

Figure 1

Experimental workflow. 1) FFPE tissue specimens were obtained; 2) a 1.5 cm 1.5 × 1 cm x 5 µm slice of the specimen was scraped into a microcentrifuge tube; 3) paraffin was removed with heptane; 4) disulfide bonds were reduced with dithiotreitol (DTT) and alkylated with iodoacetamide; 5) specimens were digested overnight with trypsin; 6) peptides were isolated; 7) peptides were analyzed via LC-MS/MS; and 8) bioinformatics analysis was performed.

Figure 2

Distribution of proteins among the three cohorts. Venn diagrams showing unique and overlapping proteins among the three cohorts. Also indicated in the figure are references to the tables in which these sets of proteins are listed. AIP: autoimmune pancreatitis; CP: chronic pancreatitis; PC: pancreatic cancer