Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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Kidney protein profiling of Wilms' tumor patients by analysis of formalin-fixed paraffin-embedded tissue samples.

Author(s): Hammer E, Ernst FD, Thiele A, Karanam NK, Kujath C, Evert M, Völker U, Barthlen W

Publication: Clin Chim Acta, 2014, Vol. 433, Page 235-41

PubMed ID: 24680863 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of using FFPE rather than frozen specimens and inter- and intraindividual variability on protein identification in normal adjacent and kidney tumor specimens. 3 kidney tumor and normal adjacent paired specimens were used for the comparison between specimens snap-frozen in liquid nitrogen and FFPE specimens.

   Summary of Findings:

   66% of the 1731 proteins identified by MS were found in both FFPE and frozen specimen. An additional 24% (420 of 1731) of proteins were found just in frozen specimens, and 9% (154 of 1731) were found just in FFPE specimens. Finally, 72% of the proteins found to have >2 fold difference in expression between frozen Wilms’ tumor and normal adjacent tissue were also found to be differentially expressed between FFPE tumor and normal adjacent specimens from the same patient. 66% of the proteins identified were found in all three replicates of the same frozen kidney specimen, and 62% of proteins identified were common among all three patients.

   Biospecimens

   • Tissue - Kidney

   Preservative Types

   • Frozen
   • Formalin

   Diagnoses:

   • Neoplastic - Pediatric
   • Neoplastic - Normal Adjacent
   • Neoplastic - Carcinoma
   • Neoplastic - Other

   Platform:

   Analyte	Technology Platform
   Peptide	MS/MS
   Protein	MS/MS

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
   Biospecimen Aliquots and Components	Biospecimen heterogeneity	Intratumoral sampling (exact positions not specified)
   Preaquisition	Diagnosis/ patient condition	Wilms' tumor Normal adjacent

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2. Study Purpose

   The purpose of this study was to determine the effects tumor status and analysis method on protein expression in FFPE kidney specimens. 7 FFPE specimens from pediatric patients (1 year 7 months to 8 years 9 months of age) were used to compare protein expression between Wilms' tumor and normal adjacent specimens.

   Summary of Findings:

   The authors identified 259 proteins (29% of 879) with >2 fold differential expression between normal adjacent and tumor tissue by MS. Most of these proteins (183 of 259) were expressed at lower levels in the tumor tissue and tended to be involved in metabolism. IHC staining confirmed expression differences for Ezrin, Sodium/hydrogen Exchanger Regulatory Factor (NHERF1), transforming growth factor beta (TGF-β1), collagen type 1 alpha 1 (Col1A1), vimentin, LIM and SH3 domain protein 1 (LASP1), and collagen.

   Biospecimens

   • Tissue - Kidney

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Normal Adjacent
   • Neoplastic - Pediatric
   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   Protein	MS/MS
   Protein	Immunohistochemistry
   Peptide	MS/MS

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   MS/MS Specific	Technology platform	IHC
   Immunohistochemistry Specific	Targeted peptide/protein	Ezrin NHERF1 TGF-β1 Col1A1 Vimentin LASP1 Collagen
   Preaquisition	Diagnosis/ patient condition	Wilms’ tumor Normal adjacent tissue

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