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Updated: May 3, 2026
The Use of Reverse Phase Protein Arrays RPPA to Explore Protein Expression Variation within Individual Renal Cell Cancers
Published on: January 22, 2013
MALDI imaging mass spectrometry profiling of proteins and lipids in clear cell renal cell carcinoma
Elizabeth Ellen Jones1, Thomas W Powers, Benjamin A Neely
1Department of Cell and Molecular Pharmacology, MUSC Proteomics Center, Medical University of South Carolina, Charleston, SC, USA.
Abstract:
Reducing the incidence and mortality rates for clear cell renal cell carcinoma (ccRCC) remains a significant clinical challenge with poor 5-year survival rates. A unique tissue cohort was assembled of matched ccRCC and distal nontumor tissues (n = 20) associated with moderate risk of disease progression, half of these from individuals who progressed to metastatic disease and the other half who remained disease free. These tissues were used for MALDI imaging MS profiling of proteins in the 2-20 kDa range, resulting in a panel of 108 proteins that had potential disease-specific expression patterns. Protein lysates from the same tissues were analyzed by MS/MS, resulting in identification of 56 proteins of less than 20 kDa molecular weight. The same tissues were also used for global lipid profiling analysis by MALDI-FT-ICR MS. From the cumulative protein and lipid expression profile data, a refined panel of 26 proteins and 39 lipid species was identified that could either distinguish tumor from nontumor tissues, or tissues from recurrent disease progressors from nonrecurrent disease individuals. This approach has the potential to not only improve prognostic assessment and enhance postoperative surveillance, but also to inform on the underlying biology of ccRCC progression.
Insights
This study identifies specific proteins and lipids in clear cell renal cell carcinoma (ccRCC) tissues. These biomarkers can help distinguish between tumor and normal tissues and predict ccRCC recurrence risk.
Area of Science:
- Biochemistry
- Proteomics
- Lipidomics
- Oncology
Background:
- Clear cell renal cell carcinoma (ccRCC) presents a significant clinical challenge with high mortality and low survival rates.
- Effective prognostic markers for ccRCC progression and recurrence are critically needed.
Purpose of the Study:
- To identify protein and lipid biomarkers for ccRCC diagnosis and prognosis.
- To analyze proteomic and lipidomic profiles in ccRCC tissues to understand disease progression.
Main Methods:
- Utilized MALDI imaging mass spectrometry (MS) for protein profiling (2-20 kDa) and MS/MS for protein identification.
- Performed global lipid profiling using MALDI-FT-ICR MS.
- Analyzed matched ccRCC and non-tumor tissues from patients with varying disease progression outcomes.
Main Results:
- Identified 108 proteins with potential disease-specific expression patterns.
- Identified 56 proteins (<20 kDa) and 39 lipid species.
- Developed a refined panel of 26 proteins and 39 lipids capable of distinguishing tumor from non-tumor tissues and predicting ccRCC recurrence.
Conclusions:
- The identified protein and lipid profiles show potential for improving ccRCC prognostic assessment and postoperative surveillance.
- This multi-omics approach offers insights into the underlying biology of ccRCC progression.
