Grade-dependent Proteomics Characterization of Kidney Cancer

Abstract

Kidney cancer is frequently metastatic on presentation at which point the disease is associated with a 95% mortality. Assessment of tumor grade on pathological examination is the most powerful means for prognostication as well as for stratification of patients into those who might respond to conventional or targeted therapy. Although there exist several grading systems in common use, all suffer from significant disparity among observers. In an attempt to objectify this process as well as to acquire grade-specific mechanistic information, we performed LC-MS/MS-based proteomics analysis on 50 clear cell kidney cancers equally distributed among normal tissues and Fuhrman grades 1-4. Initial experiments confirmed the utility of using archived formalinfixed paraffin-embedded samples for LC-MS/MS-based proteomics analysis, and the LC-MS/MS findings were validated by extensive immunoblotting. We now show that changes among many biochemical processes and pathways are strongly grade-dependent with the glycolytic and amino acid synthetic pathways highly represented. In addition, proteins relating to acute phase and xenobiotic metabolism signaling are highly represented. Self-organized mapping of proteins with similar patterns of expression led to the creation of a heat map that will be useful in grade characterization as well as in future research relating to oncogenic mechanisms and targeted therapies for kidney cancer. Molecular & Cellular Proteomics 8:971-985, 2009. Kidney cancer (or renal cell carcinoma (RCC)1 ) is the seventh most common malignancy, the 10th most common cause of cancer death in men, and the ninth most common cancer in women. In 2009, an estimated 13,000 deaths (8,100 men and 4,900 women) will occur in the United States. The disease is frequently asymptomatic; a third of cases are diagnosed when the disease is already metastatic at which time it has 95% mortality (1).Assessment of tumor grade is the most powerful available means to date of determining tumor prognosis; thus objective criteria for assessing grade are essential such that prognostication is unambiguous. In addition, grade criteria are useful in stratifying patients into those most likely to respond to conventional as well as new targeted therapies. There exist several systems for assigning tumor grade in RCC, although most pathologists utilize the Fuhrman grading system. As is evidenced by the abundance of extant grading systems (2), there appears to be a general lack of consensus and thus considerable variability in assigning tumor grades. Objective criteria for grade assignment utilizing specific protein markers will be useful in objectifying this process and thereby allowing for more accurate prognostication. Furthermore assessment of the biological basis of the differences among grades, as evidenced by diverse biochemical pathways altered in a grade-specific fashion, will lead to the development of novel diagnostic assays as well as therapeutic interventions.Once objective grading criteria are put forth, molecular mechanisms by which ...

Underexpressed CNDP2 Participates in Gastric Cancer Growth Inhibition through Activating the MAPK Signaling Pathway

“…The protein was found to be upregulated in breast and renal cell carcinoma (9,10). Furthermore, it has been suggested that CNDP2 has distinct patterns of expression within grades in kidney cancer (19). There has been a lack of direct evidence, however, as to what role CNDP2 plays in these cancers.…”

Molecular Portrait of Clear Cell Renal Cell Carcinoma: An Integrative Analysis of Gene Expression and Genomic Copy Number Profiling

“…Noticeably, recent grade-dependent proteomic characterization reported that MYC, HIF-1 and p53 are the major hubs of the network obtained analyzing formalin-fixed paraffin embedded ccRCC tissues (Perroud et al, 2009). Chen et al analyzed the correlation between chromosome aberrations and clinical pathological variables, including tumor stage and nuclear grade, and observed a significant association between LOH at chromosomes 9, 14q and 18q and higher nuclear grade.…”

“…As recently reviewed by Pal et al (Pal et al, 2010), several gene expression and proteomic studies carried out on fresh and archival ccRCC tissues (Perroud, 2009;Seliger, 2009) evidenced a series of molecular processes and pathways involved in ccRCC tumorigenesis (Banumathy & Cairns, 2010) and indicated that ccRCC progression is strictly associated to the adaptation of cancer cells to low oxygen levels (Baldewijns, 2010;Bristow & Hill, 2008) and to their continuous proliferation even in the presence of compromised DNA repair mechanisms (Semenza, 2008). These results find an additional confirmation from the analysis of genomic data presented in this chapter.…”

Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini

“…Several quantitative proteomic techniques have been utilized to investigate FFPE tissues, such as trypsin-mediated 18 O labeling (2), isobaric tag for relative and absolute quantitation (iTRAQ) (39 -41), label-free quantitation (42)(43)(44)(45)(46), and chemical dimethylation (47). The successful application of iTRAQ and chemical dimethylation are especially noteworthy, as these labeling techniques target primary amines, which is of importance to N-terminal degradomic analysis.…”