Mining Tissue Microarray Data to Uncover Combinations of Biomarker Expression Patterns that Improve Intermediate Staging and Grading of Clear Cell Renal Cell Cancer

Abstract

Purpose: Tumor stage and nuclear grade are the most important prognostic parameters of clear cell renal cell carcinoma (ccRCC). The progression risk of ccRCC remains difficult to predict particularly for tumors with organ-confined stage and intermediate differentiation grade. Elucidating molecular pathways deregulated in ccRCC may point to novel prognostic parameters that facilitate planning of therapeutic approaches.Experimental Design: Using tissue microarrays, expression patterns of 15 different proteins were evaluated in over 800 ccRCC patients to analyze pathways reported to be physiologically controlled by the tumor suppressors von Hippel-Lindau protein and phosphatase and tensin homologue (PTEN). Tumor staging and grading were improved by performing variable selection using Cox regression and a recursive bootstrap elimination scheme.Results: Patients with pT2 and pT3 tumors that were p27 and CAIX positive had a better outcome than those with all remaining marker combinations. A prolonged survival among patients with intermediate grade (grade 2) correlated with both nuclear p27 and cytoplasmic PTEN expression, as well as with inactive, nonphosphorylated ribosomal protein S6. By applying graphical log-linear modeling for over 700 ccRCC for which the molecular parameters were available, only a weak conditional dependence existed between the expression of p27, PTEN, CAIX, and p-S6, suggesting that the dysregulation of several independent pathways are crucial for tumor progression.Conclusions: The use of recursive bootstrap elimination, as well as graphical log-linear modeling for comprehensive tissue microarray (TMA) data analysis allows the unraveling of complex molecular contexts and may improve predictive evaluations for patients with advanced renal cancer. Clin Cancer Res; 16(1); 88-98. ©2010 AACR.The last decades have shown an incidental increase of patients diagnosed with renal cell carcinoma (RCC) with clear cell RCC (ccRCC) being the most frequent and aggressive subtype (1, 2). Patients with local tumors have a significantly better outcome as these cancers can be treated with radical or partial nephrectomy, whereas the 5-year survival rate of metastatic ccRCC remains poor. However, even in patients with organ-confined ccRCC, the 10-year cancer-specific death rates vary from 10% to 38% in pT1a and pT2 tumors, respectively (3).To date, the best available predictor of the postoperative clinical course of localized RCCs is tumor stage at presentation (4, 5). Nevertheless, a significant difference of outcome exists within the same stage. Additional prognostic parameters are routinely used to refine prognosis in RCC patients. After tumor stage, the second most important prognostic parameter is the nuclear differentiation grade (6). Three-and four-tired grading systems are commonly applied for tumor grading. More than 50% of ccRCCs are classified as moderately differentiated, implying an intermediate risk of tumor recurrence (7), which is not informative for the clinician to stratify therapy. Therefo...

Spontaneous Peripheral T-cell Responses toward the Tumor-Associated Antigen Cyclin D1 in Patients with Clear Cell Renal Cell Carcinoma

“…Cyclin D1 is a cell-cycle regulator crucial for the G 1 -S transition (35) and is overexpressed in many cancers including colorectal and breast carcinoma (36,37). We found that cyclin D1 was overexpressed in 43% of the primary ccRCC samples, a finding that was similar to the previous published data (38)(39)(40).…”

“…There is no association identified between Cyclin D1 expression and ccRCC prognosis (40), although Cyclin D1 overexpression is associated with shorter patient survival in other cancers and thus represents an interesting therapeutic target (44). However, cyclin D1 is difficult to target as it is expressed in the cytosol and lacks intrinsic enzymatic activity.…”

Computational pathology: Challenges and promises for tissue analysis

“…Two modern approaches within the scope of computational pathology try to solve this question from a frequentist [89] and a Bayesian [87] point of view.…”

VHL mutations and dysregulation of pVHL- and PTEN-controlled pathways in multilocular cystic renal cell carcinoma

“…The control group consisted of 40 pT1 and pT2 clear cell renal cell carcinomas with low Fuhrman differentiation grade (1 and 2) from a recently published study. 4 …”

“…3 Recently, we comprehensively analyzed pVHL-and phosphatase and tensin homolog (PTEN)-controlled pathways in 4800 clear cell renal cell carcinoma patients. 4 It was shown that the expression status of p27, PTEN, carbonic anhydrase 9 (CAIX) and phosphorylated ribosomal protein S6 is crucial for the biological behavior of sporadic clear cell renal cell carcinoma.…”