Tumor heterogeneity: how could we use it to achieve better clinical outcomes?

Differences in tumors related to location, tissue type, and histological subtype have been well documented for decades. Tumors are also molecularly very diverse. In this short review we describe the current classification schemes for tumor heterogeneity. We enlist the various drivers of tumor heterogeneity generation and comment on their clinical significance. New molecular techniques promise to assess tumor heterogeneity at affordable cost, so that these techniques can soon enter the clinic. While tumor heterogeneity currently represents a major unfavorable barrier in the field of oncology, it may also be a key in revolutionizing cancer diagnosis and treatment. Information regarding tumor heterogeneity has the potential to provide more thorough prognostic information, guide more efficacious combination treatment regimens, and lead to the development of novel therapeutic strategies and identification of new targets. For these gains to be realized, assessment of tumor heterogeneity needs to be incorporated into current diagnostic protocols but standardized and reproducible assessment methods are required. Fortunately, when these advances are realized, tumor heterogeneity has the potential to improve clinical outcomes.

CAIX Immunostaining in Non-neoplastic Renal Diseases.

BACKGROUND/AIM: Carbonic anhydrase 9 (CAIX) is a transmembrane metalloenzyme that regulates cellular adhesion, proliferation, and intra/extracellular pH. It is expressed primarily through a hypoxia-inducible factor 1 (HIF-1)-dependent mechanism. Its over-expression is closely related to somatic mutations in the Von Hippel-Lindau (VHL) gene. Studies have shown that it is over-expressed in renal cell carcinoma. In this study, we aimed to assess the value of CAIX immunostaining as an ancillary diagnostic tool in renal malignancies and medical renal diseases. PATIENTS AND METHODS: Slides of kidney tumors and medical kidney diseases were selected to evaluate CAIX expression. Intensity and staining patterns of CAIX were independently assessed by two pathologists. RESULTS: Our results showed strong and diffuse box-like membranous staining pattern in the majority of the clear cell renal cell carcinoma (ccRCC) cases (47/59 cases; 94%). A strong, diffuse cup-shaped staining pattern was observed in clear cell papillary RCC. Variable positivity was observed in other RCC (renal cell carcinoma) subtypes. In non-neoplastic renal conditions, the majority of the cases were negative for CAIX, and only a few cases demonstrated patchy non-specific staining. Of note, a single case of transplanted kidney biopsy taken because of delayed graft function showed a focal area of dilated tubules lined by cells with clear cytoplasm and enlarged nuclei with prominent nucleoli. This area showed diffuse membranous staining for CAIX.  Two cases of end-stage renal disease showed a focal circumferential membranous staining pattern for CAIX in dilated tubules. CONCLUSION: The CAIX immunoreactivity observed in these three cases could be indicative of an early-stage renal cell neoplasm and warrants further investigation.

An integrated proteomic and peptidomic assessment of the normal human urinome.

BACKGROUND: Urine represents an ideal source of clinically relevant biomarkers as it contains a large number of proteins and low molecular weight peptides. The comprehensive characterization of the normal urinary proteome and peptidome can serve as a reference for future biomarker discovery. Proteomic and peptidomic analysis of urine can also provide insight into normal physiology and disease pathology, especially for urogenital diseases. METHODS: We developed an integrated proteomic and peptidomic analytical protocol in normal urine. We employed ultrafiltration to separate protein and peptide fractions, which were analyzed separately using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on the Q-Exactive mass spectrometer. RESULTS: By analyzing six urines from healthy individuals with advanced age, we identified 1754 proteins by proteomic analysis and 4543 endogenous peptides, arising from 566 proteins by peptidomic analysis. Overall, we identified 2091 non-redundant proteins by this integrated approach. In silico protease activity analysis indicated that metalloproteases are predominantly involved in the generation of the endogenous peptide signature. In addition, a number of proteins that were detected in normal urine have previously been implicated in various urological malignancies, including bladder cancer and renal cell carcinoma (RCC). CONCLUSIONS: We utilized a highly sensitive proteomics approach that enabled us to identify one of the largest sets of protein identifications documented in normal human urine. The raw proteomics and peptidomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD003595.