Identification of novel snoRNA-based biomarkers for clear cell renal cell carcinoma from urine-derived extracellular vesicles

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of RCC with high rates of metastasis. Targeted therapies such as tyrosine kinase and checkpoint inhibitors have improved treatment success, but therapy-related side effects and tumor recurrence remain a challenge. As a result, ccRCC still have a high mortality rate. Early detection before metastasis has great potential to improve outcomes, but no suitable biomarker specific for ccRCC is available so far. Therefore, molecular biomarkers derived from body fluids have been investigated over the past decade. Among them, RNAs from urine-derived extracellular vesicles (EVs) are very promising.

METHODS

RNA was extracted from urine-derived EVs from a cohort of 78 subjects (54 ccRCC patients, 24 urolithiasis controls). RNA-seq was performed on the discovery cohort, a subset of the whole cohort (47 ccRCC, 16 urolithiasis). Reads were then mapped to the genome, and expression was quantified based on 100 nt long contiguous genomic regions. Cluster analysis and differential region expression analysis were performed with adjustment for age and gender. The candidate biomarkers were validated by qPCR in the entire cohort. Receiver operating characteristic, area under the curve and odds ratios were used to evaluate the diagnostic potential of the models.

RESULTS

An initial cluster analysis of RNA-seq expression data showed separation by the subjects' gender, but not by tumor status. Therefore, the following analyses were done, adjusting for gender and age. The regions differentially expressed between ccRCC and urolithiasis patients mainly overlapped with small nucleolar RNAs (snoRNAs). The differential expression of four snoRNAs (SNORD99, SNORD22, SNORD26, SNORA50C) was validated by quantitative PCR. Confounder-adjusted regression models were then used to classify the validation cohort into ccRCC and tumor-free subjects. Corresponding accuracies ranged from 0.654 to 0.744. Models combining multiple genes and the risk factors obesity and hypertension showed improved diagnostic performance with an accuracy of up to 0.811 for SNORD99 and SNORA50C (p = 0.0091).

CONCLUSIONS

Our study uncovered four previously unrecognized snoRNA biomarkers from urine-derived EVs, advancing the search for a robust, easy-to-use ccRCC screening method.

Evaluation of MicroRNAs as Non-Invasive Diagnostic Markers in Urinary Cells from Patients with Suspected Prostate Cancer

Currently used tumor markers for early diagnosis of prostate cancer (PCa) are often lacking sufficient specificity and sensitivity. Therefore, the diagnostic potential of selected microRNAs in comparison to serum PSA levels and PSA density (PSAD) was explored. A panel of 12 PCa-associated microRNAs was quantified by qPCR in urinary sediments from 50 patients with suspected PCa undergoing prostate biopsy, whereupon PCa was detected in 26 patients. Receiver operating characteristic (ROC) curve analyses revealed a potential for non-invasive urine-based PCa detection for miR-16 (AUC = 0.744, p = 0.012; accuracy = 76%) and miR-195 (AUC = 0.729, p = 0.017; accuracy = 70%). While serum PSA showed an insufficient diagnostic value (AUC = 0.564, p = 0.656; accuracy = 50%) in the present cohort, PSAD displayed an adequate diagnostic performance (AUC = 0.708, p = 0.031; accuracy = 70%). Noteworthy, the combination of PSAD with the best candidates miR-16 and miR-195 either individually or simultaneously improved the diagnostic power (AUC = 0.801–0.849, p < 0.05; accuracy = 76–90%). In the sub-group of patients with PSA ≤ 10 ng/mL (n = 34), an inadequate diagnostic power of PSAD alone (AUC = 0.595, p = 0.524; accuracy = 68%) was markedly surpassed by miR-16 and miR-195 individually as well as by their combination with PSAD (AUC = 0.772–0.882, p < 0.05; accuracy = 74–85%). These findings further highlight the potential of urinary microRNAs as molecular markers with high clinical performance. Overall, these results need to be validated in a larger patient cohort.

Urinary MicroRNAs as Potential Markers for Non-Invasive Diagnosis of Bladder Cancer

Currently, voided urine cytology (VUC) serves as the gold standard for the detection of bladder cancer (BCa) in urine. Despite its high specificity, VUC has shortcomings in terms of sensitivity. Therefore, alternative biomarkers are being searched, which might overcome these disadvantages as a useful adjunct to VUC. The aim of this study was to evaluate the diagnostic potential of the urinary levels of selected microRNAs (miRs), which might represent such alternative biomarkers due to their BCa-specific expression. Expression levels of nine BCa-associated microRNAs (miR-21, -96, -125b, -126, -145, -183, -205, -210, -221) were assessed by quantitative PCR in urine sediments from 104 patients with primary BCa and 46 control subjects. Receiver operating characteristic (ROC) curve analyses revealed a diagnostic potential for miR-96, -125b, -126, -145, -183, and -221 with area under the curve (AUC) values between 0.605 and 0.772. The combination of the four best candidates resulted in sensitivity, specificity, positive and negative predictive values (NPV), and accuracy of 73.1%, 95.7%, 97.4%, 61.1%, and 80.0%, respectively. Combined with VUC, sensitivity and NPV could be increased by nearly 8%, each surpassing the performance of VUC alone. The present findings suggested a diagnostic potential of miR-125b, -145, -183, and -221 in combination with VUC for non-invasive detection of BCa in urine.

Quantification of MicroRNAs in Urine-Derived Specimens

MicroRNAs are small noncoding RNAs which regulate the expression of genes involved in a multitude of cellular processes. Dysregulation of microRNAs and-in consequence-of the affected pathways is frequently observed in numerous pathologies including cancers. Therefore, tumor-related alterations in microRNA expression and function can reflect molecular processes of tumor onset and progression qualifying microRNAs as potential diagnostic and prognostic biomarkers.In particular, microRNAs with differential expression in bladder cancer (BCa) might represent promising tools for noninvasive tumor detection in urine. This would be helpful not only for diagnostic and monitoring purposes but also for therapeutic decisions. Detection and quantification of BCa-associated microRNAs in urine can be performed using the cellular sediment, which also contains BCa cells, or in exosomes originating from those cells. Methods for isolation of exosomes from urine, extraction of total RNA from cells and exosomes as well as techniques for RNA quantification, reverse transcription, and qPCR-based quantification of microRNA expression levels are described herein.

Diagnostic and prognostic value of bladder cancer-related transcript markers in urine

PURPOSE

Since cytology as the current "gold standard" for noninvasive detection of bladder cancer (BCa) is characterized by a relatively low sensitivity, urinary transcript levels of survivin (SVV), Ki-67 and cytokeratin 20 (CK20) were evaluated as alternative or complementary biomarkers. Furthermore, their prognostic value was investigated.

METHODS

Voided urine samples from 105 BCa patients and 156 controls were included. Total RNA was isolated from urine pellets and reverse-transcribed into cDNA. Expression levels of SVV, Ki-67 and CK20 were determined by quantitative PCR and normalized to the housekeeping gene TBP. Diagnostic performance of transcript markers and cytology was assessed by receiver operating characteristic (ROC) curve analyses. The prognostic value of the transcript markers was calculated by Cox proportional hazards models.

RESULTS

ROC analyses resulted in AUC values between 0.71 (Ki-67) and 0.86 (CK20), indicating an appropriate diagnostic power. Using specifically defined cutoff values, the expression levels of the assessed biomarkers were significantly higher in urine specimens from BCa patients compared to control group (Mann-Whitney U test p < 0.001). Specificity ranged from 75% (SVV) to 84% (CK20) and sensitivity from 56% (Ki-67) to 87% (CK20). In combination with cytology, the sensitivity increased up to 97% (CK20). With regard to prognostic power, only SVV showed a significant, but not independent impact on the risk of recurrence (p = 0.008).

CONCLUSIONS

Quantitative assessment of tumor-related transcript markers, particularly of CK20, may serve as a noninvasive method to identify patients with BCa. Moreover, SVV appears to be useful as a marker for a high risk of recurrence.

Prognostic impact of urokinase-type plasminogen activator system components in clear cell renal cell carcinoma patients without distant metastasis

Background

Members of the urokinase-type plasminogen activator (uPA) system including uPA, its receptor uPAR and the plasminogen activator inhibitor 1 (PAI-1) play an important role in tumour invasion and progression in a variety of tumour types. Since the majority of clear cell renal cell carcinoma (ccRCC) shows distant metastasis at time of diagnosis or later, the interplay of uPA, uPAR and PAI-1 might be of importance in this process determining the patients’ outcome.

Methods

Corresponding pairs of malignant and non-malignant renal tissue specimens were obtained from 112 ccRCC patients without distant metastasis who underwent tumour nephrectomy. Tissue extracts prepared from fresh-frozen tissue samples by detergent extraction were used for the determination of antigen levels of uPA, uPAR and PAI-1 by ELISA. Antigen levels were normalised to protein concentrations and expressed as ng per mg of total protein.

Results

Antigen levels of uPA, uPAR, and PAI-1 correlated with each other in the malignant tissue specimens (r_s=0.51-0.65; all P<0.001). Antigen levels of uPA system components were significantly higher in tissue extracts of non-organ confined tumours (pT3+4) compared to organ-confined tumours (pT1+2; all P<0.05). Significantly elevated levels of uPAR and PAI-1 were also observed in high grade ccRCC. When using median antigen levels as cut-off points, all three uPA system factors were significant predictors for disease-specific survival (DSS) in univariate Cox’s regression analyses. High levels of uPA and uPAR remained independent predictors for DSS with HR=2.86 (95% CI 1.07-7.67, P=0.037) and HR=4.70 (95% CI 1.51-14.6, P=0.008), respectively, in multivariate Cox’s regression analyses. A combination of high antigen levels of uPA and/or uPAR further improved the prediction of DSS in multivariate analysis (HR=14.5, 95% CI 1.88-111.1, P=0.010). Moreover, high uPA and/or uPAR levels defined a patient subgroup of high risk for tumour-related death in ccRCC patients with organ-confined disease (pT1+2) (HR=9.83, 95% CI 1.21-79.6, P=0.032).

Conclusions

High levels of uPA and uPAR in tumour tissue extracts are associated with a significantly shorter DSS of ccRCC patients without distant metastases.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2407-14-974) contains supplementary material, which is available to authorized users.

Abstract 39: Expression of uPA-system members correlate with the clinico-pathological parameters of PCa patients

Background: Members of the urokinase-type plasminogen activator (uPA) system play an important role in tumor progression and angiogenesis in different human malignancies including breast, kidney, colon, stomach and prostate cancer (PCa). The objective of this study was to determine the mRNA expression and protein levels of uPA system components in tissue specimens and serum samples, respectively, from patients with PCa, and to assess their potential association with clinic-pathological parameters and overall survival (OS).

Material and methods: mRNA levels of uPA, its receptor (uPAR) and its inhibitor type 1 (PAI-1) were analyzed in corresponding malignant and adjacent non-malignant prostate tissue specimens from 132 PCa patients. Relative mRNA expression levels were determined by quantitative PCR and normalized to the reference gene TATA-box-binding protein. Pre-operative serum samples from 81 of the 132 PCa patients and 36 patients with benign prostatic hyperplasia (BPH) were analyzed for antigen levels of uPA system members by ELISA.

Results: mRNA levels of the uPA system components displayed significant correlations with each other in the tumor tissues (uPA vs. uPAR: rs = 0.550; uPA vs. PAI-1: rs = 0.552; uPAR vs. PAI-1: rs = 0.643; all P &lt; 0.001). A significantly decreased uPA mRNA expression in PCa tissue compared to the corresponding non-malignant tissue specimens was detected (data not shown). High mRNA expression of uPA and PAI-1 was significantly associated with a high Gleason score (P = 0.001 and P = 0.007, respectively; Fig. 2). Antigen levels of uPA and soluble uPAR (suPAR) in serum correlated weakly, but significantly, with each other (rs = 0.382, P &lt; 0.001). A significant association was found between elevated suPAR concentrations in serum and poor OS of PCa patients (P = 0.022, log rank test). In multivariate Cox's regression analysis (adj. for age, lymph node status, tumor stage and Gleason sum) a high suPAR level was associated with a 7.12-fold increased risk of death (P=0.027).

Conclusion: The observed association of high suPAR levels with poor survival of PCa patients is consistent with published data on patients afflicted with other types of solid cancer and strongly suggests a general prognostic impact of uPAR antigen levels in serum of cancer patients.

Citation Format: Omar Al-Janabi, Helge Taubert, Andrea Lohse-Fischer, Michael Fröhner, Sven Wach, Robert Stöhr, Bastian Keck, Max Burger, Wolf Wieland, Kati Erdmann, Manfred P. Wirth, Bernd Wullich, Gustavo Baretton, Viktor Magdolen, Matthias Kotzsch, Susanne Füssel. Expression of uPA-system members correlate with the clinico-pathological parameters of PCa patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 39. doi:10.1158/1538-7445.AM2014-39

Abstract 4683: Correlation of transcript levels of members of the urokinase-type plasminogen activator system with clinico-pathological parameters in prostate cancer

Background: Members of the urokinase-type plasminogen activator (uPA) system play an important role in tumor progression and angiogenesis in different human malignancies including breast, kidney, colon, stomach and prostate cancer (PCa). Aim of the study was to characterize mRNA expression levels of members of the uPA system in tissue specimens from primary PCa and their potential association with clinico-pathological parameters.

Methods: Transcript levels of members of the uPA system, i.e., uPA, uPA receptor (uPAR) and plasminogen activator inhibitor type 1 (PAI-1) were analyzed in a cohort of 132 corresponding pairs of malignant and adjacent non-malignant prostate tissue samples. Relative gene expression levels were determined by quantitative PCR (qPCR) and normalized to the reference gene TATA-box-binding protein (TBP). Potential correlations between the three markers themselves and the clinico-pathological parameters were assessed by Spearman's Rho test and by Fisher's exact test.

Results: There were no significant differences in expression levels of uPA system genes between the corresponding malignant and non-malignant tissue specimens. Transcript levels of all members of the uPA system displayed a significant correlation with each other in the tumor tissues. At stratifying uPA, uPAR and PAI-1 expression levels by the median a significant correlation between an elevated expression of uPA and PAI-1 was correlated with higher Gleason score (P = 0.001 and P = 0.007). In addition, a significant positive correlation between uPAR transcript levels and tumor stage was detected (P = 0.025).

Conclusion: Our results demonstrate that mRNA expression levels of members of the uPA system correlated with each other and with clinico-pathological parameters. We suggest that transcript levels of uPA system members can be helpful markers for the study of tumor behavior of prostate cancer.

Citation Format: Omar Al-Janabi, Helge Taubert, Sven Wach, Robert Stöhr, Maximilian Burger, Wolf Ferdinand Wieland, Andrea Lohse-Fischer, Michael Fröhner, Manfred P. Wirth, Bernd Wullich, Viktor Magdolen, Matthias Kotzsch, Susanne Fuessel. Correlation of transcript levels of members of the urokinase-type plasminogen activator system with clinico-pathological parameters in prostate cancer . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4683. doi:10.1158/1538-7445.AM2013-4683