The value of a comprehensive primary outcome - results of a negative randomized control trial in the non-muscle invasive bladder cancer population.

INTRODUCTION American Urological Association (AUA) guidelines recommend intravesical chemotherapy to be given following transurethral resection of a bladder tumor. Prior studies have shown the benefit of mitomycin as well as gemcitabine. However, no study has compared the two agents. MATERIALS AND METHODS: The study was designed as an open label 1:1:1 randomized controlled trial, comparing intravesical mitomycin, gemcitabine and saline as a single intraoperative instillation immediately following transurethral resection of suspected bladder tumor. Primary endpoint was any grade ≥ 3 events according to NCI CTCAE Version 4.03, this captures any return trip to the operating room for recurrence of cancer or other event (benign bladder/urethra). Secondary endpoints were progression free survival for urothelial cell carcinoma and adverse events. RESULTS: A total of 82 patients were enrolled and randomized, unfortunately the trial was suspended early due to protocol deviations. In an intention to treat analysis, freedom from grade > 3 events at 2 years was 74.8% in the no treatment arm, 51.0% in the mitomycin arm, and 56.0% in the gemcitabine arm (p = 0.81). Freedom from cancer recurrence for all patients was 62.3%. In the no treatment arm, it was 78.8%, and 50.7% and 63.6% in the mitomycin arm and gemcitabine arm respectively. (p = 0.28). In a univariate analysis, the only patient variable significantly associated with the primary outcome was pathologic T stage (p < 0.002). CONCLUSION: This study provides an example of a novel, patient centered primary outcome with the goal of determining which treatment paradigms provide the greatest oncologic and clinic benefit.

Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) has been previously classified into putative discrete prognostic subtypes by gene expression profiling. To investigate the robustness of these proposed subtype classifications, we evaluated 12 public datasets, together with a new dataset of 265 ccRCC gene expression profiles. Consensus clustering showed unstable subtype and principal component analysis (PCA) showed a continuous spectrum both within and between datasets. Considering the lack of discrete delineation and continuous spectrum observed, we developed a continuous quantitative prognosis score (Continuous Linear Enhanced Assessment of RCC, or CLEAR score). Prognostic performance was evaluated in independent cohorts from The Cancer Genome Atlas (TCGA) (n = 414) and EMBL-EBI (n = 53), CLEAR score demonstrated both superior prognostic estimates and inverse correlation with anti-angiogenic tyrosine-kinase inhibition in comparison to previously proposed discrete subtyping classifications. Inverse correlation with high-dose interleukin-2 outcomes was also observed for the CLEAR score. Multiple somatic mutations (VHL, PBRM1, SETD2, KDM5C, TP53, BAP1, PTEN, MTOR) were associated with the CLEAR score. Application of the CLEAR score to independent expression profiling of intratumoral ccRCC regions demonstrated that average intertumoral heterogeneity exceeded intratumoral expression heterogeneity. Wider investigation of cancer biology using continuous approaches may yield insights into tumor heterogeneity; single cell analysis may provide a key foundation for this approach.

Prevalence of Proteinuria and Other Abnormalities in Urinalysis Performed in the Urology Clinic.

OBJECTIVE: To compare the prevalence of proteinuria in the urology clinic with other outpatient settings. Chronic kidney disease is classified according to cause, glomerular filtration rate, and proteinuria. Proteinuria may be more prevalent in patients with known chronic kidney disease, renal disorders (benign or malignant), or after urologic surgery. METHODS: A cross-sectional study of 3 populations undergoing urinalysis (UA) testing was carried out: general outpatients (n = 20,334), urology outpatients (n = 5023), and kidney cancer patients (n = 1016). Proteinuria was classified under Kidney Disease: Improving Global Outcomes guidelines: A1 (<30 mg), A2 (30-300 mg), and A3 (>300 mg). RESULTS: Proteinuria was detected throughout a community-based health system in 8.6% of UA (8.2%: A2; 0.4%: A3). In comparison, 18.6% of urology office-performed UA had proteinuria (16.0%: A2, 2.5%: A3) (P < .0001 vs non-urology). Kidney cancer patients were more likely to have proteinuria (17.9%: A2, 3.8%: A3). The proportion with A3 was significantly higher in urology and kidney cancer patients when compared with other outpatients (each P < .0001), and in the kidney cancer subgroup compared with all urology patients (P < .0001). Additional abnormalities were frequently present on microscopic analysis of UA in the urology clinic, including hematuria (20.9%), pyuria (21.8%), and bacteriuria (3.1%). CONCLUSION: The value of UA in the urology clinic as a screening test for proteinuria and other conditions appears high, with >56% having at least 1 abnormality. The population risk of proteinuria in the urology clinic is 18.5%, which is higher than that observed in non-urology clinics. Patients with kidney cancer appear more likely to have proteinuria than the average urology patient. We recommend evaluation of urology patients with UA to identify proteinuria.

Randomized trial finds that prostate cancer genetic risk score feedback targets prostate-specific antigen screening among at-risk men.

BACKGROUND: Prostate-specific antigen (PSA) screening may reduce death due to prostate cancer but leads to the overdiagnosis of many cases of indolent cancer. Targeted use of PSA screening may reduce overdiagnosis. Multimarker genomic testing shows promise for risk assessment and could be used to target PSA screening. METHODS: To test whether counseling based on the family history (FH) and counseling based on a genetic risk score (GRS) plus FH would differentially affect subsequent PSA screening at 3 months (primary outcome), a randomized trial of FH versus GRS plus FH was conducted with 700 whites aged 40 to 49 years without prior PSA screening. Secondary outcomes included anxiety, recall, physician discussion at 3 months, and PSA screening at 3 years. Pictographs versus numeric presentations of genetic risk were also evaluated. RESULTS: At 3 months, no significant differences were observed in the rates of PSA screening between the FH arm (2.1%) and the GRS-FH arm (4.5% with GRS-FH vs. 2.1% with FH: χ2 = 3.13, P = .077); however, PSA screening rates at 3 months significantly increased with given risk in the GRS-FH arm (P = .013). Similar results were observed for discussions with physicians at 3 months and PSA screening at 3 years. Average anxiety levels decreased after the individual cancer risk was provided (P = .0007), with no differences between groups. Visual presentation by pictographs did not significantly alter comprehension or anxiety. CONCLUSIONS: This is likely the first randomized trial of multimarker genomic testing to report genomic targeting of cancer screening. This study found little evidence of concern about excess anxiety or overuse/underuse of PSA screening when multimarker genetic risks were provided to patients. Cancer 2016;122:3564-3575. © 2016 American Cancer Society.

Critical appraisal of first-generation renal tumor complexity scoring systems: Creation of a second-generation model of tumor complexity.

OBJECTIVE: To investigate whether a combination of variables from each nephrometry system improves performance. There are 3 first-generation systems that quantify tumor complexity: R.E.N.A.L. nephrometry score (RNS), preoperative aspects and dimensions used for an anatomical (PADUA) classification (PC), and centrality index (CI). Although each has been subjected to validation and comparative analysis, to our knowledge, no work has been done to combine variables from each method to optimize their performance. PATIENTS AND METHODS: Scores were assigned to each of 276 patients undergoing partial nephrectomy (PN) or radical nephrectomy (RN). Individual components of all 3 systems were evaluated in multivariable logistic regression analysis of surgery type (PN vs. RN) and combined into a "second-generation model." RESULTS: In multivariable analysis, each scoring system was a significant predictor of PN vs. RN (P<0.0001). Of the first-generation systems, CI was most highly correlated with surgery type (area under the curve [AUC] = 0.91), followed by RNS (AUC = 0.90) and PC (AUC = 0.88). Each individual component of these scoring systems was also a predictor of surgery type (P<0.0001). In a multivariable model incorporating each component individually, 4 were independent predictors of surgery type (each P<0.005): tumor size (RNS and PC), nearness to the collecting system (RNS), location along the lateral rim (PC), and centrality (CI). A novel model in which these 4 variables were rescaled outperformed each first-generation system (AUC = 0.91). CONCLUSIONS: Optimization of first-generation models of renal tumor complexity results in a novel scoring system, which strongly predicts surgery type. This second-generation model should aid comprehension, but future work is still needed to establish the most clinically useful model.

Exome-wide Sequencing Shows Low Mutation Rates and Identifies Novel Mutated Genes in Seminomas.

BACKGROUND: Testicular germ cell tumors are the most common cancer diagnosed in young men, and seminomas are the most common type of these cancers. There have been no exome-wide examinations of genes mutated in seminomas or of overall rates of nonsilent somatic mutations in these tumors. OBJECTIVE: The objective was to analyze somatic mutations in seminomas to determine which genes are affected and to determine rates of nonsilent mutations. DESIGN, SETTING, AND PARTICIPANTS: Eight seminomas and matched normal samples were surgically obtained from eight patients. INTERVENTION: DNA was extracted from tissue samples and exome sequenced on massively parallel Illumina DNA sequencers. Single-nucleotide polymorphism chip-based copy number analysis was also performed to assess copy number alterations. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The DNA sequencing read data were analyzed to detect somatic mutations including single-nucleotide substitutions and short insertions and deletions. The detected mutations were validated by independent sequencing and further checked for subclonality. RESULTS AND LIMITATIONS: The rate of nonsynonymous somatic mutations averaged 0.31 mutations/Mb. We detected nonsilent somatic mutations in 96 genes that were not previously known to be mutated in seminomas, of which some may be driver mutations. Many of the mutations appear to have been present in subclonal populations. In addition, two genes, KIT and KRAS, were affected in two tumors each with mutations that were previously observed in other cancers and are presumably oncogenic. CONCLUSIONS: Our study, the first report on exome sequencing of seminomas, detected somatic mutations in 96 new genes, several of which may be targetable drivers. Furthermore, our results show that seminoma mutation rates are five times higher than previously thought, but are nevertheless low compared to other common cancers. Similar low rates are seen in other cancers that also have excellent rates of remission achieved with chemotherapy. PATIENT SUMMARY: We examined the DNA sequences of seminomas, the most common type of testicular germ cell cancer. Our study identified 96 new genes in which mutations occurred during seminoma development, some of which might contribute to cancer development or progression. The study also showed that the rates of DNA mutations during seminoma development are higher than previously thought, but still lower than for other common solid-organ cancers. Such low rates are also observed among other cancers that, like seminomas, show excellent rates of disease remission after chemotherapy.

Surgeon assessment of renal preservation with partial nephrectomy provides information comparable to measurement of volume preservation with 3-dimensional image analysis.

PURPOSE: The strongest predictors of renal function after partial nephrectomy are the preoperative glomerular filtration rate and the amount of preserved parenchyma. Measuring volume preservation by 3-dimensional imaging is accurate but time-consuming. Percent functional volume preservation was designed to replace surgeon assessment of volume preservation with a less labor intensive, objective assessment. We compared volume preservation with 3-dimensional imaging, percent functional volume preservation and surgeon assessment of volume preservation as predictors of renal function after partial nephrectomy. MATERIALS AND METHODS: We calculated volume preservation with 3-dimensional imaging, percent functional volume preservation and surgeon assessment of volume preservation in 41 patients with preoperative and postoperative cross-sectional imaging available. Surgeon assessment was validated internally in another 75 patients. Short-term and long-term renal function was assessed with univariate and multivariate linear regression models. RESULTS: Median parenchymal preservation was 85% (range 37% to 105%) by 3-dimensional imaging, 91% (range 51% to 114%) by percent functional preservation and 88% (range 45% to 99%) by surgeon assessment. Each method strongly correlated with nadir glomerular filtration rate (r(2) = 0.75, 0.65 and 0.78) and latest glomerular filtration rate (r(2) = 0.65, 0.66 and 0.67, respectively, each p <0.0001). Univariate analysis revealed that age, preoperative glomerular filtration rate, renal nephrometry score and each assessment were significant predictors of renal function (p <0.05). On multivariate analysis parenchymal preservation was the strongest predictor (p <0.0001). Models using volume preservation with 3-dimensional imaging, percent functional volume preservation and surgeon assessment of volume preservation were statistically similar in the ability to predict the nadir and latest glomerular filtration rates. In an additional validation cohort surgeon assessment remained strongly correlated with nadir glomerular filtration rate (r(2) = 0.74) and latest glomerular filtration rate (r(2) = 0.73, each p <0.0001). CONCLUSIONS: Surgeon assessment of volume preservation provides a reliable estimate of renal functional preservation with characteristics comparable to those of more time intensive alternatives. We propose that surgeon assessment of volume preservation should be routinely reported to facilitate analysis of partial nephrectomy outcomes.

CUL3 and NRF2 mutations confer an NRF2 activation phenotype in a sporadic form of papillary renal cell carcinoma.

Sustained activation of the stress-regulated transcription factor NRF2 (NFE2L2) is a prominent feature of many types of cancer, implying that mutations driving NRF2 may be important to tumor progression. In hereditary type 2 papillary renal cell carcinoma (PRCC2, also known as hereditary leiomyomatosis and renal cell cancer), NRF2 activation is a direct consequence of the accumulation of intracellular fumarate, a result of fumarate hydratase (FH) inactivation, but it is not clear how NRF2 may be activated in sporadic forms of PRCC2. Here we show that somatic mutations in NRF2, CUL3, and SIRT1 are responsible for driving the NRF2 activation phenotype in sporadic PRCC2. Transcriptome sequencing revealed the expression pattern of mutant alleles of NRF2, CUL3, and SIRT1 and also confirmed NRF2 activation in clinical specimens. Our results show a convergence in somatic mutations in sporadic PRCC2 with FH mutation in hereditary PRCC2.

Differential use of partial nephrectomy for intermediate and high complexity tumors may explain variability in reported utilization rates.

PURPOSE: Partial nephrectomy has become a reference standard for tumors amenable to a kidney sparing approach but reported utilization rates vary widely. The R.E.N.A.L. (radius, exophytic/endophytic, nearness of tumor to collecting system or sinus, anterior/posterior, location relative to polar lines and hilar tumor touching main renal artery or vein) nephrometry score was developed to standardize the reporting of tumor complexity with applicability in academic and community based settings. We hypothesized that tumor and surgeon factors account for variable use of partial nephrectomy. MATERIALS AND METHODS: Clinical and R.E.N.A.L. nephrometry score data were analyzed on 1,433 cases performed between 2004 and 2011 by a total of 19 surgeons with varying partial nephrectomy utilization rates (0% to 100%) who practiced at a total of 2 academic centers and 1 community based health system. RESULTS: Partial nephrectomy use increased during the study period from 36% before 2007 to 73% for 2010 to 2012 (p <0.0001). Increasing proportions of intermediate and high R.E.N.A.L. nephrometry score tumors were treated with partial nephrectomy during this time (35% to 86% and 11% to 36%, respectively, p <0.0001). Partial nephrectomy use was stable for low complexity tumors at 91% overall. Individual surgeons performed partial nephrectomy for 0% to 100% of intermediate complexity and 0% to 45% of high complexity tumors. On multivariable analysis surgery year, tumor size, each R.E.N.A.L. nephrometry score component, surgeon and annual surgeon volume predicted partial vs radical nephrectomy (each p <0.05). On multivariable analysis several surgeon factors, including surgeon volume, setting, fellowship training, and proportional use of minimally invasive and robotic partial nephrectomy, were associated with higher partial nephrectomy use (each p <0.002). CONCLUSIONS: Surgeon and tumor factors contribute significantly to the choice of partial nephrectomy. The significant variation in partial nephrectomy use by individual surgeons appears to be caused by differential treatment for intermediate and high complexity tumors. This may be due to surgical volume, training, setting and the use of minimally invasive techniques.

Expression of the PTTG1 oncogene is associated with aggressive clear cell renal cell carcinoma.

The pituitary tumor transforming gene (PTTG1) is a recently discovered oncogene implicated in malignant progression of both endocrine and nonendocrine malignancies. Clear cell renal cell carcinoma (ccRCC) is cytogenetically characterized by chromosome 3p deletions that harbor the ccRCC-related von Hippel-Lindau, PBRM1, BAP1, and SETD2 tumor suppressor genes, along with chromosome 5q amplifications where the significance has been unclear. PTTG1 localizes to the chromosome 5q region where amplifications occur in ccRCC. In this study, we report a functional role for PTTG1 in ccRCC tumorigenesis. PTTG1 was amplified in ccRCC, overexpressed in tumor tissue, and associated with high-grade tumor cells and poor patient prognosis. In preclinical models, PTTG1 ablation reduced tumorigenesis and invasion. An analysis of gene expression affected by PTTG1 indicated an association with invasive and metastatic disease. PTTG1-dependent expression of the RhoGEF proto-oncogene ECT2 was observed in a number of ccRCC cell lines. Moreover, ECT2 expression correlated with PTTG1 expression and poor clinical features. Together, our findings reveal features of PTTG1 that are consistent with its identification of an oncogene amplified on chromsome 5q in ccRCC, where it may offer a novel therapeutic target of pathologic significance in this disease.

RENAL nephrometry score predicts surgery type independent of individual surgeon's use of nephron-sparing surgery.

OBJECTIVE: To evaluate whether surgeon factors, such as training and experience, have a strong impact on selection of surgical approach for treating renal cancers. Nephron-sparing surgery (NSS) has become the reference standard for tumors that are amenable to such an approach. Tumor size and configuration are important predictors of usage of NSS. The RENAL nephrometry score (RNS) has been developed to standardize reporting of tumor complexity, but the performance of this method within individual surgeons' practices, particularly in the community-based setting, has not been evaluated previously. METHODS: Clinical data and RNS were collected retrospectively for 300 cases performed by 5 different surgeons with varying NSS usage rates (31-74%). RESULTS: Mean RNS for patients undergoing NSS (6.0) and radical nephrectomy (RN) (9.3) differed significantly (P <.0001), as did tumor size (2.8 vs 6.3 cm, P <.0001). RNS was a better predictor of surgery type (R(2) = .55) than was tumor size (R(2) = .43) for all 5 surgeons. In univariable analysis, individual surgeon, surgery year, glomerular filtration rate, tumor size, RNS, and each RNS component predicted NSS vs RN (each P <.05). In multivariable analysis, surgeon, tumor size, exophytic amount, and nearness to collecting system were independent predictors of NSS usage (P <.001). CONCLUSION: Despite significant variation in NSS usage by individual surgeons at a community-based health system, RNS appears to be valid for both low and high usage. With increasing usage of NSS worldwide, RNS appears to reflect current patterns and may inform future practice for surgeons of all backgrounds.

Increasing use of kidney sparing approaches for localized renal tumors in a community based health system: impact on renal functional outcomes.

PURPOSE: The use of partial nephrectomy and other kidney sparing approaches in national databases lags far behind practice patterns at major academic centers. The reasons and impact of this disparity are largely unknown. We examined the trend in kidney sparing approaches in a community based health care system to examine associated factors and impact on renal function. MATERIALS AND METHODS: We evaluated the records of all patients who underwent intervention for suspicious renal lesions at a single health care system between 1998 and 2010. Demographic, pathological and functional data were collected in an institutional review board approved database. RESULTS: During the 12 study years a kidney sparing approach was used in 35% of patients with localized renal tumors. A clear increase in the proportion of patients undergoing a kidney sparing approach was observed, including 11%, 23% and 49% during successive 4-year periods. A kidney sparing approach was used in 81% of patients with tumors 4 cm or less during 2009 to 2010. Although high volume (greater than 20 cases annually), more recently graduating (2001 or later) and fellowship trained surgeons had higher kidney sparing approach use overall (each p <0.03), the proportion of patients who underwent a kidney sparing approach increased with time in all study groups (p <0.0001). The renal functional loss in patients who underwent a kidney sparing approach and radical nephrectomy was 2% and 30%, respectively (p <0.001). CONCLUSIONS: The kidney sparing approach rate in a community based health care system can approach rates at major academic centers. This practice pattern appears related to the addition of recent graduates and urological oncologists but also to a change in long-standing practice patterns of other community urologists. These data suggest that the use of kidney sparing approaches nationwide and the associated renal functional benefits may continue to increase.

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.

The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ∼3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (also known as KDM6A), JARID1C (also known as KDM5C) and SETD2 (ref. 2). These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodelling complex gene PBRM1 (ref. 4) as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes.

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.

Interleukin-8 mediates resistance to antiangiogenic agent sunitinib in renal cell carcinoma.

The broad spectrum kinase inhibitor sunitinib is a first-line therapy for advanced clear cell renal cell carcinoma (ccRCC), a deadly form of kidney cancer. Unfortunately, most patients develop sunitinib resistance and progressive disease after about 1 year of treatment. In this study, we evaluated the mechanisms of resistance to sunitinib to identify the potential tactics to overcome it. Xenograft models were generated that mimicked clinical resistance to sunitinib. Higher microvessel density was found in sunitinib-resistant tumors, indicating that an escape from antiangiogenesis occurred. Notably, escape coincided with increased secretion of interleukin-8 (IL-8) from tumors into the plasma, and coadministration of an IL-8 neutralizing antibody resensitized tumors to sunitinib treatment. In patients who were refractory to sunitinib treatment, IL-8 expression was elevated in ccRCC tumors, supporting the concept that IL-8 levels might predict clinical response to sunitinib. Our results reveal IL-8 as an important contributor to sunitinib resistance in ccRCC and a candidate therapeutic target to reverse acquired or intrinsic resistance to sunitinib in this malignancy.

Microarray gene expression profiling using core biopsies of renal neoplasia.

We investigate the feasibility of using microarray gene expression profiling technology to analyze core biopsies of renal tumors for classification of tumor histology. Core biopsies were obtained ex-vivo from 7 renal tumors-comprised of four histological subtypes-following radical nephrectomy using 18-gauge biopsy needles. RNA was isolated from these samples and, in the case of biopsy samples, amplified by in vitro transcription. Microarray analysis was then used to quantify the mRNA expression patterns in these samples relative to non-diseased renal tissue mRNA. Genes with significant variation across all non-biopsy tumor samples were identified, and the relationship between tumor and biopsy samples in terms of expression levels of these genes was then quantified in terms of Euclidean distance, and visualized by complete linkage clustering. Final pathologic assessment of kidney tumors demonstrated clear cell renal cell carcinoma (4), oncocytoma (1), angiomyolipoma (1) and adrenalcortical carcinoma (1). Five of the seven biopsy samples were most similar in terms of gene expression to the resected tumors from which they were derived in terms of Euclidean distance. All seven biopsies were assigned to the correct histological class by hierarchical clustering. We demonstrate the feasibility of gene expression profiling of core biopsies of renal tumors to classify tumor histology.

Activation of the PI3K/AKT pathway induces urothelial carcinoma of the renal pelvis: identification in human tumors and confirmation in animal models.

Urothelial carcinoma of the renal pelvis is a deadly disease with an unclear tumorigenic mechanism. We conducted gene expression profiling on a set of human tumors of this type and identified a phosphatidylinositol 3-kinase (PI3K)/AKT activation expression signature in 76.9% (n = 13) of our samples. Sequence analysis found both activating mutations of PIK3CA (13.6%, n = 22) and loss of heterozygosity at the PTEN locus (25%, n = 8). In contrast, none of the other subtypes of kidney neoplasms (e.g., clear-cell renal cell carcinoma) harbored PIK3CA mutations (n = 87; P < 0.001). Immunohistochemical analysis of urothelial carcinoma samples found loss of PTEN protein expression (36.4%, n = 11) and elevation of phosphorylated mammalian target of rapamycin (mTOR; 63.6%, n = 11). To confirm the role of the PI3K/AKT pathway in urothelial carcinoma, we generated mice containing biallelic inactivation of Pten in the urogenital epithelia. These mice developed typical renal pelvic urothelial carcinomas, with an incidence of 57.1% in mice older than 1 year. Laser capture microdissection followed by PCR confirmed the deletion of Pten exons 4 and 5 in the animal tumor cells. Immunohistochemical analyses showed increased phospho-mTOR and phospho-S6K levels in the animal tumors. Renal lymph node metastases were found in 15.8% of the animals with urothelial carcinoma. In conclusion, we identified and confirmed an important role for the PI3K/AKT pathway in the development of urothelial carcinoma and suggested that inhibitors of this pathway (e.g., mTOR inhibitor) may serve as effective therapeutic agents.

Somatic pairing of chromosome 19 in renal oncocytoma is associated with deregulated EGLN2-mediated [corrected] oxygen-sensing response.

Chromosomal abnormalities, such as structural and numerical abnormalities, are a common occurrence in cancer. The close association of homologous chromosomes during interphase, a phenomenon termed somatic chromosome pairing, has been observed in cancerous cells, but the functional consequences of somatic pairing have not been established. Gene expression profiling studies revealed that somatic pairing of chromosome 19 is a recurrent chromosomal abnormality in renal oncocytoma, a neoplasia of the adult kidney. Somatic pairing was associated with significant disruption of gene expression within the paired regions and resulted in the deregulation of the prolyl-hydroxylase EGLN2 [corrected] a key protein that regulates the oxygen-dependent degradation of hypoxia-inducible factor (HIF). Overexpression of EGLN2 [corrected] in renal oncocytoma increased ubiquitin-mediated destruction of HIF and concomitantly suppressed the expression of several HIF-target genes, including the pro-death BNIP3L gene. The transcriptional changes that are associated with somatic pairing of chromosome 19 mimic the transcriptional changes that occur following DNA amplification. Therefore, in addition to numerical and structural chromosomal abnormalities, alterations in chromosomal spatial dynamics should be considered as genomic events that are associated with tumorigenesis. The identification of EGLN2 as a significantly deregulated gene that maps within the paired chromosome region directly implicates defects in the oxygen-sensing network to the biology of renal oncocytoma.

Identification of copy number alterations and its association with pathological features in clear cell and papillary RCC.

We report and characterize the copy number alterations (CNAs) in 35 clear cell and 12 papillary renal cell carcinomas (RCC) using Affymetrix 100K SNP arrays. Novel gain and loss regions are identified in both subtypes. In addition, statistically significant CNA are detected and associated with the pathological features: VHL mutation status, tumor grades, and sarcomatoid component in clear cell RCC and in types 1 and 2 of papillary RCC. Florescence in situ hybridization confirmed the copy number gain in the transforming growth factor, beta-induced gene (TGFBI), which is a possible oncogene for clear cell RCC.

Detection of DNA copy number changes and oncogenic signaling abnormalities from gene expression data reveals MYC activation in high-grade papillary renal cell carcinoma.

Papillary renal cell carcinoma (RCC) represents 10% to 15% of adult renal neoplasms; however, the molecular genetic events that are associated with the development and progression of sporadic papillary RCC remain largely unclear. Papillary RCCs can be divided into two subtypes based on histologic, cytogenetic, and gene expression differences. Type 1 tumors ( approximately 60-70%) are generally low grade with favorable outcome, whereas type 2 tumors ( approximately 30-40%) are associated with increased cytogenetic complexity, high tumor grade, and poor prognosis. In this study, computational analysis of gene expression data derived from papillary RCC revealed that a transcriptional signature indicative of MYC pathway activation is present in high-grade type 2 papillary RCC. The MYC signature is associated with amplification of chromosome 8q and overexpression of MYC that maps to chromosome 8q24. The importance of MYC activation was confirmed by both pharmacologic and short interfering RNA-mediated inhibition of active Myc signaling in a cell line model of type 2 papillary RCC. These results provide both computational and genetic evidence that activation of Myc is associated with the aggressiveness of papillary type 2 RCC. Therefore, it will be useful to consider inhibition of components of the MYC signaling pathway as avenues for therapeutic intervention in high-grade papillary RCC.