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https://www.readbyqxmd.com/read/28338654/tfeb-vegfa-6p21-1-co-amplified-renal-cell-carcinoma-a-distinct-entity-with-potential-implications-for-clinical-management
#1
Sounak Gupta, Sarah H Johnson, George Vasmatzis, Binu Porath, Jeannette G Rustin, Priya Rao, Brian A Costello, Bradley C Leibovich, R Houston Thompson, John C Cheville, William R Sukov
A subset of renal cell carcinomas shows TFEB overexpression secondary to MALAT1-TFEB gene fusion. As alternate mechanisms of TFEB overexpression are likely to have the same effect, we sought to determine the frequency of amplification of TFEB and the adjacent VEGFA gene at 6p21.1. As patients with metastatic renal cell carcinomas are managed with anti-VEGF therapies, we retrospectively assessed therapeutic response in patients with amplified tumors. Amplification status was analyzed for 875 renal cell carcinomas from our institution, a consultative case and 794 cases from The Cancer Genome Atlas...
March 24, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28338236/hsa-mir-3199-2-and-hsa-mir-1293-as-novel-prognostic-biomarkers-of-papillary-renal-cell-carcinoma-by-cox-ratio-risk-regression-model-screening
#2
Wen Luo, Lei Wang, Mao-Hua Luo, Yu-Zhu Huang, Hua Yang, Yu Zhou, Hong-Tao Jia, Xiu-Xin Wang
Papillary renal cell carcinoma(PRCC) is the second most common and aggressive renal cell carcinoma. Identification of novel microRNA biomarkers could be beneficial for the diagnosis and prognosis of PRCCpatients.We aimed to screen differentially expressed miRNAs that can act as prognostic factors and to predict the survival of PRCC patients. High-throughput data of miRNAs of 274 PRCC samples were downloaded from TCGA(The Cancer Genome Atlas) dataset and interested miRNAs were identified. Hierarchical clustering and principal component analysis (PCA) were performed on these miRNAs...
March 24, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28266251/an-integrated-analysis-of-cancer-genes-in-clear-cell-renal-cell-carcinoma
#3
Jin Li, Liping Guo, Zisheng Ai
AIM: This study was performed to detect driver genes and implement integrated analyses on these drivers in clear cell renal cell carcinoma (ccRCC). METHODS: Driver genes and pathways were predicted by OncodriveFM and Dendrix using 39,636 somatic mutations from The Cancer Genome Atlas, followed by DNA methylation, copy number variation, differential expression and survival analyses. RESULTS: Overall, 342 driver genes and 106 pathways were determined by OncodriveFM, two driver genes by Dendrix...
April 2017: Future Oncology
https://www.readbyqxmd.com/read/28260718/loss-of-setd2-but-not-h3k36me3-correlates-with-aggressive-clinicopathological-features-of-clear-cell-renal-cell-carcinoma-patients
#4
Lei Liu, Renbo Guo, Xiang Zhang, Yiran Liang, Feng Kong, Jue Wang, Zhonghua Xu
Recent studies facilitated by DNA sequencing identified the histone modifying gene SETD2 as the second most frequent mutant gene in sporadic clear cell renal cell carcinoma (ccRCC) patients. SETD2 functions as a tumor suppressor in ccRCC. However, its clinical association and biological functions are not fully delineated. The aim of this study is to evaluate the clinical significance of SETD2 in ccRCC patients. SETD2 and its canonical histone modification product H3K36me3 were analyzed by immunohistochemistry (IHC) in 155 ccRCC patients from two independent cohorts retrospectively...
March 6, 2017: Bioscience Trends
https://www.readbyqxmd.com/read/28260099/identification-of-prognostic-genes-in-kidney-renal-clear-cell-carcinoma-by-rna%C3%A2-seq-data-analysis
#5
Yanqin Gu, Linfeng Lu, Lingfeng Wu, Hao Chen, Wei Zhu, Yi He
The present study aimed to analyze RNA-seq data of kidney renal clear cell carcinoma (KIRC) to identify prognostic genes. RNA‑seq data were downloaded from The Cancer Genome Atlas. Feature genes with a coefficient of variation (CV) >0.5 were selected using the genefilter package in R. Gene co‑expression networks were constructed with the WGCNA package. Cox regression analysis was performed using the survive package. Furthermore, a functional enrichment analysis was conducted using Database for Annotation, Visualization and Integrated Discovery tools...
February 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28257806/pseudohypoxia-induced-by-mir-126-deactivation-promotes-migration-and-therapeutic-resistance-in-renal-cell-carcinoma
#6
Weijun Liu, Hanxiang Chen, Nathan Wong, Wesley Haynes, Callie M Baker, Xiaowei Wang
Pseudohypoxia plays a central role in the progression and therapeutic resistance of clear cell renal cell carcinoma (ccRCC); however, the underlying mechanisms are poorly understood. MicroRNA miR-126 has decreased expression in metastatic or relapsed ccRCC as compared to primary tumors, but the mechanisms by which miR-126 is implicated in RCC remain unknown. Through RNA-seq profiling to evaluate the impact of overexpression or CRISPR knockout of miR-126, we have identified SERPINE1 as a miR-126-5p target regulating cell motility, and SLC7A5 as a miR-126-3p target regulating the mTOR/HIF pathway...
February 28, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28252459/renal-cell-carcinoma-molecular-characterization-and-evolving-treatment-paradigms
#7
Mark W Ball, Eric A Singer, Ramaprasad Srinivasan
PURPOSE OF REVIEW: The treatment landscape of advanced renal cell carcinoma (RCC) continues to shift as both new targeted therapies and immunotherapies show efficacy in treating the disease. Contemporary insights into the molecular characterization of RCC are likely to fuel the development of additional therapies. This review summarizes recent advancements in the biologic characterization of RCC and discusses newly approved therapies and ongoing studies in the treatment of advanced RCC...
March 1, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28236887/ajkd-atlas-of-renal-pathology-nephrocalcinosis-and-acute-phosphate-nephropathy
#8
Agnes B Fogo, Mark A Lusco, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
March 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28236886/ajkd-atlas-of-renal-pathology-2-8-dihydroxyadeninuria
#9
Mark A Lusco, Agnes B Fogo, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
March 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28236885/ajkd-atlas-of-renal-pathology-oxalosis
#10
Agnes B Fogo, Mark A Lusco, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
March 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28152509/microrna-210-3p-depletion-by-crispr-cas9-promoted-tumorigenesis-through-revival-of-twist1-in-renal-cell-carcinoma
#11
Hirofumi Yoshino, Masaya Yonemori, Kazutaka Miyamoto, Syuichi Tatarano, Satoshi Kofuji, Nijiro Nohata, Masayuki Nakagawa, Hideki Enokida
Previous studies showed that five miRNAs (miR-885-5p, miR-1274, miR-210-3p, miR-224 and miR-1290) were upregulated the most in clear cell renal cell carcinoma (ccRCC). Our focus was to understand from a clinical standpoint the functional consequences of upregulating miR-210-3p. Towards this, we utilized the CRISPR/Cas9 gene editing system to deplete miR-210-3p in RCC cell lines (786-o, A498 and Caki2) and characterized the outcomes. We observed that miR-210-3p depletion dramatically increased tumorigenesis, including altering the morphology of A498 and Caki2 cells in a manner characteristic of epithelial-mesenchymal transition (EMT)...
February 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28115067/ajkd-atlas-of-renal-pathology-bile-nephrosis
#12
Mark A Lusco, Agnes B Fogo, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
February 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28115066/ajkd-atlas-of-renal-pathology-myoglobin-cast-nephropathy
#13
Behzad Najafian, Agnes B Fogo, Mark A Lusco, Charles E Alpers
No abstract text is available yet for this article.
February 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28115065/ajkd-atlas-of-renal-pathology-osmotic-tubular-injury
#14
Agnes B Fogo, Mark A Lusco, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
February 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28109319/for-robust-big-data-analyses-a-collection-of-150-important-pro-metastatic-genes
#15
REVIEW
Yan Mei, Jun-Ping Yang, Chao-Nan Qian
Metastasis is the greatest contributor to cancer-related death. In the era of precision medicine, it is essential to predict and to prevent the spread of cancer cells to significantly improve patient survival. Thanks to the application of a variety of high-throughput technologies, accumulating big data enables researchers and clinicians to identify aggressive tumors as well as patients with a high risk of cancer metastasis. However, there have been few large-scale gene collection studies to enable metastasis-related analyses...
January 21, 2017: Chinese Journal of Cancer
https://www.readbyqxmd.com/read/28108243/tpx2-as-a-prognostic-indicator-and-potential-therapeutic-target-in-clear-cell-renal-cell-carcinoma
#16
Zachary A Glaser, Harold D Love, Shunhua Guo, Lan Gellert, Sam S Chang, Stanley Duke Herrell, Daniel A Barocas, David F Penson, Michael S Cookson, Peter E Clark
OBJECTIVES: Our aims were to determine if targeting protein for Xklp2 (TPX2) is correlated with clear cell renal cell carcinoma (ccRCC) histology and oncologic outcomes using The Cancer Genome Atlas (TCGA) and an institutional tissue microarray (TMA). METHODS: Clinicopathological data obtained from the TCGA consisted of 415 samples diagnosed with ccRCC. A TMA was constructed from tumors of 207 patients who underwent radical nephrectomy for ccRCC. TPX2 expression by immunohistochemistry on TMA was assessed by a genitourinary pathologist...
January 17, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28063846/systematic-expression-analysis-of-mitochondrial-complex-i-identifies-ndufs1-as-a-biomarker-in-clear-cell-renal-cell-carcinoma
#17
Jörg Ellinger, Mirjam Poss, Maria Brüggemann, Arabella Gromes, Doris Schmidt, Nadja Ellinger, Yuri Tolkach, Dimo Dietrich, Glen Kristiansen, Stefan C Müller
INTRODUCTION: Mitochondrial dysfunction is common in cancer, and the mitochondrial electron transport chain is often affected in carcinogenesis. So far, little is known about the expression of the mitochondrial complex I (NADH:ubiquinone oxidoreductase) subunits in clear-cell renal-cell carcinoma (ccRCC). MATERIALS AND METHODS: An expression profile of the mitochondrial complex I subunits was determined using the NextBio database. Subsequently, the expression of selected subunits was experimentally validated on mRNA (quantitative real-time polymerase chain reaction) and protein (Western blot analysis, immunohistochemistry) level...
December 1, 2016: Clinical Genitourinary Cancer
https://www.readbyqxmd.com/read/28052770/a-systematic-search-strategy-identifies-cubilin-as-independent-prognostic-marker-for-renal-cell-carcinoma
#18
Gabriela Gremel, Dijana Djureinovic, Marjut Niinivirta, Alexander Laird, Oscar Ljungqvist, Henrik Johannesson, Julia Bergman, Per-Henrik Edqvist, Sanjay Navani, Naila Khan, Tushar Patil, Åsa Sivertsson, Mathias Uhlén, David J Harrison, Gustav J Ullenhag, Grant D Stewart, Fredrik Pontén
BACKGROUND: There is an unmet clinical need for better prognostic and diagnostic tools for renal cell carcinoma (RCC). METHODS: Human Protein Atlas data resources, including the transcriptomes and proteomes of normal and malignant human tissues, were searched for RCC-specific proteins and cubilin (CUBN) identified as a candidate. Patient tissue representing various cancer types was constructed into a tissue microarray (n = 940) and immunohistochemistry used to investigate the specificity of CUBN expression in RCC as compared to other cancers...
January 4, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28048816/mo-de-207b-05-predicting-gene-mutations-in-renal-cell-carcinoma-based-on-ct-imaging-features-validation-using-tcga-tcia-datasets
#19
X Chen, Z Zhou, K Thomas, J Wang
PURPOSE: The goal of this work is to investigate the use of contrast enhanced computed tomographic (CT) features for the prediction of mutations of BAP1, PBRM1, and VHL genes in renal cell carcinoma (RCC). METHODS: For this study, we used two patient databases with renal cell carcinoma (RCC). The first one consisted of 33 patients from our institution (UT Southwestern Medical Center, UTSW). The second one consisted of 24 patients from the Cancer Imaging Archive (TCIA), where each patient is connected by a unique identi?er to the tissue samples from the Cancer Genome Atlas (TCGA)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28029655/identifying-prognostic-biomarkers-based-on-aberrant-dna-methylation-in-kidney-renal-clear-cell-carcinoma
#20
Guang Chen, Yihan Wang, Lu Wang, Wanhai Xu
The outcome of kidney renal clear cell carcinoma (KIRC) differs even among individuals with similar clinical characteristics. DNA methylation is regarded as a regulator of gene expression in cancers, which may be a molecular marker of prognosis. In this study, we aimed to mine novel methylation markers of the prognosis of KIRC. We revealed a total of 2793 genes differentially methylated in their promoter regions (DMGs) and 2979 differentially expressed genes (DEGs) in KIRC tissues compared with normal tissues using The Cancer Genome Atlas datasets...
December 24, 2016: Oncotarget
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