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https://www.readbyqxmd.com/read/29158991/ndufa4l2-is-associated-with-clear-cell-renal-cell-carcinoma-malignancy-and-is-regulated-by-elk1
#1
Lei Wang, Zhiqiang Peng, Kaizhen Wang, Yijun Qi, Ying Yang, Yue Zhang, Xinyuan An, Shudong Luo, Junfang Zheng
Background: Clear cell renal cell carcinoma (ccRCC) is the most common and lethal cancer of the adult kidney. However, its pathogenesis has not been fully understood till now, which hinders the therapeutic development of ccRCC. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) was found to be upregulated and play an important role in ccRCC. We aimed to further investigate the underlying mechanisms by which NDUFA4L2 exerted function and its expression level was upregulated...
2017: PeerJ
https://www.readbyqxmd.com/read/29152119/a-genome-wide-comprehensively-analyses-of-long-noncoding-rna-profiling-and-metastasis-associated-lncrnas-in-renal-cell-carcinoma
#2
Xue Xu, Yongcan Xu, Chuanqin Shi, Baoyu Wang, Xiang Yu, Yanfen Zou, Tao Hu
Recently, a growing number of studies have indicated that long noncoding RNAs (lncRNAs) are emerging as new critical regulators of tumorigenesis and prognostic markers in multiple cancers. However, the expression pattern of lncRNAs and their contributions in renal cell carcinoma (RCC) remains poorly understood. In this study, we performed a genome-wide comprehensively analysis of lncRNAs profiling and clinical relevance to provide valuable lncRNA candidates for the further study in RCC. RCC and non-tumor tissues RNA sequencing data, and microarray data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), then, these data were annotated and analyzed to find dysregulated lncRNAs in RCC...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136101/identification-of-topological-features-in-renal-tumor-microenvironment-associated-with-patient-survival
#3
Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani, Qianjin Feng, Kun Huang
Motivation: As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However traditional qualitative and/or semi-quantitative parameters obtained by pathologist's visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29132830/characterizing-recurrent-and-lethal-small-renal-masses-in-clear-cell-renal-cell-carcinoma-using-recurrent-somatic-mutations
#4
Brandon J Manley, Ed Reznik, Mazyar Ghanaat, Mahyar Kashan, Maria F Becerra, Jozefina Casuscelli, Daniel Tennenbaum, Almedina Redzematovic, Maria I Carlo, Yusuke Sato, Maria Arcila, Martin H Voss, Darren R Feldman, Robert J Motzer, Paul Russo, Jonathan Coleman, James J Hsieh, Ari A Hakimi
INTRODUCTION: Small renal masses (SRMs) with evidence of clear cell renal cell carcinoma (ccRCC) are understudied. Current algorithms for the management of SRMs include surgical resection, ablation, and active surveillance. We sought to identify genomic biomarkers that could potentially refine the management of ccRCC in SRMs, especially in patients being evaluated for active surveillance. METHODS: We identified patients who had SRMs (4cm or less) at time of surgery, had sequencing performed on their primary tumor and had a diagnosis of ccRCC...
November 10, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/29113256/nudt-expression-is-predictive-of-prognosis-in-patients-with-clear-cell-renal-cell-carcinoma
#5
Yue Wang, Fangning Wan, Kun Chang, Xiaolin Lu, Bo Dai, Dingwei Ye
The nudix hydroxylase (NUDT) family of genes may have notable roles in cancer growth and metastasis. The present study aimed to determine the prognostic ability of NUDT genes in clear cell renal cell carcinoma (ccRCC). Data from 509 patients with ccRCC was obtained from The Cancer Genome Atlas (TCGA) database and 192 patient samples from Fudan University Shanghai Cancer Center (FUSCC) were analyzed in the present study. The expression profile of NUDT gene family members in the TCGA cohort was obtained from the TCGA RNA sequencing database...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29108259/copy-number-variations-and-expression-of-mpdz-are-prognostic-biomarkers-for-clear-cell-renal-cell-carcinoma
#6
Yong-Sheng Huang, Wen-Bin Liu, Fei Han, Jun-Tang Yang, Xiang-Lin Hao, Hong-Qiang Chen, Xiao Jiang, Li Yin, Lin Ao, Zhi-Hong Cui, Jia Cao, Jin-Yi Liu
The vital copy number variation (CNV) plays a crucial role in clear cell renal cell carcinoma (ccRCC). MPDZ inhibit cell polarity associate with osmotic pressure response and cancer-related biological processes. In order to clarify the role of the CNV of MPDZ in the progression of ccRCC, we analyzed the CNV and expression of MPDZ and prognosis in ccRCC patients from The Cancer Genome Atlas data portal. Notably, we found that the deletion of MPDZ was the common CNV, which was present in 28.65% of ccRCC patients...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29092949/integrative-analysis-of-histopathological-images-and-genomic-data-predicts-clear-cell-renal-cell-carcinoma-prognosis
#7
Jun Cheng, Jie Zhang, Yatong Han, Xusheng Wang, Xiufen Ye, Yuebo Meng, Anil Parwani, Zhi Han, Qianjin Feng, Kun Huang
In cancer, both histopathologic images and genomic signatures are used for diagnosis, prognosis, and subtyping. However, combining histopathologic images with genomic data for predicting prognosis, as well as the relationships between them, has rarely been explored. In this study, we present an integrative genomics framework for constructing a prognostic model for clear cell renal cell carcinoma. We used patient data from The Cancer Genome Atlas (n = 410), extracting hundreds of cellular morphologic features from digitized whole-slide images and eigengenes from functional genomics data to predict patient outcome...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29080693/s100a12-in-renal-and-cardiovascular-diseases
#8
REVIEW
Alireza Nazari, Hossein Khorramdelazad, Gholamhossein Hassanshahi, Andrew S Day, Atlas Mashayekhi Sardoo, Elnaz Tahmooresi Fard, Mehdi Abedinzadeh, Ali Esmaeili Nadimi
Expression of S100A12, a small calcium-binding protein, by neutrophils and monocytes/macrophages induces proinflammatory responses via ligation with the receptor for advanced glycation end-products (RAGE) and subsequent activation of intracellular signal transduction pathways such as the nuclear factor (NF)-κB pathway. Although S100A12 has been demonstrated to be a useful biomarker during inflammatory conditions, its precise role in the pathogenesis of renal and cardiovascular diseases has not been fully understood...
October 30, 2017: Life Sciences
https://www.readbyqxmd.com/read/29073630/microrna-30a-5p-inhibits-the-growth-of-renal-cell-carcinoma-by-modulating-grp78-expression
#9
Changlin Wang, Licheng Cai, Jing Liu, Gang Wang, Haoming Li, Xiaoxiong Wang, Wanhai Xu, Minghua Ren, Li Feng, Pinghuang Liu, Cheng Zhang
BACKGROUND/AIMS: MiR-30a-5p, a member of the microRNA-30 family (miR-30), is known to function as a tumor suppressor in several different cancers. However, the expression levels, biological function, and underlying mechanisms of miR-30a-5p in renal cell carcinoma (RCC) remain unclear. Glucose-regulated protein78 (GRP78) is a common cancer biomarker and promotes the growth and survival of cancer cells. The expression of GRP78 has been reported to be modulated by miR-30a in neurons. In this study, the expression profile of miR-30a-5p in clear cell renal cell carcinoma (ccRCC) and its effect on ccRCC through regulating GRP78 expression was investigated...
October 27, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29067547/low-levels-of-psma-expression-limit-the-utility-of-18-f-dcfpyl-pet-ct-for-imaging-urothelial-carcinoma
#10
Scott P Campbell, Alexander S Baras, Mark W Ball, Max Kates, Noah M Hahn, Trinity J Bivalacqua, Michael H Johnson, Martin G Pomper, Mohamad E Allaf, Steven P Rowe, Michael A Gorin
OBJECTIVE: To explore the clinical utility of PSMA-targeted (18)F-DCFPyL PET/CT in patients with metastatic urothelial carcinoma. METHODS: Three patients with metastatic urothelial carcinoma were imaged with (18)F-DCFPyL PET/CT. All lesions with perceptible radiotracer uptake above background were considered positive. Maximum standardized uptake values were recorded for each detected lesion and findings on (18)F-DCFPyL PET/CT were compared to those on conventional imaging studies...
October 24, 2017: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/29055354/ajkd-atlas-of-renal-pathology-fibronectin-glomerulopathy
#11
Mark A Lusco, Yi-Pu Chen, Hong Cheng, Hong-Rui Dong, Behzad Najafian, Charles E Alpers, Agnes B Fogo
No abstract text is available yet for this article.
November 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/29038551/a-novel-machine-learning-approach-reveals-latent-vascular-phenotypes-predictive-of-renal-cancer-outcome
#12
Nathan Ing, Fangjin Huang, Andrew Conley, Sungyong You, Zhaoxuan Ma, Sergey Klimov, Chisato Ohe, Xiaopu Yuan, Mahul B Amin, Robert Figlin, Arkadiusz Gertych, Beatrice S Knudsen
Gene expression signatures are commonly used as predictive biomarkers, but do not capture structural features within the tissue architecture. Here we apply a 2-step machine learning framework for quantitative imaging of tumor vasculature to derive a spatially informed, prognostic gene signature. The trained algorithms classify endothelial cells and generate a vascular area mask (VAM) in H&E micrographs of clear cell renal cell carcinoma (ccRCC) cases from The Cancer Genome Atlas (TCGA). Quantification of VAMs led to the discovery of 9 vascular features (9VF) that predicted disease-free-survival in a discovery cohort (n = 64, HR = 2...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28984208/unique-protein-expression-signatures-of-survival-time-in-kidney-renal-clear-cell-carcinoma-through-a-pan-cancer-screening
#13
Guangchun Han, Wei Zhao, Xiaofeng Song, Patrick Kwok-Shing Ng, Jose A Karam, Eric Jonasch, Gordon B Mills, Zhongming Zhao, Zhiyong Ding, Peilin Jia
BACKGROUND: In 2016, it is estimated that there will be 62,700 new cases of kidney cancer in the United States, and 14,240 patients will die from the disease. Because the incidence of kidney renal clear cell carcinoma (KIRC), the most common type of kidney cancer, is expected to continue to increase in the US, there is an urgent need to find effective diagnostic biomarkers for KIRC that could help earlier detection of and customized treatment strategies for the disease. Accordingly, in this study we systematically investigated KIRC's prognostic biomarkers for survival using the reverse phase protein array (RPPA) data and the high throughput sequencing data from The Cancer Genome Atlas (TCGA)...
October 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28984199/roles-of-alternative-splicing-in-modulating-transcriptional-regulation
#14
Jin Li, Yang Wang, Xi Rao, Yue Wang, Weixing Feng, Hong Liang, Yunlong Liu
BACKGROUND: The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene function by adding or removing certain protein domains, and therefore affect the activity of protein. Reverse engineering of gene regulatory networks using gene expression profiles has proven valuable in dissecting the logical relationships among multiple proteins during the transcriptional regulation. However, it is unclear whether alternative splicing of certain proteins affects the activity of other transcription factors...
October 3, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28981387/aldh1a1-and-hltf-modulate-the-activity-of-lysosomal-autophagy-inhibitors-in-cancer-cells
#15
Shengfu Piao, Rani Ojha, Vito W Rebecca, Arabinda Samanta, Xiao-Hong Ma, Quentin Mcafee, Michael C Nicastri, Meghan Buckley, Eric Brown, Jeffrey D Winkler, Phyllis A Gimotty, Ravi K Amaravadi
Lysosomal autophagy inhibitors (LAI) such as hydroxychloroquine (HCQ) have significant activity in a subset of cancer cell lines. LAIs are being evaluated in cancer clinical trials, but genetic determinants of sensitivity to LAIs are unknown, making it difficult to predict which tumors would be most susceptible. Here we characterize differentially expressed genes in HCQ-sensitive (-S) and -resistant (-R) cancer cells. Notably, expression of canonical macroautophagy/autophagy genes was not associated with sensitivity to HCQ...
October 5, 2017: Autophagy
https://www.readbyqxmd.com/read/28976794/multicenter-validation-of-enhancer-of-zeste-homolog-2-expression-as-an-independent-prognostic-marker-in-localized-clear-cell-renal-cell-carcinoma
#16
MULTICENTER STUDY
Thai Huu Ho, Payal Kapur, Jeanette E Eckel-Passow, Alana Christie, Richard W Joseph, Daniel J Serie, John C Cheville, R Houston Thompson, Farrah Homayoun, Vandana Panwar, James Brugarolas, Alexander S Parker
Purpose Enhancer of zeste homolog 2 (EZH2), a chromatin remodeler, is implicated in the pathogenesis of clear cell renal cell carcinoma (ccRCC). However, the effect of EZH2 on outcomes in localized ccRCC is unclear, and molecular biomarkers are not currently integrated into prognostic models or adjuvant therapy trials. Methods We performed Cox regression to evaluate the association of tumor-based EZH2 gene and protein expression with survival in three independent cohorts: a cohort from The Cancer Genome Atlas (n = 532), a cohort from University of Texas Southwestern Medical Center (n = 122), and a cohort from Mayo Clinic (n = 1,338)...
November 10, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28941488/ajkd-atlas-of-renal-pathology-nail-patella-syndrome-associated-nephropathy
#17
Behzad Najafian, Kelly Smith, Mark A Lusco, Charles E Alpers, Agnes B Fogo
No abstract text is available yet for this article.
October 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28938589/a-five-long-non-coding-rna-signature-to-improve-prognosis-prediction-of-clear-cell-renal-cell-carcinoma
#18
Da Shi, Qinghua Qu, Qimeng Chang, Yilin Wang, Yaping Gui, Dong Dong
Recent works have reported that long non-coding RNAs (lncRNAs) play critical roles in tumorigenesis and prognosis of cancers, suggesting the potential utility of lncRNAs as cancer prognostic markers. However, lncRNA signatures in predicting the survival of patients with clear cell renal cell carcinoma (ccRCC) remain unknown. In this study, we attempted to identify lncRNA signatures and their prognostic values in ccRCC. Using lncRNA expression profiling data in 440 ccRCC tumors from The Cancer Genome Atlas (TCGA) data, a five-lncRNA signature (AC069513...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938536/integrating-omics-data-and-protein-interaction-networks-to-prioritize-driver-genes-in-cancer
#19
Tiejun Zhang, Di Zhang
Although numerous approaches have been proposed to discern driver from passenger, identification of driver genes remains a critical challenge in the cancer genomics field. Driver genes with low mutated frequency tend to be filtered in cancer research. In addition, the accumulation of different omics data necessitates the development of algorithmic frameworks for nominating putative driver genes. In this study, we presented a novel framework to identify driver genes through integrating multi-omics data such as somatic mutation, gene expression, and copy number alterations...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28931862/long-non-coding-rna-hotair-promotes-cell-migration-by-upregulating-insulin-growth-factor-binding-protein-2-in-renal-cell-carcinoma
#20
Hiromichi Katayama, Keiichi Tamai, Rie Shibuya, Mao Nakamura, Mai Mochizuki, Kazunori Yamaguchi, Sadafumi Kawamura, Tatsuo Tochigi, Ikuro Sato, Takamasa Okanishi, Kunie Sakurai, Wataru Fujibuchi, Yoichi Arai, Kennichi Satoh
Renal cell carcinoma (RCC) is one of the most lethal urologic cancers. About one-third of RCC patients already have distal metastasis at the time of diagnosis. There is growing evidence that Hox antisense intergenic RNA (HOTAIR) plays essential roles in metastasis in several types of cancers. However, the precise mechanism by which HOTAIR enhances malignancy remains unclear, especially in RCC. Here, we demonstrated that HOTAIR enhances RCC-cell migration by regulating the insulin growth factor-binding protein 2 (IGFBP2) expression...
September 20, 2017: Scientific Reports
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