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Renal atlas

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https://www.readbyqxmd.com/read/29038551/a-novel-machine-learning-approach-reveals-latent-vascular-phenotypes-predictive-of-renal-cancer-outcome
#1
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
#2
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
#3
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
#4
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
#5
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)...
October 4, 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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28902136/dual-strands-of-pre-mir-149-inhibit-cancer-cell-migration-and-invasion-through-targeting-foxm1-in-renal-cell-carcinoma
#10
Atsushi Okato, Takayuki Arai, Yasutaka Yamada, Sho Sugawara, Keiichi Koshizuka, Lisa Fujimura, Akira Kurozumi, Mayuko Kato, Satoko Kojima, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
Our recent studies revealed that dual strands of certain pre-microRNAs, e.g., pre-miR-144, pre-miR-145, and pre-miR-150, act as antitumor microRNAs (miRNAs) in several cancers. The involvement of passenger strands of miRNAs in cancer pathogenesis is a novel concept in miRNA research. The analysis of a miRNA expression signature in clear cell renal cell carcinoma (ccRCC) has revealed that the guide strand of pre-miR-149 is significantly downregulated in cancer tissues. The aims of this study were to investigate the functional significance of miR-149's guide strand (miR-149-5p) and passenger strand (miR-149-3p), and to identify the oncogenic genes regulated by these miRNAs in ccRCC cells...
September 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28900502/a-bap1-mutation-specific-microrna-signature-predicts-clinical-outcomes-in-clear-cell-renal-cell-carcinoma-patients-with-wild-type-bap1
#11
Yu-Zheng Ge, Lu-Wei Xu, Chang-Cheng Zhou, Tian-Ze Lu, Wen-Tao Yao, Ran Wu, You-Cai Zhao, Xiao Xu, Zhi-Kai Hu, Min Wang, Xiao-Bing Yang, Liu-Hua Zhou, Bing Zhong, Zheng Xu, Wen-Cheng Li, Jia-Geng Zhu, Rui-Peng Jia
Background: Clear cell renal cell carcinoma (ccRCC) is the most prevalent histologic subtype of kidney cancers in adults, which could be divided into two distinct subgroups according to the BRCA1 associated protein-1 (BAP1) mutation status. In the current study, we comprehensively analyzed the genome-wide microRNA (miRNA) expression profiles in ccRCC, with the aim to identify the differentially expressed miRNAs between BAP1 mutant and wild-type tumors, and generate a BAP1 mutation-specific miRNA signature for ccRCC patients with wild-type BAP1...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28894827/the-genetic-landscape-of-programmed-death-ligand-1-pd-l1-alterations-in-head-and-neck-cancer
#12
Thomas E Heineman, Adam Widman, Edward C Kuan, Maie St John
OBJECTIVES: Nivolumab has recently been shown in the phase III clinical trial CheckMate-141 to have superior survival rates compared to the current standard of care chemotherapy for recurrent or metastatic platinum-resistant head and neck squamous cell carcinoma (HNSCC). Nivolumab targets the immune inhibitory receptor programmed cell death 1 (PD-1). Programmed cell death ligand 1 (PD-L1) genomics have been poorly characterized in the context of HNSCC, including expression levels of PD-L1 in individual tumors as well as related up or down-regulated genes that might function as co-targets...
June 2017: Laryngoscope Investigative Otolaryngology
https://www.readbyqxmd.com/read/28878000/dissecting-hematopoietic-and-renal-cell-heterogeneity-in-adult-zebrafish-at-single-cell-resolution-using-rna-sequencing
#13
Qin Tang, Sowmya Iyer, Riadh Lobbardi, John C Moore, Huidong Chen, Caleb Lareau, Christine Hebert, McKenzie L Shaw, Cyril Neftel, Mario L Suva, Craig J Ceol, Andre Bernards, Martin Aryee, Luca Pinello, Iain A Drummond, David M Langenau
Recent advances in single-cell, transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. In this study, we used massively parallel, single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune-cell deficiencies within DNA-protein kinase catalytic subunit (prkdc), interleukin-2 receptor γ a (il2rga), and double-homozygous-mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants...
October 2, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28860812/an-integrated-analysis-for-long-noncoding-rnas-and-micrornas-with-the-mediated-competing-endogenous-rna-network-in-papillary-renal-cell-carcinoma
#14
Chuiguo Huang, Naijun Yuan, Liying Wu, Xiaofu Wang, Junqiang Dai, Pan Song, Fengxi Li, Changbao Xu, Xinghua Zhao
Papillary renal cell carcinoma (PRCC) is the second most common subtype of renal cell carcinoma, and it lacks effective therapeutic targets and prognostic molecular biomarkers. Attention has been increasingly focused on long noncoding RNAs (lncRNAs), which can act as competing endogenous RNA (ceRNA) to compete for shared microRNAs (miRNAs) in the tumorigenesis of human tumors. Therefore, to clarify the functional roles of lncRNAs with respect to the mediated ceRNA network in PRCC, we comprehensively integrated expression profiles, including data on mRNAs, lncRNAs and miRNAs obtained from 289 PRCC tissues and 32 normal tissues in The Cancer Genome Atlas...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28842062/ajkd-atlas-of-renal-pathology-ckd-of-unknown-cause-ckdu-%C3%A2-mesoamerican-nephropathy
#15
Mark A Lusco, Agnes B Fogo, Annika Östman Wernerson, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
September 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28835003/regulation-of-pharmacogene-expression-by-microrna-in-the-cancer-genome-atlas-tcga-research-network
#16
Nayoung Han, Yun-Kyoung Song, Gilbert J Burckart, Eunhee Ji, In-Wha Kim, Jung Mi Oh
Individual differences in drug responses are associated with genetic and epigenetic variability of pharmacogene expression. We aimed to identify the relevant miRNAs which regulate pharmacogenes associated with drug responses. The miRNA and mRNA expression profiles derived from data for normal and solid tumor tissues in The Cancer Genome Atlas (TCGA) Research Network. Predicted miRNAs targeted to pharmacogenes were identified using publicly available databases. A total of 95 pharmacogenes were selected from cholangiocarcinoma and colon adenocarcinoma, as well as kidney renal clear cell, liver hepatocellular, and lung squamous cell carcinomas...
September 1, 2017: Biomolecules & Therapeutics
https://www.readbyqxmd.com/read/28834287/partial-nephrectomy-margin-imaging-using-structured-illumination-microscopy
#17
Mei Wang, David B Tulman, Andrew B Sholl, Sree H Mandava, Michael M Maddox, Benjamin R Lee, J Quincy Brown
Partial nephrectomy (PN) is the recommended procedure over radical nephrectomy (RN) for patients with renal masses < 4 cm in diameter (Stage T1a). Patients with > 4 cm renal masses can also be treated with PN, but have a higher risk for positive surgical margins. Positive surgical margins (PSM), when present, are indicative of poor clinical outcomes. The current gold-standard histopathology method is not well-suited for the identification of PSM intra-operatively due to processing time and destructive nature...
August 21, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28831388/a-new-network-based-strategy-for-predicting-the-potential-mirna-mrna-interactions-in-tumorigenesis
#18
Jiwei Xue, Fanfan Xie, Junmei Xu, Yuan Liu, Yu Liang, Zhining Wen, Menglong Li
MicroRNA (miRNA) plays an important role in the degradation and inhibition of mRNAs and is a kind of essential drug targets for cancer therapy. To facilitate the clinical cancer research, we proposed a network-based strategy to identify the cancer-related miRNAs and to predict their targeted genes based on the gene expression profiles. The strategy was validated by using the data sets of acute myeloid leukemia (AML), breast invasive carcinoma (BRCA), and kidney renal clear cell carcinoma (KIRC). The results showed that in the top 20 miRNAs ranked by their degrees, 90...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28827104/comprehensive-evaluation-of-prostate-specific-membrane-antigen-expression-in-the-vasculature-of-renal-tumors-implications-for-imaging-studies-and-prognostic-role
#19
Sophia Spatz, Yuri Tolkach, Klaus Jung, Carsten Stephan, Jonas Busch, Bernhard Ralla, Anja Rabien, Georg Feldmann, Peter Brossart, Ralph A Bundschuh, Hojjat Ahmadzadehfar, Markus Essler, Marieta Toma, Stefan C Müller, Jörg Ellinger, Stefan Hauser, Glen Kristiansen
PURPOSE: Prostate-specific membrane antigen (PSMA) is expressed by endothelium of many tumors. The aim of the study was to find a rationale for PSMA-based imaging and to investigate the prognostic role of vascular PSMA expression in patients with renal cell carcinoma (RCC). MATERIALS AND METHODS: Two-hundred fifty seven patients with RCC were included with a median follow-up exceeding 10.0 years. PSMA expression on the tumor vessels was detected by immunohistochemistry...
August 18, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28819401/identification-and-validation-of-soluble-carrier-family-expression-signature-for-predicting-poor-outcome-of-renal-cell-carcinoma
#20
Wan Fangning, Ma Chunguang, Zhang Hailiang, Shi Guohai, Zhu Yao, Dai Bo, Shen Yijun, Zhu Yiping, Ye Dingwei
The soluble carrier (SLC) family plays an important role in cell metabolism. The purpose of the current study was to screen SLCs as potential prognostic factors in clear cell renal cell carcinoma (ccRCC). A total of 509 patients with ccRCC from The Cancer Genome Atlas (TCGA) cohort were enrolled in this study. The expression profile of SLCs was obtained from the TCGA RNAseq database. Metadata of the TCGA cohort, including age, sex, TNM stage, tumor grade, American Joint Committee on Cancer stage, laterality, and overall survival, were collected...
2017: Journal of Cancer
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