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Renal atlas

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https://www.readbyqxmd.com/read/28694034/insertion-and-deletion-derived-tumour-specific-neoantigens-and-the-immunogenic-phenotype-a-pan-cancer-analysis
#1
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir, Tim Chambers, Roberto Salgado, Peter Savas, Sherene Loi, Nicolai J Birkbak, Laurent Sansregret, Martin Gore, James Larkin, Sergio A Quezada, Charles Swanton
BACKGROUND: The focus of tumour-specific antigen analyses has been on single nucleotide variants (SNVs), with the contribution of small insertions and deletions (indels) less well characterised. We investigated whether the frameshift nature of indel mutations, which create novel open reading frames and a large quantity of mutagenic peptides highly distinct from self, might contribute to the immunogenic phenotype. METHODS: We analysed whole-exome sequencing data from 5777 solid tumours, spanning 19 cancer types from The Cancer Genome Atlas...
July 7, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28662155/a-three-microrna-signature-as-a-diagnostic-and-prognostic-marker-in-clear-cell-renal-cancer-an-in-silico-analysis
#2
Bin Liang, Jianying Zhao, Xuan Wang
Accumulating evidence has demonstrated that some specific miRNAs were aberrantly expressed in renal clear cell carcinoma and participated in many biological processes. The aim of this study was to investigate a panel of miRNA signature for diagnosis and prognosis of renal clear cell carcinoma (KIRC). Here, we performed a comprehensive analysis for miRNA expression profiles and corresponding clinical information of 516 KIRC patients from The Cancer Genome Atlas (TCGA). In the study, a total of 63 differentially expressed miRNAs were identified, of which 34 were up-regulated and 29 were down-regulated...
2017: PloS One
https://www.readbyqxmd.com/read/28646986/ajkd-atlas-of-renal-pathology-lecithin-cholesterol-acyltransferase-lcat-deficiency
#3
Behzad Najafian, Mark A Lusco, Laura S Finn, Charles E Alpers, Agnes B Fogo
No abstract text is available yet for this article.
July 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28646985/ajkd-atlas-of-renal-pathology-anti-tubular-basement-membrane-antibody-disease
#4
Mark A Lusco, Agnes B Fogo, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
July 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28646984/ajkd-atlas-of-renal-pathology-chronic-interstitial-nephritis
#5
Agnes B Fogo, Mark A Lusco, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
July 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28646318/primary-renal-paragangliomas-and-renal-neoplasia-associated-with-pheochromocytoma-paraganglioma-analysis-of-von-hippel-lindau-vhl-succinate-dehydrogenase-sdhx-and-transmembrane-protein-127-tmem127
#6
Sounak Gupta, Jun Zhang, Dragana Milosevic, John R Mills, Stefan K Grebe, Steven C Smith, Lori A Erickson
Alterations of von Hippel-Lindau (VHL), succinate dehydrogenase (SDHX), and TMEM127 have been associated with the development of pheochromocytomas (PCs) and paragangliomas (PGLs) and are also associated with the development of renal neoplasms. This study involved 2 primary renal PGL and 12 cases of PC/PGL with associated renal neoplasia with a mean follow up of 74 months. Germline VHL and SDHX mutation status was obtained from the medical record. Immunohistochemistry for SDHB and mutation analysis for TMEM127 was performed, in addition to analysis of The Cancer Genome Atlas datasets for SDHX and TMEM127 mutated renal cell carcinomas (RCCs)...
June 23, 2017: Endocrine Pathology
https://www.readbyqxmd.com/read/28634536/telavancin-a-novel-semisynthetic-lipoglycopeptide-agent-to-counter-the-challenge-of-resistant-gram-positive-pathogens
#7
REVIEW
Biswadeep Das, Chayna Sarkar, Debasmita Das, Amit Gupta, Arnav Kalra, Shubham Sahni
Telavancin (TD-6424), a semisynthetic lipoglycopeptide vancomycin-derivative, is a novel antimicrobial agent developed by Theravance for overcoming resistant Gram-positive bacterial infections, specifically methicillin-resistant Staphylococcus aureus (MRSA). The US Food and Drug Administration (USFDA) had approved telavancin in 2009 for the treatment of complicated skin and skin structure infections (cSSSIs) caused by Gram-positive bacteria, including MRSA (S. aureus, Streptococcus agalactiae, Streptococcus pyogenes, Streptococcus anginosus group, or Enterococcus faecalis)...
March 2017: Therapeutic Advances in Infectious Disease
https://www.readbyqxmd.com/read/28614790/genomic-landscape-and-evolution-of-metastatic-chromophobe-renal-cell-carcinoma
#8
Jozefina Casuscelli, Nils Weinhold, Gunes Gundem, Lu Wang, Emily C Zabor, Esther Drill, Patricia I Wang, Gouri J Nanjangud, Almedina Redzematovic, Amrita M Nargund, Brandon J Manley, Maria E Arcila, Nicholas M Donin, John C Cheville, R Houston Thompson, Allan J Pantuck, Paul Russo, Emily H Cheng, William Lee, Satish K Tickoo, Irina Ostrovnaya, Chad J Creighton, Elli Papaemmanuil, Venkatraman E Seshan, A Ari Hakimi, James J Hsieh
Chromophobe renal cell carcinoma (chRCC) typically shows ~7 chromosome losses (1, 2, 6, 10, 13, 17, and 21) and ~31 exonic somatic mutations, yet carries ~5%-10% metastatic incidence. Since extensive chromosomal losses can generate proteotoxic stress and compromise cellular proliferation, it is intriguing how chRCC, a tumor with extensive chromosome losses and a low number of somatic mutations, can develop lethal metastases. Genomic features distinguishing metastatic from nonmetastatic chRCC are unknown. An integrated approach, including whole-genome sequencing (WGS), targeted ultradeep cancer gene sequencing, and chromosome analyses (FACETS, OncoScan, and FISH), was performed on 79 chRCC patients including 38 metastatic (M-chRCC) cases...
June 15, 2017: JCI Insight
https://www.readbyqxmd.com/read/28592388/characterization-of-clinical-cases-of-advanced-papillary-renal-cell-carcinoma-via-comprehensive-genomic-profiling
#9
Sumanta K Pal, Siraj M Ali, Evgeny Yakirevich, Daniel M Geynisman, Jose A Karam, Julia A Elvin, Garrett M Frampton, Xuan Huang, Douglas I Lin, Mark Rosenzweig, Doron Lipson, Philip J Stephens, Jeffrey S Ross, Vincent A Miller, Neeraj Agarwal, Brian Shuch, Toni K Choueiri, Jon H Chung
BACKGROUND: Papillary renal cell carcinoma (PRCC) is a rare subset of RCC. The Cancer Genome Atlas (TCGA) data largely reflect localized disease, and there are limited data for advanced PRCC. OBJECTIVE: To characterize the frequency of genomic alterations (GAs) in patients with advanced PRCC for whom comprehensive genomic profiling (CGP) was performed in the context of routine clinical care. DESIGN, SETTING, AND PARTICIPANTS: Formalin-fixed, paraffin-embedded tissue was obtained for 169 consecutive patients with confirmed PRCC...
May 30, 2017: European Urology
https://www.readbyqxmd.com/read/28546287/immune-atlases-created-for-kidney-lung-cancers
#10
(no author information available yet)
Two groups of researchers have generated the first comprehensive "immune atlases" of clear cell renal cell carcinoma and early lung adenocarcinoma. Their work better illuminates the tumor immune microenvironment and may lead to more effective immunotherapy strategies.
May 25, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28543182/prognostic-significance-of-promoter-cpg-island-methylation-of-obesity-related-genes-in-patients-with-nonmetastatic-renal-cell-carcinoma
#11
Julia Mendoza-Pérez, Jian Gu, Luis A Herrera, Nizar M Tannir, Shanyu Zhang, Surena Matin, Jose A Karam, Christopher G Wood, Xifeng Wu
BACKGROUND: Greater than 40% of renal cell carcinoma (RCC) cases in the United States are attributed to excessive body weight. Moreover, obesity also may be linked to RCC prognosis. However, the molecular mechanisms underlying these associations are unclear. In the current study, the authors evaluated the role of promoter methylation in obesity-related genes in RCC tumorigenesis and disease recurrence. METHODS: Paired tumors (TU) and normal adjacent (N-Adj) tissues from 240 newly diagnosed and previously untreated white patients with RCC were examined...
May 23, 2017: Cancer
https://www.readbyqxmd.com/read/28532640/ajkd-atlas-of-renal-pathology-kidney-disease-in-primary-sj%C3%A3-gren-syndrome
#12
Agnes B Fogo, Mark A Lusco, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
June 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28532639/ajkd-atlas-of-renal-pathology-tubulointerstitial-nephritis-with%C3%A2-uveitis
#13
Mark A Lusco, Agnes B Fogo, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
June 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28532638/ajkd-atlas-of-renal-pathology-type-iii-collagen%C3%A2-glomerulopathy
#14
Agnes B Fogo, Mark A Lusco, Behzad Najafian, Charles E Alpers
No abstract text is available yet for this article.
June 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://www.readbyqxmd.com/read/28512261/a-five-long-non-coding-rna-signature-to-improve-prognosis-prediction-of-clear-cell-renal-cell-carcinoma
#15
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...
April 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28489074/analysis-of-renal-cancer-cell-lines-from-two-major-resources-enables-genomics-guided-cell-line-selection
#16
Rileen Sinha, Andrew G Winer, Michael Chevinsky, Christopher Jakubowski, Ying-Bei Chen, Yiyu Dong, Satish K Tickoo, Victor E Reuter, Paul Russo, Jonathan A Coleman, Chris Sander, James J Hsieh, A Ari Hakimi
The utility of cancer cell lines is affected by the similarity to endogenous tumour cells. Here we compare genomic data from 65 kidney-derived cell lines from the Cancer Cell Line Encyclopedia and the COSMIC Cell Lines Project to three renal cancer subtypes from The Cancer Genome Atlas: clear cell renal cell carcinoma (ccRCC, also known as kidney renal clear cell carcinoma), papillary (pRCC, also known as kidney papillary) and chromophobe (chRCC, also known as kidney chromophobe) renal cell carcinoma. Clustering copy number alterations shows that most cell lines resemble ccRCC, a few (including some often used as models of ccRCC) resemble pRCC, and none resemble chRCC...
May 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28475899/an-immune-atlas-of-clear-cell-renal-cell-carcinoma
#17
Stéphane Chevrier, Jacob Harrison Levine, Vito Riccardo Tomaso Zanotelli, Karina Silina, Daniel Schulz, Marina Bacac, Carola Hermine Ries, Laurie Ailles, Michael Alexander Spencer Jewett, Holger Moch, Maries van den Broek, Christian Beisel, Michael Beda Stadler, Craig Gedye, Bernhard Reis, Dana Pe'er, Bernd Bodenmiller
Immune cells in the tumor microenvironment modulate cancer progression and are attractive therapeutic targets. Macrophages and T cells are key components of the microenvironment, yet their phenotypes and relationships in this ecosystem and to clinical outcomes are ill defined. We used mass cytometry with extensive antibody panels to perform in-depth immune profiling of samples from 73 clear cell renal cell carcinoma (ccRCC) patients and five healthy controls. In 3.5 million measured cells, we identified 17 tumor-associated macrophage phenotypes, 22 T cell phenotypes, and a distinct immune composition correlated with progression-free survival, thereby presenting an in-depth human atlas of the immune tumor microenvironment in this disease...
May 4, 2017: Cell
https://www.readbyqxmd.com/read/28470573/bsnd-is-a-novel-immunohistochemical-marker-for-oncocytic-salivary-gland-tumors
#18
Kazuya Shinmura, Hisami Kato, Yuichi Kawanishi, Takaharu Kamo, Yusuke Inoue, Katsuhiro Yoshimura, Kenta Sugiyama, Kiyoshi Misawa, Seiji Hosokawa, Hiroyuki Mineta, Haruhiko Sugimura
BSND protein, which is involved in chloride transport, is expressed in normal kidney and the inner ear and is known as an immunohistochemical marker for chromophobe renal cell carcinoma (RCC) and renal oncocytoma; however, other organs and tumor types exhibiting BSND expression have not yet been reported. In this study, we investigated the expression of BSND using data from the Cancer Genome Atlas (TCGA) database and by performing immunohistochemical analyses. As a result, we found that BSND was also expressed in the striated duct cells of normal salivary glands...
May 3, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28459210/the-long-noncoding-rna-urothelial-carcinoma-associated-1-overexpression-as-a-poor-prognostic-biomarker-in-clear-cell-renal-cell-carcinoma
#19
Yang Wang, Wen Gao, Jiali Xu, Yizhi Zhu, Lingxiang Liu
Long noncoding RNA urothelial carcinoma-associated 1 has previously played important roles in cancer. However, its role is still unknown in clear cell renal cell carcinoma. We utilized the most recent molecular and clinical data of clear cell renal cell carcinoma from The Cancer Genome Atlas project, and the relationship between urothelial carcinoma-associated 1 expression and the clinicopathological features was analyzed. Our results indicated that urothelial carcinoma-associated 1 overexpression was associated with male ( p = 0...
May 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28434822/current-and-potential-imaging-applications-of-ferumoxytol-for-magnetic-resonance-imaging
#20
REVIEW
Gerda B Toth, Csanad G Varallyay, Andrea Horvath, Mustafa R Bashir, Peter L Choyke, Heike E Daldrup-Link, Edit Dosa, John Paul Finn, Seymur Gahramanov, Mukesh Harisinghani, Iain Macdougall, Alexander Neuwelt, Shreyas S Vasanawala, Prakash Ambady, Ramon Barajas, Justin S Cetas, Jeremy Ciporen, Thomas J DeLoughery, Nancy D Doolittle, Rongwei Fu, John Grinstead, Alexander R Guimaraes, Bronwyn E Hamilton, Xin Li, Heather L McConnell, Leslie L Muldoon, Gary Nesbit, Joao P Netto, David Petterson, William D Rooney, Daniel Schwartz, Laszlo Szidonya, Edward A Neuwelt
Contrast-enhanced magnetic resonance imaging is a commonly used diagnostic tool. Compared with standard gadolinium-based contrast agents, ferumoxytol (Feraheme, AMAG Pharmaceuticals, Waltham, MA), used as an alternative contrast medium, is feasible in patients with impaired renal function. Other attractive imaging features of i.v. ferumoxytol include a prolonged blood pool phase and delayed intracellular uptake. With its unique pharmacologic, metabolic, and imaging properties, ferumoxytol may play a crucial role in future magnetic resonance imaging of the central nervous system, various organs outside the central nervous system, and the cardiovascular system...
July 2017: Kidney International
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