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The cancer genome atlas

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https://www.readbyqxmd.com/read/29473345/cgb5-expression-is-independently-associated-with-poor-overall-survival-and-recurrence-free-survival-in-patients-with-advanced-gastric-cancer
#1
Yuxin Yang, Yonghong Shi, Yanjuan Hou, Ying Lu, Jinliang Yang
The human CGB5 gene encodes chorionic gonadotropin (hCG)β 5, which is aberrantly expressed in trophoblastic neoplasm and in some non-trophoblastic neoplasms. Fucntional studies observed that it involved tumor initiation, growth, and metastatic outgrowth. In this study, using data from the International Cancer Genome Consortium (ICGC) and the Cancer Genome Atlas (TCGA)-stomach adenocarcinoma (STAD), we assessed the independent prognostic value of CGB5 expression in patients with primary gastric cancer (GC)...
February 23, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29473328/lncrna-hotair-influences-cell-growth-migration-invasion-and-apoptosis-via-the-mir-20a-5p-hmga2-axis-in-breast-cancer
#2
Wenyan Zhao, Donghua Geng, Shuqiang Li, Zhaofu Chen, Ming Sun
To study the regulatory effect of lncRNA HOTAIR/miR-20a-5p/HMGA2 axis on breast cancer (BC) cell growth, cell mobility, invasiveness, and apoptosis. The microarray data of lncRNAs and mRNAs with differential expression in BC tissues were analyzed in the Cancer Genome Atlas (TCGA) database. LncRNA HOX transcript antisense RNA (lncRNA HOTAIR) expression in BC was assessed by qRT-PCR. Cell viability was confirmed using MTT and colony formation assay. Cell apoptosis was analyzed by TdT-mediated dUTP nick-end labeling (TUNEL) assay...
February 23, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29473326/prediction-of-radiotherapy-response-with-a-5-microrna-signature-based-nomogram-in-head-and-neck-squamous-cell-carcinoma
#3
Lin Chen, Yihui Wen, Jingwei Zhang, Wei Sun, Vivian W Y Lui, Yi Wei, Fenghong Chen, Weiping Wen
Radiotherapy is unlikely to benefit all patients with head and neck squamous cell carcinoma (HNSCC). Therefore, novel method is warranted to predict the radiotherapy response. Our study aimed to construct a microRNA (miRNA)-based nomogram to predict clinical outcomes of patients with HNSCC receiving radiotherapy. We screened out 56 differential miRNAs by analyzing 44 paired tumor and adjacent normal samples miRNA expression profiles from The Cancer Genome Atlas (TCGA). A total of 307 patients with HNSCC receiving adjuvant radiotherapy were randomly divided into a training set (n = 154) and a validation set (n = 153)...
February 23, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29472156/novel-biomarkers-in-bladder-cancer
#4
REVIEW
Michael L Cheng, Gopa Iyer
A sea change has occurred in the treatment options available for metastatic urothelial bladder cancer with the recent Food and Drug Administration approval of 5 immune checkpoint blockade agents for patients who have progressed on platinum-based chemotherapy or are not candidates for cisplatin. Additionally, comprehensive characterization of the landscape of genomic alterations in this disease through The Cancer Genome Atlas and other efforts has detected numerous potential targets for small molecule inhibitors...
February 19, 2018: Urologic Oncology
https://www.readbyqxmd.com/read/29471873/mircancerdb-a-database-for-correlation-analysis-between-microrna-and-gene-expression-in-cancer
#5
Mahmoud Ahmed, Huynh Nguyen, Trang Lai, Deok Ryong Kim
OBJECTIVES: microRNAs regulate expression of target genes by specifically binding to their transcripts, subsequently leading to translational inhibition or mRNA degradation. Gene regulation by microRNAs has been implicated in a wide range of physiological and pathological conditions. Here, we leverage the use of public-access data and the available genomic annotations to pre-calculate the correlation of the expression of a large number of microRNAs with gene at the mRNA and protein level in the context of cancers...
February 7, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29471435/immune-infiltration-in-invasive-lobular-breast-cancer
#6
Christine Desmedt, Roberto Salgado, Marco Fornili, Giancarlo Pruneri, Gert Van den Eynden, Gabriele Zoppoli, Françoise Rothé, Laurence Buisseret, Soizic Garaud, Karen Willard-Gallo, David Brown, Yacine Bareche, Ghizlane Rouas, Christine Galant, François Bertucci, Sherene Loi, Giuseppe Viale, Angelo Di Leo, Andrew R Green, Ian O Ellis, Emad A Rakha, Denis Larsimont, Elia Biganzoli, Christos Sotiriou
Background: Invasive lobular breast cancer (ILC) is the second most common histological subtype of breast cancer after invasive ductal cancer (IDC). Here, we aimed at evaluating the prevalence, levels, and composition of tumor-infiltrating lymphocytes (TILs) and their association with clinico-pathological and outcome variables in ILC, and to compare them with IDC. Methods: We considered two patient series with TIL data: a multicentric retrospective series (n = 614) and the BIG 02-98 study (n = 149 ILC and 807 IDC)...
February 20, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29470520/association-between-expression-of-random-gene-sets-and-survival-is-evident-in-multiple-cancer-types-and-may-be-explained-by-sub-classification
#7
Yishai Shimoni
One of the goals of cancer research is to identify a set of genes that cause or control disease progression. However, although multiple such gene sets were published, these are usually in very poor agreement with each other, and very few of the genes proved to be functional therapeutic targets. Furthermore, recent findings from a breast cancer gene-expression cohort showed that sets of genes selected randomly can be used to predict survival with a much higher probability than expected. These results imply that many of the genes identified in breast cancer gene expression analysis may not be causal of cancer progression, even though they can still be highly predictive of prognosis...
February 22, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29468160/adhesion-gpcrs-in-kidney-development-and-disease
#8
REVIEW
Salvador Cazorla-Vázquez, Felix B Engel
Chronic kidney disease (CKD) represents the fastest growing pathology worldwide with a prevalence of >10% in many countries. In addition, kidney cancer represents 5% of all new diagnosed cancers. As currently no effective therapies exist to restore kidney function after CKD- as well as cancer-induced renal damage, it is important to elucidate new regulators of kidney development and disease as new therapeutic targets. G protein-coupled receptors (GPCRs) represent the most successful class of pharmaceutical targets...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29464064/translational-study-reveals-a-two-faced-role-of-rbm3-in-pancreatic-cancer-and-suggests-its-potential-value-as-a-biomarker-for-improved-patient-stratification
#9
Emelie Karnevi, Liv Ben Dror, Adil Mardinoglu, Jacob Elebro, Margareta Heby, Sven-Erik Olofsson, Björn Nodin, Jakob Eberhard, William Gallagher, Mathias Uhlén, Karin Jirström
Periampullary adenocarcinoma, including pancreatic cancer, is a heterogeneous group of tumors with dismal prognosis, partially due to lack of reliable targetable and predictive biomarkers. RNA-binding motif protein 3 (RBM3) has previously been shown to be an independent prognostic and predictive biomarker in several types of cancer. Herein, we examined the prognostic value of RBM3 in periampullary adenocarcinoma, as well as the effects following RBM3 suppression in pancreatic cancer cells in vitro . RBM3 mRNA levels were examined in 176 pancreatic cancer patients from The Cancer Genome Atlas...
January 19, 2018: Oncotarget
https://www.readbyqxmd.com/read/29459674/identification-of-novel-prognosis-related-genes-associated-with-cancer-using-integrative-network-analysis
#10
YongKiat Wee, Yining Liu, Jiachun Lu, Xiaoyan Li, Min Zhao
Prognosis identifies the seriousness and the chances of survival of a cancer patient. However, it remains a challenge to identify the key cancer genes in prognostic studies. In this study, we collected 2064 genes that were related to prognostic studies by using gene expression measurements curated from published literatures. Among them, 1820 genes were associated with copy number variations (CNVs). The further functional enrichment on 889 genes with frequent copy number gains (CNGs) revealed that these genes were significantly associated with cancer pathways including regulation of cell cycle, cell differentiation and mitogen-activated protein kinase (MAPK) cascade...
February 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29456764/integrative-analysis-of-the-epigenetic-basis-of-muscle-invasive-urothelial-carcinoma
#11
Thomas Sanford, Maxwell V Meng, Reema Railkar, Piyush K Agarwal, Sima P Porten
Background: Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer. Methods: Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29456741/overexpression-of-flavin-containing-monooxygenase-5-predicts-poor-prognosis-in-patients-with-colorectal-cancer
#12
Tong Zhang, Ping Yang, Jianchang Wei, Wanglin Li, Junbin Zhong, Huacui Chen, Jie Cao
The present study investigated the expression and clinical significance of flavin-containing monooxygenase 5 (FMO5) in colorectal cancer (CRC). The expression of FMO5 was detected by immunohistochemistry in 208 colon cancer tissues and 8 normal colon tissues. Then, the correlations of FMO5 expression with several clinicopathological features were evaluated. FMO5 mRNA expression from The Cancer Genome Atlas dataset was assessed for further validation. In addition, the association of the expression of FMO5 with prognosis was further evaluated by Kaplan-Meier survival curves and Cox proportional hazards model...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29456732/two-protein-coding-genes-act-as-a-novel-clinical-signature-to-predict-prognosis-in-patients-with-ovarian-serous-cystadenocarcinoma
#13
Jue Zhang, Meng Xu, Han Gao, Jin-Chen Guo, Yu-Lin Guo, Miao Zou, Xu-Feng Wu
Ovarian cancer is the seventh most common type of cancer and the eighth most common cause of cancer-associated mortality among women. A number of studies have hypothesized that the expression status of certain genes may be used to predict prognosis in ovarian cancer. In the present study, the RNA expression data from next-generation sequencing and the clinical information of 413 patients from The Cancer Genome Atlas dataset was downloaded to identify the association between gene-expression level and the survival time of the patients with ovarian serous cystadenocarcinoma...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29456628/identification-of-influential-observations-in-high-dimensional-cancer-survival-data-through-the-rank-product-test
#14
Eunice Carrasquinha, André Veríssimo, Marta B Lopes, Susana Vinga
Background: Survival analysis is a statistical technique widely used in many fields of science, in particular in the medical area, and which studies the time until an event of interest occurs. Outlier detection in this context has gained great importance due to the fact that the identification of long or short-term survivors may lead to the detection of new prognostic factors. However, the results obtained using different outlier detection methods and residuals are seldom the same and are strongly dependent of the specific Cox proportional hazards model selected...
2018: BioData Mining
https://www.readbyqxmd.com/read/29456550/genomic-analysis-revealed-new-oncogenic-signatures-in-tp53-mutant-hepatocellular-carcinoma
#15
Venkatesh Kancherla, Samir Abdullazade, Matthias S Matter, Manuela Lanzafame, Luca Quagliata, Guglielmo Roma, Yujin Hoshida, Luigi M Terracciano, Charlotte K Y Ng, Salvatore Piscuoglio
The TP53 gene is the most commonly mutated gene in human cancers and mutations in TP53 have been shown to have either gain-of-function or loss-of-function effects. Using the data generated by The Cancer Genome Atlas, we sought to define the spectrum of TP53 mutations in hepatocellular carcinomas (HCCs) and their association with clinicopathologic features, and to determine the oncogenic and mutational signatures in TP53 -mutant HCCs. Compared to other cancer types, HCCs harbored distinctive mutation hotspots at V157 and R249, whereas common mutation hotspots in other cancer types, R175 and R273, were extremely rare in HCCs...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29455299/prostate-specific-membrane-antigen-in-breast-cancer-a-comprehensive-evaluation-of-expression-and-a-case-report-of-radionuclide-therapy
#16
Yuri Tolkach, Heidrun Gevensleben, Ralph Bundschuh, Aydan Koyun, Daniela Huber, Christina Kehrer, Thomas Hecking, Mignon-Denise Keyver-Paik, Christina Kaiser, Hojjat Ahmadzadehfar, Markus Essler, Walther Kuhn, Glen Kristiansen
PURPOSE: Prostate-specific membrane antigen (PSMA), a protein product of the folate hydrolase 1 (FOLH1) gene, is gaining increasing acceptance as a target for positron emission tomography/computer tomography (PET/CT) imaging in patients with several cancer types, including breast cancer. So far, PSMA expression in breast cancer endothelia has not been sufficiently characterized. METHODS: This study comprised 315 cases of invasive carcinoma of no special type (NST) and lobular breast cancer (median follow-up time 9...
February 17, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29454310/in-vitro-and-in-silico-validation-of-ca3-and-fhl1-downregulation-in-oral-cancer
#17
Cláudia Maria Pereira, Ana Carolina de Carvalho, Felipe Rodrigues da Silva, Matias Eliseo Melendez, Roberta Cardim Lessa, Valéria Cristina C Andrade, Luiz Paulo Kowalski, André L Vettore, André Lopes Carvalho
BACKGROUND: Aberrant methylation is a frequent event in oral cancer. METHODS: In order to better characterize these alterations, a search for genes downregulated by aberrant methylation in oral squamous cell carcinoma (OSCC) was conducted through the mining of ORESTES dataset. Findings were further validated in OSCC cell lines and patients' samples and confirmed using TCGA data. Differentially expressed genes were identified in ORESTES libraries and validated in vitro using RT-PCR in HNSCC cell-lines and OSCC tumor samples...
February 17, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29453919/genetic-and-epigenetic-differences-of-benign-and-malignant-pheochromocytomas-and-paragangliomas-ppgls
#18
Fatemeh Khatami, Mahsa Mohammadamoli, Seyed Mohammad Tavangar
Pheochromocytomas and paragangliomas (PPGLs) are tumors arising from the adrenal medulla and sympathetic/parasympathetic paraganglia, respectively. According to Th e Cancer Genome Atlas (TCGA), approximately 40% of PPGLs are due to germ line mutations in one of 16 susceptibility genes, and a further 30% are due to somatic alterations in at least seven main genes (VHL, EPAS1, CSDE1, MAX, HRAS, NF1, RET, and possibly KIF1B). Th e diagnosis of malignant PPGL was straight forward in most cases as it was defined as presence of PPGL in non-chromaffin tissues...
January 1, 2018: Endocrine Regulations
https://www.readbyqxmd.com/read/29453409/a-potential-prognostic-long-noncoding-rna-signature-to-predict-recurrence-among-er-positive-breast-cancer-patients-treated-with-tamoxifen
#19
Kang Wang, Jie Li, Yong-Fu Xiong, Zhen Zeng, Xiang Zhang, Hong-Yuan Li
Limited predictable long noncoding RNA (lncRNA) signature was reported in tamoxifen resistance among estrogen receptor (ER)-positive breast cancer (BC) patients. The aim of this study was to identify and assess prognostic lncRNA signature to predict recurrence among ER-positive BC patients treated with tamoxifen. Cohorts from Gene Expression Omnibus (GEO) (n = 298) and The Cancer Genome Atlas (TCGA) (n = 160) were defined as training and validation cohort, respectively. BC relapse associated lnRNAs was identify within training cohort, and the predictable value of recurrence was assessed in both cohorts...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29452772/metabolic-and-lipidomic-reprogramming-in-renal-cell-carcinoma-subtypes-reflects-regions-of-tumor-origin
#20
Elke Schaeffeler, Florian Büttner, Anna Reustle, Verena Klumpp, Stefan Winter, Steffen Rausch, Pascale Fisel, Jörg Hennenlotter, Stephan Kruck, Arnulf Stenzl, Judith Wahrheit, Denise Sonntag, Marcus Scharpf, Falko Fend, Abbas Agaimy, Arndt Hartmann, Jens Bedke, Matthias Schwab
BACKGROUND: Renal cell carcinoma (RCC) consists of prognostic distinct subtypes derived from different cells of origin (eg, clear cell RCC [ccRCC], papillary RCC [papRCC], and chromophobe RCC [chRCC]). ccRCC is characterized by lipid accumulation and metabolic alterations, whereas data on metabolic alterations in non-ccRCC are limited. OBJECTIVE: We assessed metabolic alterations and the lipid composition of RCC subtypes and ccRCC-derived metastases. Moreover, we elucidated the potential of metabolites/lipids for subtype classification and identification of therapeutic targets...
February 13, 2018: European Urology Focus
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