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https://www.readbyqxmd.com/read/28723760/bioinformatics-analysis-to-identify-the-critical-genes-micrornas-and-long-noncoding-rnas-in-melanoma
#1
Qian Zhang, Yang Wang, Jiulong Liang, Yaguang Tian, Yu Zhang, Kai Tao
Melanoma, which is usually induced by ultraviolet light exposure and the following DNA damage, is the most dangerous skin cancer. The purpose of the present study was to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the ArrayExpress database, which included 21 primary melanoma samples and 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing data of cutaneous melanoma were downloaded from The Cancer Genome Atlas database. After identifying the differentially expressed genes (DEGs) using Limma package, enrichment analysis and protein-protein interaction (PPI) network analysis were performed separately for them using DAVID software and Cytoscape software...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28723667/resistance-to-ctla-4-checkpoint-inhibition-reversed-through-selective-elimination-of-granulocytic-myeloid-cells
#2
Paul E Clavijo, Ellen C Moore, Jianhong Chen, Ruth J Davis, Jay Friedman, Young Kim, Carter Van Waes, Zhong Chen, Clint T Allen
PURPOSE: Local immunosuppression remains a critical problem that limits clinically meaningful response to checkpoint inhibition in patients with head and neck cancer. Here, we assessed the impact of MDSC elimination on responses to CTLA-4 checkpoint inhibition. EXPERIMENTAL DESIGN: Murine syngeneic carcinoma immune infiltrates were characterized by flow cytometry. Granulocytic MDSCs (gMDSCs) were depleted and T-lymphocyte antigen-specific responses were measured...
June 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28719033/identification-of-driver-copy-number-alterations-in-diverse-cancer-types-and-application-in-drug-repositioning
#3
Wenbin Zhou, Zhangxiang Zhao, Ruiping Wang, Yue Han, Chengyu Wang, Fan Yang, Ya Han, Haihai Liang, Lishuang Qi, Chenguang Wang, Zheng Guo, Yunyan Gu
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside in recurrently aberrant genomic regions, including a large number of genes or non-coding genes, which remain a challenge for decoding the SCNAs involved in carcinogenesis. Here, we propose a new approach to comprehensively identify drivers, using 8740 cancer samples involving 18 cancer types from The Cancer Genome Atlas (TCGA)...
July 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28718916/the-genetic-landscape-of-endometrial-clear-cell-carcinomas
#4
Deborah F DeLair, Kathleen A Burke, Pier Selenica, Raymond S Lim, Sasinya N Scott, Sumit Middha, Abhinita S Mohanty, Donavan T Cheng, Michael F Berger, Robert A Soslow, Britta Weigelt
Clear cell carcinoma of the endometrium is a rare type of endometrial cancer generally associated with an aggressive clinical behavior. Here we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs) and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs...
July 18, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28718375/emp3-is-induced-by-twist1-2-and-regulates-epithelial-to-mesenchymal-transition-of-gastric-cancer-cells
#5
Ming Han, Wanpeng Xu
In this study, we aimed to explore new downstream effectors of TWIST1/2 in inducing epithelial-to-mesenchymal transition in gastric cancer. Bioinformatic data mining was performed using data in The Cancer Genome Atlas Stomach Adenocarcinoma. Survival curves were generated using Kaplan-Meier plotter. Gastric cancer cell lines (AGS and SGC-7901) were used as in vitro cell model to investigate the regulative effect of TWIST1/2 on epithelial membrane protein 3 expression and the progression of epithelial-to-mesenchymal transition...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28718365/tmem88-ccl14-and-clec3b-as-prognostic-biomarkers-for-prognosis-and-palindromia-of-human-hepatocellular-carcinoma
#6
Xin Zhang, Jin-Xiang Wan, Zun-Ping Ke, Feng Wang, Hai-Xia Chai, Jia-Qiang Liu
Hepatocellular carcinoma is one of the most mortal and prevalent cancers with increasing incidence worldwide. Elucidating genetic driver genes for prognosis and palindromia of hepatocellular carcinoma helps managing clinical decisions for patients. In this study, the high-throughput RNA sequencing data on platform IlluminaHiSeq of hepatocellular carcinoma were downloaded from The Cancer Genome Atlas with 330 primary hepatocellular carcinoma patient samples. Stable key genes with differential expressions were identified with which Kaplan-Meier survival analysis was performed using Cox proportional hazards test in R language...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28717245/development-and-validation-of-a-three-gene-prognostic-signature-for-patients-with-hepatocellular-carcinoma
#7
Binghua Li, Wendu Feng, Ouyang Luo, Tiancheng Xu, Yajuan Cao, Hongyan Wu, Decai Yu, Yitao Ding
Hepatocellular carcinoma (HCC) is the leading cause of cancer-related death worldwide, because recurrence often occurs in most HCC patients undergoing hepatectomy. It is necessary to identify patients with high risk for recurrence and adopt effective therapies. An obstacle to monitor patients at high risk for poor prognosis has been the lack of useful predictive biomarkers. Fortunately, recent progress in system biology allows to screen the biomarkers for HCC prognosis in a high-throughput manner. In this study, we performed systematic Kaplan-Meier survival analysis of the whole mRNA transcriptomics based on the Cancer Genome Atlas project (TCGA) and developed a three-gene prognostic signature composing of three genes UPB1, SOCS2 and RTN3...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717182/widespread-alternative-exon-usage-in-clinically-distinct-subtypes-of-invasive-ductal-carcinoma
#8
Sunniva Stordal Bjørklund, Anshuman Panda, Surendra Kumar, Michael Seiler, Doug Robinson, Jinesh Gheeya, Ming Yao, Grethe I Grenaker Alnæs, Deborah Toppmeyer, Margit Riis, Bjørn Naume, Anne-Lise Børresen-Dale, Vessela N Kristensen, Shridar Ganesan, Gyan Bhanot
Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716985/two-microrna-signatures-for-malignancy-and-immune-infiltration-predict-overall-survival-in-advanced-epithelial-ovarian-cancer
#9
Ilya Korsunsky, Janaki Parameswaran, Iuliana Shapira, John Lovecchio, Andrew Menzin, Jill Whyte, Lisa Dos Santos, Sharon Liang, Tawfiqul Bhuiya, Mary Keogh, Houman Khalili, Cassandra Pond, Anthony Liew, Andrew Shih, Peter K Gregersen, Annette T Lee
MicroRNAs have been established as key regulators of tumor gene expression and as prime biomarker candidates for clinical phenotypes in epithelial ovarian cancer (EOC). We analyzed the coexpression and regulatory structure of microRNAs and their co-localized gene targets in primary tumor tissue of 20 patients with advanced EOC in order to construct a regulatory signature for clinical prognosis. We performed an integrative analysis to identify two prognostic microRNA/mRNA coexpression modules, each enriched for consistent biological functions...
July 17, 2017: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/28714987/comparison-of-algorithms-for-the-detection-of-cancer-drivers-at-subgene-resolution
#10
Eduard Porta-Pardo, Atanas Kamburov, David Tamborero, Tirso Pons, Daniela Grases, Alfonso Valencia, Nuria Lopez-Bigas, Gad Getz, Adam Godzik
Understanding genetic events that lead to cancer initiation and progression remains one of the biggest challenges in cancer biology. Traditionally, most algorithms for cancer-driver identification look for genes that have more mutations than expected from the average background mutation rate. However, there is now a wide variety of methods that look for nonrandom distribution of mutations within proteins as a signal for the driving role of mutations in cancer. Here we classify and review such subgene-resolution algorithms, compare their findings on four distinct cancer data sets from The Cancer Genome Atlas and discuss how predictions from these algorithms can be interpreted in the emerging paradigms that challenge the simple dichotomy between driver and passenger genes...
July 17, 2017: Nature Methods
https://www.readbyqxmd.com/read/28714863/dna-methylation-based-immune-response-signature-improves-patient-diagnosis-in-multiple-cancers
#11
Jana Jeschke, Martin Bizet, Christine Desmedt, Emilie Calonne, Sarah Dedeurwaerder, Soizic Garaud, Alexander Koch, Denis Larsimont, Roberto Salgado, Gert Van den Eynden, Karen Willard Gallo, Gianluca Bontempi, Matthieu Defrance, Christos Sotiriou, François Fuks
BACKGROUND: The tumor immune response is increasingly associated with better clinical outcomes in breast and other cancers. However, the evaluation of tumor-infiltrating lymphocytes (TILs) relies on histopathological measurements with limited accuracy and reproducibility. Here, we profiled DNA methylation markers to identify a methylation of TIL (MeTIL) signature that recapitulates TIL evaluations and their prognostic value for long-term outcomes in breast cancer (BC). METHODS: MeTIL signature scores were correlated with clinical endpoints reflecting overall or disease-free survival and a pathologic complete response to preoperative anthracycline therapy in 3 BC cohorts from the Jules Bordet Institute in Brussels and in other cancer types from The Cancer Genome Atlas...
July 17, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28714374/screening-key-genes-and-mirnas-in-early-stage-colon-adenocarcinoma-by-rna-sequencing
#12
Jixi Liu, Fang Liu, Xiaoou Li, Xin Song, Lei Zhou, Jianzheng Jie
Colon adenocarcinoma is the third leading cause of cancer-related deaths across the world, developing novel and non-invasive diagnostic and prognostic biomarkers for the early-stage colon adenocarcinoma at molecular level is essential. In our study, RNA-sequencing was performed to identify the differentially expressed genes and miRNAs (DEmiRNAs) in early-stage colon adenocarcinoma compared to tissues of precancerous lesions, colonic intraepithelial neoplasia. The DEmiRNA-target interaction network was constructed and functional annotation of targets of DEmiRNAs was performed...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28714367/parp-1-serves-as-a-novel-molecular-marker-for-hepatocellular-carcinoma-in-a-southern-chinese-zhuang-population
#13
Jiatong Li, Dongwei Dou, Ping Li, Wenqi Luo, Wenxin Lv, Chengdong Zhang, Xiaowei Song, Yuan Yang, Yuening Zhang, Yanzhen Xu, Feifan Xiao, Yan Wei, Jian Qin, Hongtao Li, Xiaoli Yang
PARP-1 (poly(ADP-ribose) polymerase-1) plays an important role in tumorigenesis. Since its effects on different populations are varied, this study investigated the impact of PARP-1 on primary hepatocellular carcinoma in a Southern Chinese Zhuang population. We assessed the global PARP-1 messenger RNA expression in patients with hepatocellular carcinoma using The Cancer Genome Atlas dataset. Increased PARP-1 expression, related to alpha-fetoprotein level, was observed. The area under the receiver operating characteristic curve value was 0...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28714025/effect-of-ccl2-sirna-on-proliferation-and-apoptosis-in-the-u251-human-glioma-cell-line
#14
Bin Lu, Yue Zhou, Zhongzhou Su, Ai Yan, Peng Ding
Glioma is one of the most common types of tumor of the central nervous system. Increased expression of C‑C motif chemokine 2 (CCL2) has previously been observed in various types of cancer. The effect of CCL2 small interfering (si)RNA on the proliferation, angiogenesis and apoptosis of the glioma cell line U251 was investigated in the present study. Data on CCL2 expression in glioma and normal tissues were obtained from The Cancer Genome Atlas. A total of 30 patients with glioma were enrolled in the present study...
July 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28714017/targeting-vegfr-and-fgfr-in-head-and-neck-squamous-cell-carcinoma-in-vitro
#15
Roman C Brands, Luise M Knierim, Francesco De Donno, Valentin Steinacker, Stefan Hartmann, Axel Seher, Alexander C Kübler, Urs D A Müller-Richter
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease characterized by a tumor microenvironment (TME) that overexpresses vascular endothelial growth factor receptor (VEGFR) and fibroblast growth factor receptor (FGFR), which can lead to neovascularization, tumor growth and metastasis. Therapeutic strategies inhibiting these signaling pathways might lead to innovative HNSCC treatments. Five HNSCC cell lines were characterized based on VEGFR1-3 and FGFR1-4 expression by sqRT-PCR and treated with three different tyrosine kinase inhibitors (TKIs) (nintedanib, dovitinib and pazopanib), all of which are effective against VEGFR and FGFR family members...
July 10, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28713927/classifier-of-cross-talk-genes-predicts-the-prognosis-of-hepatocellular-carcinoma
#16
Xiaofeng Zhai, Qingfeng Xue, Qun Liu, Yuyu Guo, Zhe Chen
The present study aimed to establish a prediction model for hepatocellular carcinoma (HCC) based on the cross talk genes from important biological pathways involved in HCC. Differentially expressed genes (DEGs) for HCC were identified from mRNA profiles of GSE36376, which were mapped to protein‑protein interaction (PPI) networks from BioGrid and the human protein reference database. Then critical genes based on the deviation score and the degree of node were selected from the novel PPI network. Cross talk genes were screened from the network established based on the associations of gene‑gene, gene‑pathway and pathway‑pathway...
July 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28712776/clonal-evolution-in-paired-endometrial-intraepithelial-neoplasia-atypical-hyperplasia-and-endometrioid-adenocarcinoma
#17
Mariano Russo, James Broach, Kathryn Sheldon, Kenneth R Houser, Dajiang J Liu, Joshua Kesterson, Rebecca Phaeton, Carrie Hossler, Nadine Hempel, Maria Baker, Jordan M Newell, Richard Zaino, Joshua I Warrick
Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically-defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma...
July 13, 2017: Human Pathology
https://www.readbyqxmd.com/read/28711912/identification-of-two-novel-biomarkers-of-rectal-carcinoma-progression-and-prognosis-via-co-expression-network-analysis
#18
Min Sun, Taojiao Sun, Zhongshi He, Bin Xiong
mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied weighted gene co-expression network analysis to parse DEGs and eight clinical traits in 66 eligible RC samples...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28709407/trop2-enhances-invasion-of-thyroid-cancer-by-inducing-mmp2-through-erk-and-jnk-pathways
#19
Hongyu Guan, Zejun Guo, Weiwei Liang, Hai Li, Guohong Wei, Lijuan Xu, Haipeng Xiao, Yanbing Li
BACKGROUND: Mounting evidence has showed that Tumor-associated calcium signal transducer 2 (Trop2) is upregulated in various kinds of human cancers and plays important roles in tumorigenesis. However, the expression status and functional significance of Trop2 in thyroid cancer are largely unknown. METHODS: We first determined the expression of Trop2 by using RNAseqV2 data sets for thyroid cancer deposited on The Cancer Genome Atlas (TCGA) website. The expression of Trop2 was then confirmed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemistry assays...
July 14, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28708462/heterogeneous-enhancement-patterns-of-tumor-adjacent-parenchyma-at-mr-imaging-are-associated-with-dysregulated-signaling-pathways-and-poor-survival-in-breast-cancer
#20
Jia Wu, Bailiang Li, Xiaoli Sun, Guohong Cao, Daniel L Rubin, Sandy Napel, Debra M Ikeda, Allison W Kurian, Ruijiang Li
Purpose To identify the molecular basis of quantitative imaging characteristics of tumor-adjacent parenchyma at dynamic contrast material-enhanced magnetic resonance (MR) imaging and to evaluate their prognostic value in breast cancer. Materials and Methods In this institutional review board-approved, HIPAA-compliant study, 10 quantitative imaging features depicting tumor-adjacent parenchymal enhancement patterns were extracted and screened for prognostic features in a discovery cohort of 60 patients. By using data from The Cancer Genome Atlas (TCGA), a radiogenomic map for the tumor-adjacent parenchymal tissue was created and molecular pathways associated with prognostic parenchymal imaging features were identified...
July 14, 2017: Radiology
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