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https://www.readbyqxmd.com/read/28742980/disease-relevant-modifications-of-the-methylome-and-transcriptome-by-particulate-matter-pm2-5-from-biomass-combustion
#1
Katharina Heßelbach, Gwang-Jin Kim, Stephan Flemming, Thomas Häupl, Marc Bonin, Regina Dornhof, Stefan Günther, Irmgard Merfort, Matjaz Humar
Exposure to particulate matter (PM) is recognized as a major health hazard, but molecular responses are still insufficiently described. We analyzed the epigenetic impact of ambient PM2.5 from biomass combustion on the methylome of primary human bronchial epithelial BEAS-2B cells using the Illumina HumanMethylation450 BeadChip. The transcriptome was determined by the Affymetrix HG-U133 Plus 2.0 Array. PM2.5 induced genome wide alterations of the DNA methylation pattern, including differentially methylated CpGs in the promoter region associated with CpG islands...
July 25, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28742856/fit-for-genomic-and-proteomic-purposes-sampling-the-fitness-of-nucleic-acid-and-protein-derivatives-from-formalin-fixed-paraffin-embedded-tissue
#2
Anna Yakovleva, Jordan L Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lang, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules...
2017: PloS One
https://www.readbyqxmd.com/read/28742845/evaluation-of-k-ras-and-p53-expression-in-pancreatic-adenocarcinoma-using-the-cancer-genome-atlas
#3
Liming Lu, Jingchun Zeng
Genetic alterations in K-ras and p53 are thought to be critical in pancreatic cancer development and progression. However, K-ras and p53 expression in pancreatic adenocarcinoma have not been systematically examined in The Cancer Genome Atlas (TCGA) Data Portal. Information regarding K-ras and p53 alterations, mRNA expression data, and protein/protein phosphorylation abundance was retrieved from The Cancer Genome Atlas (TCGA) databases, and analyses were performed by the cBioPortal for Cancer Genomics. The mutual exclusivity analysis showed that events in K-ras and p53 were likely to co-occur in pancreatic adenocarcinoma (Log odds ratio = 1...
2017: PloS One
https://www.readbyqxmd.com/read/28742792/evidence-for-genetic-association-between-chromosome-1q-loci-and-predisposition-to-colorectal-neoplasia
#4
Stephanie A Schubert, Dina Ruano, Fadwa A Elsayed, Arnoud Boot, Stijn Crobach, Arantza Farina Sarasqueta, Bruce Wolffenbuttel, Melanie M van der Klauw, Jan Oosting, Carli M Tops, Ronald van Eijk, Hans Fa Vasen, Rolf Ham Vossen, Maartje Nielsen, Sergi Castellví-Bel, Clara Ruiz-Ponte, Ian Tomlinson, Malcolm G Dunlop, Pavel Vodicka, Juul T Wijnen, Frederik J Hes, Hans Morreau, Noel Fcc de Miranda, Rolf H Sijmons, Tom van Wezel
BACKGROUND: A substantial fraction of familial colorectal cancer (CRC) and polyposis heritability remains unexplained. This study aimed to identify predisposing loci in patients with these disorders. METHODS: Homozygosity mapping was performed using 222 563 SNPs in 302 index patients with various colorectal neoplasms and 3367 controls. Linkage analysis, exome and whole-genome sequencing were performed in a family affected by microsatellite stable CRCs. Candidate variants were genotyped in 10 554 cases and 21 480 controls...
July 25, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28742206/bioinformatics-analysis-of-rna-seq-data-revealed-critical-genes-in-colon-adenocarcinoma
#5
W-D Xi, Y-J Liu, X-B Sun, J Shan, L Yi, T-T Zhang
OBJECTIVE: RNA-seq data of colon adenocarcinoma (COAD) were analyzed with bioinformatics tools to discover critical genes in the disease. Relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. MATERIALS AND METHODS: RNA-seq data of COAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. False positive discovery (FDR) < 0.05 and |log2 (fold change)|>1 were set as the cut-offs to screen out differentially expressed genes (DEGs)...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28741984/multiple-ct-scans-extend-lifespan-by-delaying-cancer-progression-in-cancer-prone-mice
#6
Jennifer A Lemon, Nghi Phan, Douglas R Boreham
Computed tomography (CT) scans are a routine diagnostic imaging technique that utilize low-energy X rays with an average absorbed dose of approximately 10 mGy per clinical whole-body CT scan. The growing use of CT scans in the clinic has raised concern of increased carcinogenic risk in patients exposed to ionizing radiation from diagnostic procedures. The goal of this study was to better understand cancer risk associated with low-dose exposures from CT scans. Historically, low-dose exposure preceding a larger challenge dose increases tumor latency, but does little to impact tumor frequency in Trp53(+/-) mice...
July 25, 2017: Radiation Research
https://www.readbyqxmd.com/read/28741788/molecular-analysis-of-single-circulating-tumour-cells-following-long-term-storage-of-clinical-samples
#7
Barbara Mesquita, Dominic G Rothwell, Deborah J Burt, Francesca Chemi, Fabiola Fernandez-Gutierrez, Daniel Slane-Tan, Jenny Antonello, Mathew Carter, Louise Carter, Marina Parry, Lynsey Franklin, Richard Marais, Fiona Blackhall, Caroline Dive, Ged Brady
The CellSearch® semi-automated CTC enrichment and staining system has been established as the "gold standard" for CTC enumeration with CellSearch® CTC counts recognized by the FDA as prognostic for a number of cancers. We and others have gone on to show that molecular analysis of CellSearch® CTCs isolated shortly after CellSearch® enrichment provides another valuable layer of information that has potential clinical utility including predicting response to treatment. Although CellSearch® CTCs can be readily isolated after enrichment, the process of analysing a single CellSearch® patient sample, which may contain many CTCs, is both time consuming and costly...
July 25, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28741503/the-pushmi-pullyu-of-dna-repair-clinical-synthetic-lethality
#8
REVIEW
S Percy Ivy, Johann de Bono, Elise C Kohn
Maintenance of genomic integrity is critical for adaptive survival in the face of endogenous and exogenous environmental stress. The loss of stability and fidelity in the genome caused by cancer and cancer treatment provides therapeutic opportunities to leverage the critical balance between DNA injury and repair. Blocking repair and pushing damaged DNA through the cell cycle using therapeutic inhibitors exemplify the 'pushmi-pullyu' effect of disrupted DNA repair. DNA repair inhibitors (DNARi) can be separated into five biofunctional categories: sensors, mediators, transducers, effectors, and collaborators that recognize DNA damage, propagate injury DNA messages, regulate cell cycle checkpoints, and alter the microenvironment...
November 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28741493/derisking-drug-induced-carcinogenicity-for-novel-therapeutics
#9
REVIEW
Jonathan G Moggs, Timothy MacLachlan, Hans-Joerg Martus, Philip Bentley
Assessing the carcinogenic potential of innovative drugs spanning diverse therapeutic modalities and target biology represents a major challenge during drug development. Novel modalities, such as cell and gene therapies that involve intrinsic genetic modification of the host genome, require distinct approaches for identification of cancer hazard. We emphasize the need for customized weight-of-evidence cancer risk assessments based on mode of action that balance multiple options for preclinical identification of cancer hazard with appropriate labeling of clinical products and risk management plans...
August 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28741489/epigenomic-consequences-of-coding-and-noncoding-driver-mutations
#10
REVIEW
Xiaosai Yao, Manjie Xing, Wen Fong Ooi, Patrick Tan, Bin Tean Teh
Chromatin alterations are integral to the pathogenic process of cancer, as demonstrated by recent discoveries of frequent mutations in chromatin-modifier genes and aberrant DNA methylation states in different cancer types. Progress is being made on elucidating how chromatin alterations, and how proteins catalyzing these alterations, mechanistically contribute to tissue-specific tumorigenesis. In parallel, technologies enabling the genome-wide profiling of histone modifications have revealed the existence of noncoding driver genetic alterations in cancer...
October 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28741488/extraordinary-cancer-epigenomics-thinking-outside-the-classical-coding-and-promoter-box
#11
REVIEW
Matthew Murtha, Manel Esteller
The advent of functional genomics powered by high-throughput sequencing has given us a new appreciation of the genomic sequences that lie outside the canonical promoter-coding sequence box. These regions harbor distant regulatory elements, enhancers, super-enhancers, insulators, alternative promoters, and sequences that transcribe as noncoding RNAs (ncRNAs) such as miRNAs and long ncRNAs. These functional genomics studies have also enabled a clearer understanding of the role of the 3D structure of the genome in epigenetic regulation...
October 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28741487/difference-makers-chromosomal-instability-versus-aneuploidy-in-cancer
#12
REVIEW
Richard H van Jaarsveld, Geert J P L Kops
Human cancers harbor great numbers of genomic alterations. One of the most common alterations is aneuploidy, an imbalance at the chromosome level. Some aneuploid cancer cell populations show varying chromosome copy number alterations over time, a phenotype known as 'chromosomal instability' (CIN). Chromosome segregation errors in mitosis are the most common cause for CIN in vitro, and these are also thought to underlie the aneuploidies seen in clinical cancer samples. However, CIN and aneuploidy are different traits and they are likely to have distinct impacts on tumor evolution and clinical tumor behavior...
October 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28740869/comparing-sequencing-assays-and-human-machine-analyses-in-actionable-genomics-for-glioblastoma
#13
Kazimierz O Wrzeszczynski, Mayu O Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Vladimir Vacic, Raquel Norel, Erhan Bilal, Ewa A Bergmann, Julia L Moore Vogel, Jeffrey N Bruce, Andrew B Lassman, Peter Canoll, Christian Grommes, Steve Harvey, Laxmi Parida, Vanessa V Michelini, Michael C Zody, Vaidehi Jobanputra, Ajay K Royyuru, Robert B Darnell
OBJECTIVE: To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. METHODS: Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs...
August 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28740578/clinical-performance-of-e2fs-1-3-in-kidney-clear-cell-renal-cancer-evidence-from-bioinformatics-analysis
#14
Bin Liang, Jianying Zhao, Xuan Wang
Extensive research on the E2F transcription factor family has led to numerous insights that E2Fs were involved not only in proliferation and tumorigenesis but also in apoptosis and differentiation. In the present study, we analyzed the differential expression of E2Fs1-3 genes, and also evaluated the impact of E2Fs 1-3 genes expression on clinical outcome from the Cancer Genome Atlas (TCGA) database. The results showed that E2F1, E2F2 and E2F3 expression was increased in KIRC tissues than matched normal tissues (E2F1, P < 0...
May 2017: Genes & Cancer
https://www.readbyqxmd.com/read/28740569/dna-oncogenic-virus-induced-oxidative-stress-genomic-damage-and-aberrant-epigenetic-alterations
#15
REVIEW
Mankgopo Magdeline Kgatle, Catherine Wendy Spearman, Asgar Ali Kalla, Henry Norman Hairwadzi
Approximately 20% of human cancers is attributable to DNA oncogenic viruses such as human papillomavirus (HPV), hepatitis B virus (HBV), and Epstein-Barr virus (EBV). Unrepaired DNA damage is the most common and overlapping feature of these DNA oncogenic viruses and a source of genomic instability and tumour development. Sustained DNA damage results from unceasing production of reactive oxygen species and activation of inflammasome cascades that trigger genomic changes and increased propensity of epigenetic alterations...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/28740507/mir-195-inhibits-tumor-growth-and-metastasis-in-papillary-thyroid-carcinoma-cell-lines-by-targeting-ccnd1-and-fgf2
#16
Yali Yin, Shubin Hong, Shuang Yu, Yanrui Huang, Shuwei Chen, Yujie Liu, Quan Zhang, Yanbing Li, Haipeng Xiao
BACKGROUND: MicroRNA (miRNA) dysregulation was commonly seen in papillary thyroid carcinoma (PTC), and miR-195 was verified to be downregulated in PTC by the large data set analysis from The Cancer Genome Atlas (TCGA). Our study aimed to explore the biological functions and the underlying molecular mechanisms of miR-195 in PTC. METHODS: The relative expression of miR-195 and its target genes were assessed by quantitative RT-PCR assay in 38 pairs of PTC and the adjacent thyroid tissues...
2017: International Journal of Endocrinology
https://www.readbyqxmd.com/read/28739746/association-of-intron-microsatellite-instability-and-exon-mutational-profile-of-tp53-in-human-gastric-cancers
#17
Xueyun Huo, Xiaoqin Xiao, Shuangyue Zhang, Deshan Zhou, Zhenwen Chen
BACKGROUND/AIM: Microsatellite instability (MSI) is a hallmark of genomic instability. In gastric cancer (GC), MSI phenotype is an important molecular subgroup that is often closely correlated with elevated mutation rates on the whole genome level. However, on a single gene level, it is still unknown whether the MSI status of a gene is correlated with the mutational profile of the gene itself. MATERIALS AND METHODS: We analyzed intron MSI status and exon mutational profile of TP53 through short tandem repeat (STR) scanning and direct sequencing respectively in gastric cancers and their matched normal tissues...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28739740/global-analysis-of-mirna-mrna-interaction-network-in-breast-cancer-with-brain-metastasis
#18
Zhixin Li, Zhiqiang Peng, Siyu Gu, Junfang Zheng, Duiping Feng, Qiong Qin, Junqi He
BACKGROUND: MicroRNAs (miRNAs) have been linked to a number of cancer types including breast cancer. The rate of brain metastases is 10-30% in patients with advanced breast cancer which is associated with poor prognosis. The potential application of miRNAs in the diagnostics and therapeutics of breast cancer with brain metastasis is an area of intense interest. In an initial effort to systematically address the differential expression of miRNAs and mRNAs in primary breast cancer which may provide clues for early detection of brain metastasis, we analyzed the consequent changes in global patterns of gene expression in Gene Expression Omnibus (GEO) data set obtained by microarray from patients with in situ carcinoma and patients with brain metastasis...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28739735/knockdown-of-epha1-using-crispr-cas9-suppresses-aggressive-properties-of-ovarian-cancer-cells
#19
Yuxin Cui, B O Wu, Valentina Flamini, Bronwen A J Evans, Deshan Zhou, Wen G Jiang
BACKGROUND/AIM: Overexpression of erythropoietin-producing hepatocellular A1 (EPHA1), a member of the EPH super family, is frequently observed in various cancer types. The dysregulated interaction of EPHA1 with its ligand Ephrin A1 has been linked to the progression of ovarian cancer (OC). However, the contribution of EPHA1 in the regulation of the aggressive properties of OC cells remains unknown. MATERIALS AND METHODS: In this study we investigated the differential expression of EPHA1 in human OC cells...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28739729/the-axis-of-cxcr4-sdf-1-plays-a-role-in-colon-cancer-cell-adhesion-through-regulation-of-the-akt-and-igf1r-signalling-pathways
#20
Fei Zheng, Zhongtao Zhang, Valentina Flamini, Wen G Jiang, Yuxin Cui
BACKGROUND/AIM: Colorectal cancer (CRC) is the third most common cancer in the world. The high mortality of this tumor is mainly due to its invasive properties, as it forms metastases in multiple organs, preferentially in the liver. There has evidence showing that C-X-C chemokine receptor type 4 (CXCR-4) and its ligand, stromal cell-derived factor-1 (SDF-1), plays an important role in cancer progression and metastasis. However, the molecular mechanism underling the CRCR4-mediated CRC metastasis has not been well characterized...
August 2017: Anticancer Research
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