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https://www.readbyqxmd.com/read/28454465/microarray-based-analysis-of-gene-regulation-by-mesenchymal-stem-cells-in-breast-cancer
#1
Ming Zhang, Chang E Gao, Wen Hui Li, Yi Yang, Li Chang, Jian Dong, Yan Xin Ren, De Dian Chen
Breast cancer is one of the most common malignant tumors with a high case-fatality rate among women. The present study aimed to investigate the effects of mesenchymal stem cells (MSCs) on breast cancer by exploring the potential underlying molecular mechanisms. The expression profile of GSE43306, which refers to MDA-MB-231 cells with or without a 1:1 ratio of MSCs, was downloaded from Gene Expression Omnibus database for differentially expressed gene (DEG) screening. The Database for Annotation, Visualization and Integrated Discovery was used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454461/prognostic-value-of-mlh1-promoter-methylation-in-male-patients-with-esophageal-squamous-cell-carcinoma
#2
Dongping Wu, Xiaoying Chen, Yan Xu, Haiyong Wang, Guangmao Yu, Luping Jiang, Qingxiao Hong, Shiwei Duan
The DNA mismatch repair (MMR) gene MutL homolog 1 (MLH1) is critical for the maintenance of genomic integrity. Methylation of the MLH1 gene promoter was identified as a prognostic marker for numerous types of cancer including glioblastoma, colorectal, ovarian and gastric cancer. The present study aimed to determine whether MLH1 promoter methylation was associated with survival in male patients with esophageal squamous cell carcinoma (ESCC). Formalin-fixed, paraffin-embedded ESCC tissues were collected from 87 male patients...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454439/oct4-induces-emt-through-lef1-%C3%AE-catenin-dependent-wnt-signaling-pathway-in-hepatocellular-carcinoma
#3
Lu Sun, Tianhua Liu, Shu Zhang, Kun Guo, Yinkun Liu
Octamer 4 (Oct4), a member of the Pit-Oct-Unc transcription factor family required to maintain self-renewal and pluripotency of embryonic stem cells, has been previously identified to be associated with tumorigenesis and malignant transformation of numerous types of cancer including hepatocellular carcinoma (HCC). The present data shows that Oct4 enhances cancer stem cell properties and increases invasion ability in the Huh7 cell line. To increase understanding of the role of Oct4 in HCC, the present study used a functional genomics approach and analyzed the resulting transcriptional profiles to identify Oct4-dependent genes in Huh7...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454437/polycomb-group-expression-signatures-in-the-malignant-progression-of-gliomas
#4
Qi Hu, Weining Wu, Ailiang Zeng, Tianfu Yu, Feng Shen, Er Nie, Yingyi Wang, Ning Liu, Junxia Zhang, Yongping You
Polycomb group (PcG) proteins form at least two key complexes, namely polycomb repressive complex 1 and polycomb repressive complex 2. These complexes are involved in the progression of various cancers. Systematic research has not been conducted on the aberrant expression of PcG members in gliomas. Using the Chinese Glioma Genome Atlas data set, PcG expression patterns between normal brain tissues and glioma samples were analyzed, and a PcG-based classifier was then developed using BRB Cox regression and risk-score model...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454428/the-regulation-of-proteins-associated-with-the-cytoskeleton-by-hepatitis-b-virus-x-protein-during-hepatocarcinogenesis
#5
Fanyun Kong, Hongjuan You, Renxian Tang, Kuiyang Zheng
Hepatocellular carcinoma (HCC) is a major malignant disease worldwide, and chronic hepatitis B virus (HBV) infection is one of the primary causes for this type of cancer. Hepatitis B virus X protein (HBx) is a non-structural protein encoded by the viral genome that has significant effects on the pathogenesis of HCC. With the development of high-throughput assays and technologies, the abnormal HBx-induced expression of certain cellular proteins with assorted biological functions has been investigated. These target proteins identified by various methods include specific proteins associated with the cellular cytoskeleton, which contribute to HBx-induced hepatocarcinogenesis...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454418/epigenetic-silencing-of-protocadherin-10-in-colorectal-cancer
#6
Xian Zhong, Hong Shen, Jianshan Mao, Jiawei Zhang, Weidong Han
Colorectal cancer (CRC) is one of the most common types of malignant tumor in the world and occurs through a multi-step process resulting from the accumulation of genetic and epigenetic alterations of the genome. Although the molecular mechanisms of the pathogenesis of CRC remain unclear, the inactivation of tumor suppressor genes (TSGs) through promoter methylation serves an important role. Aberrant methylation is a well-defined marker of CRC. At present, the epigenetic silencing of protocadherin 10 (PCDH10) has been identified as an important TSG with key roles in colorectal carcinogenesis, invasion and metastasis as a frequent and early event...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454375/a-comprehensive-analysis-of-cancer-driving-mutations-and-genes-in-kidney-cancer
#7
Chengmei Long, Jinbo Jian, Xinchang Li, Gongxian Wang, Jingen Wang
An accumulation of driver mutations is important for cancer formation and progression, and leads to the disruption of genes and signaling pathways. The identification of driver mutations and genes has been the subject of numerous previous studies. The present study was performed to identify cancer-driving mutations and genes in renal cell carcinoma (RCC), prioritizing noncoding variants with a high functional impact, in order to analyze the most informative features. Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping version 2 (Polyphen2) and MutationAssessor were applied to predict deleterious mutations in the coding genome...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454321/the-loss-of-casp4-expression-is-associated-with-poor-prognosis-in-esophageal-squamous-cell-carcinoma
#8
Misako Shibamoto, Hidenari Hirata, Hidetoshi Eguchi, Genta Sawada, Noritaka Sakai, Yoshiaki Kajiyama, Koshi Mimori
Esophageal squamous cell carcinoma (ESCC) has high biological malignant potential among the various digestive tract cancers and is associated with a poor prognosis. To identify novel genes involved in tumor progression, the present study analyzed the genetic and transcriptional alterations in two clinical cohorts, totaling 157 cases of ESCC (78 cases from the discovery set and 79 cases from the validation set). From the discovery set, gene expression and copy number profiles were analyzed using expression arrays and array-comparative genomic hybridization, respectively...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454300/single-cell-genomic-profiling-of-acute-myeloid-leukemia-for-clinical-use-a-pilot-study
#9
Benedict Yan, Yongli Hu, Kenneth H K Ban, Zenia Tiang, Christopher Ng, Joanne Lee, Wilson Tan, Lily Chiu, Tin Wee Tan, Elaine Seah, Chin Hin Ng, Wee-Joo Chng, Roger Foo
Although bulk high-throughput genomic profiling studies have led to a significant increase in the understanding of cancer biology, there is increasing awareness that bulk profiling approaches do not completely elucidate tumor heterogeneity. Single-cell genomic profiling enables the distinction of tumor heterogeneity, and may improve clinical diagnosis through the identification and characterization of putative subclonal populations. In the present study, the challenges associated with a single-cell genomics profiling workflow for clinical diagnostics were investigated...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454214/genome-wide-analysis-of-gynecologic-cancer-the-cancer-genome-atlas-in-ovarian-and-endometrial-cancer
#10
Moito Iijima, Kouji Banno, Ryuichiro Okawa, Megumi Yanokura, Miho Iida, Takashi Takeda, Haruko Kunitomi-Irie, Masataka Adachi, Kanako Nakamura, Kiyoko Umene, Yuya Nogami, Kenta Masuda, Eiichiro Tominaga, Daisuke Aoki
Cancer typically develops due to genetic abnormalities, but a single gene abnormality cannot completely account for the onset of cancer. The Cancer Genome Atlas (CGA) project was conducted for the cross-sectional genome-wide analysis of numerous genetic abnormalities in various types of cancer. This approach has facilitated the identification of novel AT-rich interaction domain 1A gene mutations in ovarian clear cell carcinoma, frequent tumor protein 53 (TP53) gene mutations in high-grade ovarian serous carcinoma, and Kirsten rat sarcoma and B-rapidly accelerated fibrosarcoma proto-oncogene, serine/threonine kinase gene mutations in low-grade ovarian serous carcinoma...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454108/telomere-erosion-in-nf1-tumorigenesis
#11
Rhiannon E Jones, Julia W Grimstead, Ashni Sedani, Duncan Baird, Meena Upadhyaya
Neurofibromatosis type 1 (NF1; MIM# 162200) is a familial cancer syndrome that affects 1 in 3,500 individuals worldwide and is inherited in an autosomal dominant fashion. Malignant Peripheral Nerve Sheath Tumors (MPNSTs) represent a significant cause of morbidity and mortality in NF1 and currently there is no treatment or definite prognostic biomarkers for these tumors. Telomere shortening has been documented in numerous tumor types. Short dysfunctional telomeres are capable of fusion and it is considered that the ensuing genomic instability may facilitate clonal evolution and the progression to malignancy...
April 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28454104/rna-sequencing-based-cell-proliferation-analysis-across-19-cancers-identifies-a-subset-of-proliferation-informative-cancers-with-a-common-survival-signature
#12
Ryne C Ramaker, Brittany N Lasseigne, Andrew A Hardigan, Laura Palacio, David S Gunther, Richard M Myers, Sara J Cooper
Despite advances in cancer diagnosis and treatment strategies, robust prognostic signatures remain elusive in most cancers. Cell proliferation has long been recognized as a prognostic marker in cancer, but the generation of comprehensive, publicly available datasets allows examination of the links between cell proliferation and cancer characteristics such as mutation rate, stage, and patient outcomes. Here we explore the role of cell proliferation across 19 cancers (n = 6,581 patients) by using tissue-based RNA sequencing data from The Cancer Genome Atlas Project and calculating a 'proliferative index' derived from gene expression associated with Proliferating Cell Nuclear Antigen (PCNA) levels...
April 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28453745/percentage-of-mesenchymal-stem-cells-in-high-grade-glioma-tumor-samples-correlates-with-patient-survival
#13
Tal Shahar, Uri Rozovski, Kenneth R Hess, Anwar Hossain, Joy Gumin, Feng Gao, Gregory N Fuller, Lindsey Goodman, Erik P Sulman, Frederick F Lang
Background.: Human mesenchymal stem cells (hMSCs) have been shown to reside as stromal cells in human gliomas as glioma-associated hMSCs (GA-hMSCs), but their biological role remains unclear. Because recent evidence indicates that GA-hMSCs drive tumor cell proliferation and stemness, we hypothesized that a higher percentage of GA-hMSCs in tumors predicts poor patient prognosis. Method.: We determined the percentage of cells coexpressing GA-hMSC markers CD105+/CD73+/CD90+ from patients with newly diagnosed high-grade glioma and analyzed the association between this percentage and overall survival (OS) in 3 independent cohorts: fresh surgical glioblastoma specimens (cohort 1, N = 9), cultured tumor specimens at passage 3 (cohort 2, N = 28), and The Cancer Genome Atlas (TCGA) database...
May 1, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28453743/targeted-next-generation-sequencing-of-pediatric-neuro-oncology-patients-improves-diagnosis-identifies-pathogenic-germline-mutations-and-directs-targeted-therapy
#14
Cassie N Kline, Nancy M Joseph, James P Grenert, Jessica van Ziffle, Eric Talevich, Courtney Onodera, Mariam Aboian, Soonmee Cha, David R Raleigh, Steve Braunstein, Joseph Torkildson, David Samuel, Michelle Bloomer, Alejandra G de Alba Campomanes, Anuradha Banerjee, Nicholas Butowski, Corey Raffel, Tarik Tihan, Andrew W Bollen, Joanna J Phillips, W Michael Korn, Iwei Yeh, Boris C Bastian, Nalin Gupta, Sabine Mueller, Arie Perry, Theodore Nicolaides, David A Solomon
Background.: Molecular profiling is revolutionizing cancer diagnostics and leading to personalized therapeutic approaches. Herein we describe our clinical experience performing targeted sequencing for 31 pediatric neuro-oncology patients. Methods.: We sequenced 510 cancer-associated genes from tumor and peripheral blood to identify germline and somatic mutations, structural variants, and copy number changes. Results.: Genomic profiling was performed on 31 patients with tumors including 11 high-grade gliomas, 8 medulloblastomas, 6 low-grade gliomas, 1 embryonal tumor with multilayered rosettes, 1 pineoblastoma, 1 uveal ganglioneuroma, 1 choroid plexus carcinoma, 1 chordoma, and 1 high-grade neuroepithelial tumor...
May 1, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28453708/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#15
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C L Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453704/genomic-characterization-of-her2-positive-breast-cancer-and-response-to-neoadjuvant-trastuzumab-and-chemotherapy-results-from-the-acosog-z1041-alliance-trial
#16
R Lesurf, O L Griffith, M Griffith, J Hundal, L Trani, M A Watson, R Aft, M J Ellis, D Ota, V J Suman, F Meric-Bernstam, A M Leitch, J C Boughey, G Unzeitig, A U Buzdar, K K Hunt, E R Mardis
Background: HER2 (ERBB2) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference. Patients and methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483)...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453696/epstein-barr-virus-associated-gastric-cancer-reveals-intratumoral-heterogeneity-of-pik3ca-mutations
#17
C Böger, S Krüger, H M Behrens, S Bock, J Haag, H Kalthoff, C Röcken
Background: Recent whole-genome sequencing identified four molecular subtypes of gastric cancer (GC), of which the subgroup of Epstein-Barr virus-associated GC (EBVaGC) showed a significant enrichment of PIK3CA mutations. We here aimed to validate independently the enrichment of PIK3CA mutations in EBVaGC of a Central European GC cohort, to correlate EBV status with clinico-pathological patient characteristics and to test for a major issue of GC, intratumoral heterogeneity. Patients and methods: In a first step, 484 GCs were screened for EBV and PIK3CA hot spot mutations of exon 9/20 using EBER in situ hybridization and pyrosequencing, respectively...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453695/genetic-variants-of-dna-repair-related-genes-predict-efficacy-of-tas-102-in-patients-with-refractory-metastatic-colorectal-cancer
#18
M Suenaga, M Schirripa, S Cao, W Zhang, D Yang, S Murgioni, D Rossini, F Marmorino, A Mennitto, Y Ning, S Okazaki, M D Berger, Y Miyamoto, R Gopez, A Barzi, T Yamaguchi, F Loupakis, H-J Lenz
Background: Tri-phosphorylated trifluridine (FTD) incorporation into DNA is TAS-102's main anti-tumor action. We tested whether genetic polymorphisms in homologous recombination (HR) and cell cycle checkpoint pathway for DNA repair is associated with outcomes in refractory metastatic colorectal cancer (mCRC) patients treated with TAS-102. Patients and methods: We analyzed genomic DNA extracted from 233 samples of three cohorts: an evaluation cohort of 52 patients receiving TAS-102, a validation cohort of 129 patients receiving TAS-102 and a control cohort of 52 patients receiving regorafenib...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453687/gdisc-a-web-portal-for-integrative-analysis-of-gene-drug-interaction-for-survival-in-cancer
#19
John Christian Givhan Spainhour, Juho Lim, Peng Qiu
Summary: Survival analysis has been applied to The Cancer Genome Atlas (TCGA) data. Although drug exposure records are available in TCGA, existing survival analyses typically did not consider drug exposure, partly due to naming inconsistencies in the data. We have spent extensive effort to standardize the drug exposure data, which enabled us to perform survival analysis on drug-stratified subpopulations of cancer patients. Using this strategy, we integrated gene copy number data, drug exposure data and patient survival data to infer gene-drug interactions that impact survival...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453651/a-panoromic-view-of-personal-cancer-genomes
#20
Lidia Mateo, Oriol Guitart-Pla, Carles Pons, Miquel Duran-Frigola, Roberto Mosca, Patrick Aloy
The massive molecular profiling of thousands of cancer patients has led to the identification of many tumor type specific driver genes. However, only a few (or none) of them are present in each individual tumor and, to enable precision oncology, we need to interpret the alterations found in a single patient. Cancer PanorOmics (http://panoromics.irbbarcelona.org) is a web-based resource to contextualize genomic variations detected in a personal cancer genome within the body of clinical and scientific evidence available for 26 tumor types, offering complementary cohort- and patient-centric views...
April 27, 2017: Nucleic Acids Research
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