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https://www.readbyqxmd.com/read/29050338/tumor-infiltrating-b-cells-producing-antitumor-active-immunoglobulins-in-resected-hcc-prolong-patient-survival
#1
Stefan M Brunner, Timo Itzel, Christoph Rubner, Rebecca Kesselring, Eva Griesshammer, Matthias Evert, Andreas Teufel, Hans J Schlitt, Stefan Fichtner-Feigl
BACKGROUND & AIMS: The immunological microenvironment of HCC influences patient outcome, however, the role of B cells remains unclear. This study investigated effects of local B-cell infiltration in HCC cohorts on patient survival and immunological and molecular tumor microenvironment. RESULTS: Unsupervised gene expression analysis of full cancer transcriptomes (N=2158) revealed a highly co-regulated immunological cluster in HCC that mainly contained immunoglobulin fragments...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050299/exostosin-1-regulates-cancer-cell-stemness-in-doxorubicin-resistant-breast-cancer-cells
#2
Sarala Manandhar, Chang-Gu Kim, Sun-Hee Lee, Soo Hyun Kang, Nikita Basnet, You Mie Lee
Cancer stem cells (CSCs) are associated with cancer recurrence following radio/chemotherapy owing to their high resistance to therapeutic intervention. In this study, we investigated the role of exostoxin 1 (EXT1), an endoplasmic reticulum (ER)-residing type II transmembrane glycoprotein, in cancer cell stemness. DNA microarray analysis revealed that doxorubicin-resistant MCF7/ADR cells have high levels of EXT1 expression compared to its parental cell line, MCF7. These cells showed significantly higher populations of CSCs and larger populations of aldehyde dehydrogenase (ALDH(+)) and CD44(+)/CD24(-)cells, as compared to MCF7 cells...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050268/long-non-coding-rna-neat1-regulates-epithelial-membrane-protein-2-expression-to-repress-nasopharyngeal-carcinoma-migration-and-irradiation-resistance-through-mir-101-3p-as-a-competing-endogenous-rna-mechanism
#3
Yujia Wang, Chunting Wang, Can Chen, Fengbo Wu, Pengfei Shen, Peng Zhang, Gu He, Xiang Li
The altered expression of long non-coding RNAs (lncRNAs) is often related to carcinogenesis, metastasis and resistance to radiation or chemotherapy. In the current study, cDNA microarray analysis found that NEAT1 expression was reduced in nasopharyngeal carcinoma (NPC) patients and that it regulated NPC progression. However, the detailed mechanisms of NEAT1 in NPC were unclear. NEAT1 repressed NPC cell growth, invasion and radiation resistance in vitro and tumor metastasis in vivo. In addition, the results of an approach integrating bioinformatics, luciferase reporter assays and RNA immunoprecipitation indicated that NEAT1 antagonized miR-101-3p through a competing endogenous RNA (ceRNA) mechanism and that the interaction between NEAT1 and EMP2 was miR-101-3p dependent...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050246/nrf2-regulated-metabolic-gene-signature-as-a-prognostic-biomarker-in-non-small-cell-lung-cancer
#4
Akhileshwar Namani, Qin Qin Cui, Yihe Wu, Hongyan Wang, Xiu Jun Wang, Xiuwen Tang
Mutations in Kelch-like ECH-associated protein 1 (KEAP1) cause the aberrant activation of nuclear factor erythroid-derived 2-like 2 (NRF2), which leads to oncogenesis and drug resistance in lung cancer cells. Our study was designed to identify the genes involved in lung cancer progression targeted by NRF2. A series of microarray experiments in normal and cancer cells, as well as in animal models, have revealed regulatory genes downstream of NRF2 that are involved in wide variety of pathways. Specifically, we carried out individual and combinatorial microarray analysis of KEAP1 overexpression and NRF2 siRNA-knockdown in a KEAP1 mutant-A549 non-small cell lung cancer (NSCLC) cell line...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050230/a-potential-panel-of-two-long-non-coding-rna-signature-to-predict-recurrence-of-patients-with-laryngeal-cancer
#5
Zhigang Bai, Enhong Shi, Qiwei Wang, Zhouwei Dong, Ping Xu
Accumulating evidence has shown that aberrant lncRNA expression plays an oncogenic or tumor-suppressive role in the tumorigenesis of laryngeal cancer. However, the prognostic roles of lncRNAs in laryngeal cancer recurrence are still poorly understood. In this study, we obtained lncRNA expression profiles of 109 patients with laryngeal cancer by mining previously published gene expression microarray data from the Gene Expression Omnibus (GEO) and identified two lncRNAs associated with laryngeal cancer recurrence in the training dataset by using Cox regression analysis...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050227/identification-of-two-novel-biomarkers-of-rectal-carcinoma-progression-and-prognosis-via-co-expression-network-analysis
#6
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...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050152/-effect-of-transcription-factor-e2f1-expression-on-the-invasion-of-prostate-cancer
#7
X C Bi, X Y Pu, J M Liu, S Huang
Objective: To investigate the effect of transcription factor E2F1 on the invasion of prostate cancer and its clinical significance. Methods: A stable inhibition of E2F1 prostate cancer cell line PC3 was established. The E2F1 and relative invasion biomarker protein expression level of the transfected cells was detected by Western blot. The PC3 cells were divided into two groups: the control group and sh-E2F1 group, cell invasion assay and cell scratch test were used to detect the number of cell migration in the experiment time...
September 26, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/29050001/expression-of-angiogenic-and-inflammatory-factors-in-choroidal-neovascularisation-derived-retinal-pigment-epithelium
#8
Christoph Ehlken, Maria-Magdalena Guichard, Günther Schlunck, Anima D Bühler, Gottfried Martin, Hansjürgen T Agostini
PURPOSE: Anti-angiogenic treatment is well established in the management of exudative age-related macular degeneration (AMD), but not sufficient in all patients. The characterisation of factors driving this chronic disease could serve to identify additional treatment options. The purpose of this study was to assess gene expression patterns and distinct changes in cells derived from surgically extracted choroidal neovascularisation (CNV) membranes. MATERIALS AND METHODS: The expression of >11,000 genes was analysed by means of a microarray in cells cultured from 2 late-stage CNV membranes compared to primary human retinal pigment epithelium (RPE) and ARPE-19 cells...
October 20, 2017: Ophthalmic Research
https://www.readbyqxmd.com/read/29049375/intratumoral-heterogeneity-of-programmed-cell-death-ligand-1-expression-is-common-in-lung-cancer
#9
Sayuri Nakamura, Kentaro Hayashi, Yuki Imaoka, Yuka Kitamura, Yuko Akazawa, Kazuhiro Tabata, Ruben Groen, Tomoshi Tsuchiya, Naoya Yamasaki, Takeshi Nagayasu, Junya Fukuoka
Programmed cell death ligand-1 (PD-L1) expression may predict the response to both programmed cell death-1 and PD-L1 inhibitors in lung cancer. However, the extent of intratumoral heterogeneity of PD-L1 expression, which may cause false negative results, is largely unexplored. We aimed to assess the intratumoral heterogeneity of PD-L1 expression in surgically resected lung cancer specimens by applying a novel method of tissue microarray, namely Spiral Arrays, which enables us to observe the heterogeneity in spiral-shaped tissue cores...
2017: PloS One
https://www.readbyqxmd.com/read/29049217/identification-of-novel-therapeutic-target-genes-and-pathway-in-pancreatic-cancer-by-integrative-analysis
#10
Bangli Hu, Cheng Shi, Hai-Xing Jiang, Shan-Yu Qin
BACKGROUND: Gene alterations are crucial to the molecular pathogenesis of pancreatic cancer. The present study was designed to identify the potential candidate genes in the pancreatic carcinogenesis. METHODS: Gene Expression Omnibus database (GEO) datasets of pancreatic cancer tissue were retrieval and the differentially expressed genes (DEGs) from individual microarray data were merged. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) networks, and gene coexpression analysis were performed...
October 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29049183/identifying-key-genes-associated-with-acute-myocardial-infarction
#11
Ming Cheng, Shoukuan An, Junquan Li
BACKGROUND: This study aimed to identify key genes associated with acute myocardial infarction (AMI) by reanalyzing microarray data. METHODS: Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO database. After data preprocessing, genes without heterogeneity across different platforms were subjected to differential expression analysis between the AMI group and the control group using metaDE package. P < .05 was used as the cutoff for a differentially expressed gene (DEG)...
October 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29049013/identification-and-validation-of-fibroblast-growth-factor-12-gene-as-a-novel-potential-biomarker-in-esophageal-cancer-using-cancer-genomic-datasets
#12
Ashish Bhushan, Avninder Singh, Sujala Kapur, Bibhuti B Borthakar, Jagannath Sharma, Avdhesh K Rai, Amal C Kataki, Sunita Saxena
Esophageal squamous cell carcinoma (ESCC) has a complex, multifactorial etiology in which environmental, geographical, and genetic factors play major roles. It is the second most common cancer among men and the fourth most common among women in India, with a particularly high prevalence in Northeast India. In this study, an integrative in silico [DAVID, NCG5.0, Oncomine, Cancer Cell Line Encyclopedia, and The Cancer Genome Atlas (TCGA)] approach was used to identify the potential biomarkers by using the available three genomic datasets on ESCC from Northeast India followed by its in vitro functional validation...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29049012/transcriptome-profiling-uncovers-potential-common-mechanisms-in-fetal-trisomies-18-and-21
#13
Marija Volk, Aleš Maver, Alenka Hodžić, Luca Lovrečić, Borut Peterlin
Human trisomies have recently been investigated using transcriptomics approaches to identify the gene expression (GE) signatures characteristic of each of these specific aneuploidy conditions. We hypothesized that the viability of cells with gross genomic imbalances might be associated with the activation of resilience mechanisms that are common to different trisomies and that are reflected by specific shared GE patterns. We report in this article our microarray GE analyses of amniocytes from fetuses with viable trisomy conditions, trisomy 21 or trisomy 18, to detect such common expression signatures...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29048996/aberrant-dna-methylation-in-radon-and-or-cigarette-smoke-induced-malignant-transformation-in-beas-2b-human-lung-cell-line
#14
Huanhuan Huang, Yahui Ji, Jiayu Zhang, Zhigang Su, Mingxing Liu, Jian Tong, Cuicui Ge, Tao Chen, Jianxiang Li
It is well known that cigarette smoking (CS) and/or radon (Rn) induce malignant transformation in lung cells. To investigate the mechanisms underlying lung carcinogenesis induced by CS, Rn; or Rn followed by CS using BEAS-2B cell line derived from human bronchial epithelial cells. BEAS-2B cells were exposed to either Rn (20,000 Bq/m(3)) for 30 min or CS (20%) for 10 min or Rn followed by CS for 40 min. Global and gene-specific DNA methylation modifications were measured by microarray and methylation-specific polymerase chain reaction...
October 19, 2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/29048729/beyond-down-syndrome-phenotype-paternally-derived-isodicentric-chromosome-21-with-partial-monosomy-21q22-3
#15
Manesha Putra, Urvashi Surti, Jie Hu, Deana Steele, Michele Clemens, Devereux N Saller, Svetlana A Yatsenko, Aleksandar Rajkovic
Inverted isodicentric chromosome 21 is a rare form of chromosomal rearrangement that may result in trisomy 21; sometimes this rearrangement may also lead to segmental monosomy of the terminal long arm of chromosome 21. In this report, we describe the prenatal diagnosis and neonatal follow-up of a child with a paternally derived, de novo isodicentric chromosome 21 and a concurrent ∼1.2 Mb deletion of the 21q22.3 region [46,XX,idic(21)(q22.3)]. This child presented with unusual phenotype of Down syndrome and additional defects including esophageal atresia and tethered cord syndrome...
October 19, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29048622/enhancement-of-cytotoxic-effects-of-gemcitabine-by-dclk1-inhibition-through-suppression-of-chk1-phosphorylation-in-human-pancreatic-cancer-cells
#16
Daichi Kawamura, Yoshihiro Takemoto, Arata Nishimoto, Koji Ueno, Tohru Hosoyama, Bungo Shirasawa, Toshiki Tanaka, Naruji Kugimiya, Eijiro Harada, Kimikazu Hamano
Although gemcitabine (GEM) is frequently used in the treatment of pancreatic cancer, the effects are limited. To increase the inhibitory effect of GEM, the identification of a molecular target is needed. Recent studies have revealed that doublecortin-like kinase 1 (Dclk1) positively regulates tumor growth, invasion, metastasis, factors related to epithelial-mesenchymal transition (EMT), pluripotency, angiogenesis, and anti-apoptosis in pancreatic cancer cells. Therefore, Dclk1 is a potential therapeutic target for pancreatic cancer...
September 20, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29047401/correction-to-potent-and-reversible-lentiviral-vector-restriction-in-murine-induced-pluripotent-stem-cells
#17
Franziska K Geis, Melanie Galla, Dirk Hoffmann, Johannes Kuehle, Daniela Zychlinski, Tobias Maetzig, Juliane W Schott, Adrian Schwarzer, Christine Goffinet, Stephen P Goff, Axel Schambach
The authors wish to apologize for an error within the scale bar of the microarray heatmap in Additional File 5 of the supplementary information. Two values were incorrectly displayed on the scale bar (11 instead of 10 and 13 instead of 12).
October 18, 2017: Retrovirology
https://www.readbyqxmd.com/read/29047256/analysis-of-genes-with-alternatively-spliced-transcripts-in-the-leaf-root-panicle-and-seed-of-rice-using-a-long-oligomer-microarray-and-rna-seq
#18
Songhwa Chae, Joung Sug Kim, Kyong Mi Jun, Sang-Bok Lee, Myung Soon Kim, Baek Hie Nahm, Yeon-Ki Kim
Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes...
October 17, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/29047230/a-comprehensive-genome-wide-analysis-of-long-noncoding-rna-expression-profile-in-hepatocellular-carcinoma
#19
Hongxia Cui, Yunxing Zhang, Qiujie Zhang, Wenming Chen, Haibo Zhao, Jun Liang
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, especially in East Asia and China. Long noncoding RNAs (lncRNAs) are emerging as critical regulators that may be involved in the development and progression of cancers in humans. However, the contributions of lncRNAs to HCC development, metastasis, and recurrence remain largely unknown. In this study, we comprehensively investigated lncRNA expression profile in HCC and normal tissues using TCGA RNA sequencing data, one RNA sequencing dataset, and two microarray datasets from GEO...
October 18, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/29046940/gastric-cancer-immunohistochemical-classification-of-molecular-subtypes-and-their-association-with-clinicopathological-characteristics
#20
Eva-Maria Birkman, Naziha Mansuri, Samu Kurki, Annika Ålgars, Minnamaija Lintunen, Raija Ristamäki, Jari Sundström, Olli Carpén
Gastric cancer is traditionally divided into intestinal and diffuse histological subtypes, but recent molecular analyses have led to novel classification proposals based on genomic alterations. While the intestinal- and diffuse-type tumours are distinguishable from each other at the molecular level, intestinal-type tumours have more diverse molecular profile. The technology required for comprehensive molecular analysis is expensive and not applicable for routine clinical diagnostics. In this study, we have used immunohistochemistry and in situ hybridisation in molecular classification of gastric adenocarcinomas with an emphasis on the intestinal subtype...
October 19, 2017: Virchows Archiv: An International Journal of Pathology
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