keyword
MENU ▼
Read by QxMD icon Read
search

RNA sequencing Cancer

keyword
https://www.readbyqxmd.com/read/29333768/-effects-of-geranylgeranyltransferase-%C3%A2-gene-silencing-by-rna-interference-on-the-migration-and-invasion-of-tongue-carcinoma
#1
Chen Zhenggang, Wang Shuren, Li Jinghua, Han Jinhong, Wang Qimin, Tong Lei, Liu Wenjun, Yang Fang, Guo Qingyuan, Guo Dawei, Wang Ying
OBJECTIVE: RNA interference was used to silence geranylgeranyltransferase Ⅰ(GGTase-Ⅰ) in vitro and to study the effect of GGTase-Ⅰ on the migration and invasion of tongue squamous cancer cells. METHODS: Three small interfering RNAs (siRNA) were designed according to the GGTase-Ⅰ sequence by Genebank and were transfected into tongue squamous cancer cells Cal-27 to knock down GGTase-Ⅰ expression. The tested cells were divided into three groups, as follows: the RNA-interfered groups (GGTase-Ⅰ siRNA1, GGTase-Ⅰ siRNA 2, GGTase-Ⅰ siRNA 3), a negative control group (disrupted by random sequence NC-siRNA), and a blank control group...
December 1, 2017: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/29330429/tissue-and-serum-microrna-profile-of-oral-squamous-cell-carcinoma-patients
#2
Augusto Schneider, Berta Victoria, Yury Nunez Lopez, Wiktoria Suchorska, Wojciech Barczak, Agnieszka Sobecka, Wojciech Golusinski, Michal M Masternak, Pawel Golusinski
Head and neck cancer is characterized by malignant tumors arising from the epithelium covering the upper aerodigestive tract, and the majority of these epithelial malignancies are squamous cell carcinomas (SCCs) of the oral cavity (OSCCs). The aim of the current work was to identify miRNAs regulated in OSCC cancerous tissue when compared to a healthy adjacent tissue and to verify the presence of the same miRNAs in the circulation of these patients. For that serum samples and biopsies of healthy and tumor tissues were collected from five patients diagnosed with OSCC of the oral cavity, RNA was extracted from these samples and microRNAs libraries were prepared and sequenced...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330370/a-rna-sequencing-approach-for-the-identification-of-novel-long-non-coding-rna-biomarkers-in-colorectal-cancer
#3
Atsushi Yamada, Pingjian Yu, Wei Lin, Yoshinaga Okugawa, C Richard Boland, Ajay Goel
Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330289/brca1-through-its-e3-ligase-activity-regulates-the-transcription-factor-oct1-and-carbohydrate-metabolism
#4
Karina Vázquez-Arreguín, Jessica Maddox, Jinsuk Kang, Dongju Park, Reuben R Cano, Rachel E Factor, Thomas Ludwig, Dean Tantin
The tumor suppressor BRCA1 regulates the DNA damage response (DDR) and other processes that remain incompletely defined. Among these, BRCA1 heterodimerizes with BARD1 to ubiquitylate targets via its N-terminal E3 ligase activity. Here it is demonstrated that BRCA1 promotes oxidative metabolism by degrading Oct1 (POU2F1), a transcription factor with pro-glycolytic and tumorigenic effects. BRCA1 E3 ubiquitin ligase mutation skews cells towards a glycolytic metabolic profile while elevating Oct1 protein. CRISPR-mediated Oct1 deletion reverts the glycolytic phenotype...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330284/novel-intergenically-spliced-chimera-nfatc3-pla2g15-is-associated-with-aggressive-t-all-biology-and-outcome
#5
Jonathan Bond, Christine Tran Quang, Guillaume Hypolite, Mohamed Belhocine, Aurélie Bergon, Gaëlle Cordonnier, Jacques Ghysdael, Elizabeth Macintyre, Nicolas Boissel, Salvatore Spicuglia, Vahid Asnafi
Leukemias are frequently characterized by the expression of oncogenic fusion chimeras that normally arise due to chromosomal rearrangements. Intergenically-spliced chimeric RNAs (ISCs) are transcribed in the absence of structural genomic changes, and aberrant ISC expression is now recognized as a potential driver of cancer. To better understand these potential oncogenic drivers, high-throughput RNA-sequencing (RNA-seq) was performed on T-acute lymphoblastic leukemia (T-ALL) patient specimens (n=24) and candidate T-ALL-related ISCs were identified (n=55; a median of 4 per patient)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330282/population-dependent-intron-retention-and-dna-methylation-in-breast-cancer
#6
Dongwook Kim, Manu Shivakumar, Seonggyun Han, Michael S Sinclair, Youngji Lee, Yonglan Zheng, Olufunmilayo I Olopade, Dokyoon Kim, Younghee Lee
Regulation of gene expression by DNA methylation in gene promoter regions is well-studied; however, the effects of methylation in the gene body (exons and introns) on gene expression are comparatively understudied. Recently, hyper-methylation has been implicated in the inclusion of alternatively spliced exons; moreover, exon recognition can be enhanced by recruiting the methyl-CpG-binding protein (MeCP2) to hyper-methylated sites. This study examines if methylation status of an intron is correlated with how frequently the intron is retained during splicing using DNA methylation and RNA sequencing (RNA-seq) data from breast cancer tissue specimens in The Cancer Genome Atlas (TCGA)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330107/prostate-cancer-associated-lncrnas
#7
Yuichi Mitobe, Ken-Ichi Takayama, Kuniko Horie-Inoue, Satoshi Inoue
Long non-coding RNA (LncRNA) is defined as an RNA transcript that does not encode any protein, with a length longer than 200 nt. Based on the recent advances in high-throughput sequencing techniques, a large number of lncRNAs have been characterized as functional transcripts that play important roles in various biological processes as well as pathologic states. In a research field of prostate cancer, several key lncRNAs have been identified as new players that contribute to the pathophysiology of the disease, which is primarily regulated by androgen and its cognate receptor...
January 9, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29330104/circular-rna-an-emerging-non-coding-rna-as-a-regulator-and-biomarker-in-cancer
#8
Bing Chen, Shenglin Huang
Circular RNA (circRNA) is a type of covalently closed non-coding RNA that may regulate gene expression in eukaryotes. The recent application of high-throughput RNA sequencing and bioinformatics approaches has revealed a large number of circRNAs in human cells. Emerging evidence indicates that many circRNAs have cell-type specific expression and are linked to physiological development and various diseases. Specially, circRNAs can either serve as oncogenic stimuli or tumor suppressors in cancer. circRNAs have also been shown to be enriched and stable in extracellular fluid, indicating the potential of circRNAs as cancer biomarkers...
January 9, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29328656/design-and-synthesis-of-novel-reactive-oxygen-species-inducers-for-the-treatment-of-pancreatic-ductal-adenocarcinoma
#9
Yuting Kuang, Mario Sechi, Salvatore Nurra, Mats Ljungman, Nouri Neamati
Altering redox homeostasis provides distinctive therapeutic opportunities for the treatment of pancreatic cancer. Quinazolinediones (QDs) are novel redox modulators that we previously showed to induce potent growth inhibition in pancreatic ductal adenocarcinoma (PDAC) cell lines. Our lead optimization campaign yielded QD325 as the most potent redox modulator candidate inducing substantial reactive oxygen species (ROS) in PDAC cells. Nascent RNA sequencing following treatments with the QD compounds revealed induction of stress responses in nucleus, endoplasmic reticulum, and mitochondria of pancreatic cancer cells...
January 12, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29328404/chronic-oxymatrine-treatment-induces-resistance-and-epithelial%C3%A2-mesenchymal-transition-through-targeting-the-long-non-coding-rna-malat1-in-colorectal-cancer-cells
#10
Yibai Xiong, Jun Wang, Huirong Zhu, Lingshuang Liu, Yi Jiang
A major reason for colorectal cancer (CRC) chemoresistance is the enhanced migration and invasion of cancer cells, such as the cell acquisition of epithelial-mesenchymal transition (EMT). Long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been considered as a pro-oncogene in multiple cancers. However, the precise functional mechanism of lncRNA MALAT1 in chemoresistance and EMT is not well known. In the present study, we focused on the effect of oxymatrine on CRC cells and further investigated the role of MALAT1 in oxymatrine-induced resistance and EMT process...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29327716/genomic-heterogeneity-of-alk-fusion-breakpoints-in-non-small-cell-lung-cancer
#11
Jason N Rosenbaum, Ryan Bloom, Jason T Forys, Jeff Hiken, Jon R Armstrong, Julie Branson, Samantha McNulty, Priya D Velu, Kymberlie Pepin, Haley Abel, Catherine E Cottrell, John D Pfeifer, Shashikant Kulkarni, Ramaswamy Govindan, Eric Q Konnick, Christina M Lockwood, Eric J Duncavage
In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29326299/targeting-mutant-kras-with-crispr-cas9-controls-tumor-growth
#12
Hyongbum Henry Kim, Wonjoo Kim, Sangeun Lee, Han Sang Kim, Minjung Song, Yong Hoon Cha, Young-Hoon Kim, Jeonghong Shin, Eun-Seo Lee, Yeonsoo Joo, Jae J Song, Eun Ju Choi, Jae W Choi, Jinu Lee, Moonkyung Kang, Jong In Yook, Min Goo Lee, Yeon-Soo Kim, Soonmyung Paik
KRAS is the most frequently mutated oncogene in human tumors and its activating mutations represents important therapeutic targets. The combination of Cas9 and guide RNA from the CRISPR-Cas system recognizes a specific DNA sequence and makes a double-strand break, which enables editing of the relevant genes. Here we harnessed CRISPR to specifically target mutant KRAS alleles in cancer cells. We screened guide RNAs using a reporter system and validated them in cancer cells after lentiviral delivery of Cas9 and guide RNA...
January 11, 2018: Genome Research
https://www.readbyqxmd.com/read/29325442/pooled-generation-of-lentiviral-tetracycline-regulated-microrna-embedded-short-hairpin-rna-libraries
#13
Felix Ferdinand Adams, Thomas Hoffmann, Johannes Zuber, Dirk Heckl, Axel Schambach, Adrian Schwarzer
Short hairpin RNA (shRNA) screens are powerful tools to probe genetic dependencies in loss-of-function studies, like the identification of therapeutic targets in cancer research. Lentivirally delivered shRNAs embedded in endogenous microRNA contexts (shRNAmiRs) mediate efficient long-term suppression of target genes suitable for numerous experimental contexts and clinical applications. Here, we describe an easy-to-use laboratory protocol covering the design and pooled assembly of focused shRNAmiR libraries into an optimized, Tet-inducible all-in-one lentiviral vector, packaging of viral particles, followed by retrieval and quantification of hairpin sequences after cellular DNA-recovery...
January 12, 2018: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/29325230/protocadherin8-promotes-invasion-and-metastasis-via-laminin-subunit-%C3%AE-2-in-gastric-cancer
#14
Ying Lin, Xiaoxiao Ge, Xiaofei Zhang, Zheng Wu, Kaiyi Liu, Fengjuan Lin, Congqi Dai, Weijian Guo, Jin Li
Growing evidence suggests that protocadherins (PCDHs) play crucial roles in pathogenesis and progression of cancers including gastric cancer (GC). Protocadherin8 (PCDH8) was previously reported to be involved in metastasis of GC, but functional studies yielded inconsistent results and the molecular mechanism remained unknown. This study aimed to explore the clinical relevance, function and molecular mechanism of PCDH8 in GC. Data from the GEPIA and Kaplan-Meier plotter databases showed that high expression of PCDH8 was significantly correlated with poorer prognosis in GC...
January 11, 2018: Cancer Science
https://www.readbyqxmd.com/read/29324748/trans10-cis12-conjugated-linoleic-acid-inhibits-proliferation-and-migration-of-ovarian-cancer-cells-by-inducing-er-stress-autophagy-and-modulation-of-src
#15
Mian M K Shahzad, Mildred Felder, Kai Ludwig, Hannah R Van Galder, Matthew L Anderson, Jong Kim, Mark E Cook, Arvinder K Kapur, Manish S Patankar
The goal of this study was to investigate the anti-cancer effects of Trans10,cis12 conjugated linoleic acid (t10,c12 CLA). MTT assays and QCM™ chemotaxis 96-wells were used to test the effect of t10,c12 CLA on the proliferation and migration and invasion of cancer cells. qPCR and Western Blotting were used to determine the expression of specific factors. RNA sequencing was conducted using the Illumina platform and apoptosis was measured using a flow cytometry assay. t10,c12 CLA (IC50, 7 μM) inhibited proliferation of ovarian cancer cell lines SKOV-3 and A2780...
2018: PloS One
https://www.readbyqxmd.com/read/29324665/genome-wide-methylation-patterns-in-androgen-independent-prostate-cancer-cells-a-comprehensive-analysis-combining-medip-bisulfite-rna-and-microrna-sequencing-data
#16
Yumin Wang, Tingting Qin, Wangqiang Hu, Binghua Chen, Meijie Dai, Gang Xu
This study aimed to investigate the mechanisms underlying the development of the androgen-independent phenotype in prostate cancer. Methylation patterns were detected in androgen-independent and androgen-dependent lymph node carcinoma of the prostate (LNCaP) prostate carcinoma cells based on methylated DNA immunoprecipitation-bisulfite sequencing data and differentially methylated regions (DMRs) were identified. Differentially expressed genes (DEGs) and micro RNAs (miRNAs) with DMRs (named MDEGs and MDEmiRNAs) were identified by combining transcriptome and methylation data, and transcription factor (TF)-DEGs with DMRs in promoter (PMDEGs) and MDEmiRNA-MDEGs networks were constructed...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29322784/bioinformatic-analysis-of-changes-in-rna-polymerase-ii-transcription-stimulated-by-estradiol-in-mcf7-cells
#17
J Wu, Y Cai, G Zhao
Estradiol (E2) is the most potent estrogen and RNA polymerase II (Pol II) regulates a great mass of gene expression. This study was designed to illustrate the mechanisms of estrogen-dependent human breast cancer (BC) through Pol II. ChIP-seq data, DNase-seq data and other sequencing data of human BC MCF-7 cells were downloaded from Gene Expression Omnibus database. Each of these datasets included one control and one E2 treated sample. Sequence alignment was performed and Pol II factor binding signal was determined...
2018: Neoplasma
https://www.readbyqxmd.com/read/29321960/the-clinical-value-of-mir-193a-3p-in-non-small-cell-lung-cancer-and-its-potential-molecular-mechanism-explored-in-silico-using-rna-sequencing-and-microarray-data
#18
Xiang Gao, Rui-Xue Tang, Qiong-Ni Xie, Jia-Ying Lin, Hong-Lan Shi, Gang Chen, Zu-Yun Li
miR-193a-3p is a tumor-related miRNA playing an essential role in tumorigenesis and progression of non-small cell lung cancer (NSCLC). The objective of the present study was to investigate the relationship between miR-193a-3p expression and clinical value and to further explore the potential signaling of miR-193a-3p in the carcinogenesis of NSCLC. RNA-sequencing and microarray data were collected from the databases GEO, ArrayExpress and The Cancer Genome Atlas (TCGA). Furthermore, in silico assessments were performed to analyze the prospective pathways and networks of the target genes of miR-193a-3p...
January 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29321190/genomic-landscape-of-pancreatic-neuroendocrine-tumours-the-international-cancer-genome-consortium
#19
Andrea Mafficini, Aldo Scarpa
Neuroendocrine tumours (NETs) may arise throughout the body and are a highly heterogeneous, relatively rare class of neoplasms difficult to study also for the lack of disease models. Despite this, knowledge on their molecular alterations has expanded in the latest years, also building from genetic syndromes causing their onset. Pancreatic NETs (PanNETs) have been among the most studied, and research so far has outlined a series of recurring features, as inactivation of MEN1, VHL, TSC1/2 genes, and hyperactivation of the PI3K/mTOR pathway...
January 10, 2018: Journal of Endocrinology
https://www.readbyqxmd.com/read/29321030/crabp1-c1ql1-and-lcn2-are-biomarkers-of-differentiated-thyroid-carcinoma-and-predict-extrathyroidal-extension
#20
Ricardo Celestino, Torfinn Nome, Ana Pestana, Andreas M Hoff, A Pedro Gonçalves, Luísa Pereira, Bruno Cavadas, Catarina Eloy, Trine Bjøro, Manuel Sobrinho-Simões, Rolf I Skotheim, Paula Soares
BACKGROUND: The prognostic variability of thyroid carcinomas has led to the search for accurate biomarkers at the molecular level. Follicular thyroid carcinoma (FTC) is a typical example of differentiated thyroid carcinomas (DTC) in which challenges are faced in the differential diagnosis. METHODS: We used high-throughput paired-end RNA sequencing technology to study four cases of FTC with different degree of capsular invasion: two minimally invasive (mFTC) and two widely invasive FTC (wFTC)...
January 10, 2018: BMC Cancer
keyword
keyword
94103
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"