keyword
MENU ▼
Read by QxMD icon Read
search

RNA sequencing Breast Cancer

keyword
https://www.readbyqxmd.com/read/28811643/overexpressed-somatic-alleles-are-enriched-in-functional-elements-in-breast-cancer
#1
Paula Restrepo, Mercedeh Movassagh, Nawaf Alomran, Christian Miller, Muzi Li, Chris Trenkov, Yulian Manchev, Sonali Bahl, Stephanie Warnken, Liam Spurr, Tatiyana Apanasovich, Keith Crandall, Nathan Edwards, Anelia Horvath
Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28805661/the-foxn3-neat1-sin3a-repressor-complex-promotes-progression-of-hormonally-responsive-breast-cancer
#2
Wanjin Li, Zihan Zhang, Xinhua Liu, Xiao Cheng, Yi Zhang, Xiao Han, Yu Zhang, Shumeng Liu, Jianguo Yang, Bosen Xu, Lin He, Luyang Sun, Jing Liang, Yongfeng Shang
The pathophysiological function of the forkhead transcription factor FOXN3 remains to be explored. Here we report that FOXN3 is a transcriptional repressor that is physically associated with the SIN3A repressor complex in estrogen receptor-positive (ER+) cells. RNA immunoprecipitation-coupled high-throughput sequencing identified that NEAT1, an estrogen-inducible long noncoding RNA, is required for FOXN3 interactions with the SIN3A complex. ChIP-Seq and deep sequencing of RNA genomic targets revealed that the FOXN3-NEAT1-SIN3A complex represses genes including GATA3 that are critically involved in epithelial-to-mesenchymal transition (EMT)...
August 14, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28802528/how-young-is-too-young-in-breast-cancer-young-breast-cancer-is-not-a-unique-biological-subtype
#3
Jianfei Fu, Lunpo Wu, Wei Fu, Yinuo Tan, Tiantian Xu, Zhongwu Hong, Fan Wang, Shuguang Li
BACKGROUND: There is no uniformly adopted cutoff value to define "young patients" with breast cancer. This study was designed to determine an optimal cutoff value, to investigate prognostic factors and to explore gene expression profiles of young female breast cancer. MATERIALS AND METHODS: The Surveillance, Epidemiology, and End Results database was examined to identify cases of female breast cancer diagnosed between 2000 and 2007. The optimal cutoff value for young age was determined using the X-tile program (Yale University, version 3...
June 8, 2017: Clinical Breast Cancer
https://www.readbyqxmd.com/read/28794488/nanogrid-single-nucleus-rna-sequencing-reveals-phenotypic-diversity-in-breast-cancer
#4
Ruli Gao, Charissa Kim, Emi Sei, Theodoros Foukakis, Nicola Crosetto, Leong-Keat Chan, Maithreyan Srinivasan, Hong Zhang, Funda Meric-Bernstam, Nicholas Navin
Single cell RNA sequencing has emerged as a powerful tool for resolving transcriptional diversity in tumors, but is limited by throughput, cost and the ability to process archival frozen tissue samples. Here we develop a high-throughput 3' single-nucleus RNA sequencing approach that combines nanogrid technology, automated imaging, and cell selection to sequence up to ~1800 single nuclei in parallel. We compare the transcriptomes of 485 single nuclei to 424 single cells in a breast cancer cell line, which shows a high concordance (93...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28794284/genomic-profiling-of-er-breast-cancers-after-short-term-estrogen-suppression-reveals-alterations-associated-with-endocrine-resistance
#5
Jennifer M Giltnane, Katherine E Hutchinson, Thomas P Stricker, Luigi Formisano, Christian D Young, Monica V Estrada, Mellissa J Nixon, Liping Du, Violeta Sanchez, Paula Gonzalez Ericsson, Maria G Kuba, Melinda E Sanders, Xinmeng J Mu, Eliezer M Van Allen, Nikhil Wagle, Ingrid A Mayer, Vandana Abramson, Henry Gόmez, Monica Rizzo, Weiyi Toy, Sarat Chandarlapaty, Erica L Mayer, Jason Christiansen, Danielle Murphy, Kerry Fitzgerald, Kai Wang, Jeffrey S Ross, Vincent A Miller, Phillip J Stephens, Roman Yelensky, Levi Garraway, Yu Shyr, Ingrid Meszoely, Justin M Balko, Carlos L Arteaga
Inhibition of proliferation in estrogen receptor-positive (ER(+)) breast cancers after short-term antiestrogen therapy correlates with long-term patient outcome. We profiled 155 ER(+)/human epidermal growth factor receptor 2-negative (HER2(-)) early breast cancers from 143 patients treated with the aromatase inhibitor letrozole for 10 to 21 days before surgery. Twenty-one percent of tumors remained highly proliferative, suggesting that these tumors harbor alterations associated with intrinsic endocrine therapy resistance...
August 9, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28765883/-corrigendum-transcriptome-sequencing-of-human-breast-cancer-reveals-aberrant-intronic-transcription-in-amplicons-and-dysregulation-of-alternative-splicing-with-major-therapeutic-implications
#6
(no author information available yet)
After the publication of the article, the authors retrospectively noted that the name of Dr Dawn Jones, a postdoctoral researcher in the laboratory of Professor Christine Gosden, should have been added to the authors' list, whose contribution to the study greatly augmented the exploration of all the RNA products via adoption of the RNASeq (Illumina) methodology. All the existing authors agree to the inclusion of Dr Jones as a co‑author, with the exception of Derek Gardener, who has retired from the Institute and is no longer contactable by e-mail (although we are confident that he would not raise any objection)...
September 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28754563/changes-in-gene-expression-variability-reveal-a-stable-synthetic-lethal-interaction-network-in-brca2-ovarian-cancers
#7
Raymund Bueno, Jessica C Mar
Synthetic lethal interactions (SLIs) are robust mechanisms that provide cells with the ability to sustain viability despite having mutations in genes critical to the DNA damage response, a core cellular process. Studies in model organisms such as S. cerevisiae showed that thousands of genes important in maintaining DNA integrity cooperated in a SLI network. Two genes participate in a SLI when mutation in one gene has no effect on the cell, but mutations in both interacting genes are lethal. Furthermore in C...
July 25, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28751463/dual-src-kinase-pretubulin-inhibitor-kx-01-sensitizes-er%C3%AE-negative-breast-cancers-to-tamoxifen-through-er%C3%AE-re-expression
#8
Muralidharan Anbalagan, Mei Sheng, Brian Fleischer, Yifang Zhang, Yuanjun Gao, Van T Hoang, Margarite D Matossian, Hope E Burks, Matthew E Burow, Bridgette M Collins-Burow, David Hangauer, Brian G Rowan
Unlike breast cancer that is positive for estrogen receptor-α (ERα), there are no targeted therapies for triple negative breast cancer (TNBC). ERα is silenced in TNBC through epigenetic changes including DNA methylation and histone acetylation. Restoring ERα expression in TNBC may sensitize patients to endocrine therapy. Expression of c-Src and ERα are inversely correlated in breast cancer suggesting that c-Src inhibition may lead to re-expression of ERα in TNBC. KX-01 is a peptide substrate-targeted Src/pretubulin inhibitor in clinical trials for solid tumors...
July 27, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28751448/association-of-fgfr1-with-er%C3%AE-maintains-ligand-independent-er-transcription-and-mediates-resistance-to-estrogen-deprivation-in-er-breast-cancer
#9
Luigi Formisano, Kimberly Mae Stauffer, Christian D Young, Neil E Bhola, Angel L Guerrero-Zotano, Valerie M Jansen, Monica M Estrada, Katherine E Hutchinson, Jennifer M Giltnane, Luis J Schwarz, Yao Lu, Justin M Balko, Olivier Deas, Stefano Cairo, Jean-Gabriel Judde, Ingrid A Mayer, Melinda Sanders, Teresa C Dugger, Roberto Bianco, Thomas Stricker, Carlos L Arteaga
FGFR1 amplification occurs in ~15% of ER+ human breast cancers. We investigated mechanisms by which FGFR1 amplification confers antiestrogen resistance to ER+ breast cancer.<br /><br />Experimental Design: ER+ tumors from patients treated with letrozole before surgery were subjected to Ki67 immunohistochemistry, FGFR1 FISH, and RNA-sequencing. ER+/FGFR1 amplified breast cancer cells and patient-derived xenografts (PDXs) were treated with FGFR1 siRNA or the FGFR tyrosine kinase inhibitor lucitanib...
July 27, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28750120/association-between-genomic-metrics-and-immune-infiltration-in-triple-negative-breast-cancer
#10
Thomas Karn, Tingting Jiang, Christos Hatzis, Nicole Sänger, Ahmed El-Balat, Achim Rody, Uwe Holtrich, Sven Becker, Giampaolo Bianchini, Lajos Pusztai
Importance: Why some triple-negative breast cancers (TNBCs) have high and others have low immune cell infiltration is unknown. Understanding how immune surveillance shapes the cancer genome could help in the selection of patients and the development of more effective immunotherapy strategies. Objective: To examine the association between genomic metrics and the extent of immune infiltration in TNBCs. Design, Setting, and Participants: This study, performed from June 1, 2015, through January 31, 2017, used DNA and RNA sequencing data and messenger RNA expression results from The Cancer Genome Atlas (TCGA) breast cancer data set (n = 1215) to calculate previously described immune metagene expression values and histologic lymphocyte counts to quantify immune infiltration and assign prognostic categories to TNBCs...
July 27, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28739310/identification-of-new-tsga10-transcript-variants-in-human-testis-with-conserved-regulatory-rna-elements-in-5-untranslated-region-and-distinct-expression-in-breast-cancer
#11
Pouya Salehipour, Mahsa Nematzadeh, Maryam Beigom Mobasheri, Mandana Afsharpad, Kamran Mansouri, Mohammad Hossein Modarressi
Testis specific gene antigen 10 (TSGA10) is a cancer testis antigen involved in the process of spermatogenesis. TSGA10 could also play an important role in the inhibition of angiogenesis by preventing nuclear localization of HIF-1α. Although it has been shown that TSGA10 messenger RNA (mRNA) is mainly expressed in testis and some tumors, the transcription pattern and regulatory mechanisms of this gene remain largely unknown. Here, we report that human TSGA10 comprises at least 22 exons and generates four different transcript variants...
July 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28738804/oncogenic-long-noncoding-rna-landscape-in-breast-cancer
#12
Shouping Xu, Dejia Kong, Qianlin Chen, Yanyan Ping, Da Pang
BACKGROUND: Few long noncoding RNAs (lncRNAs) that act as oncogenic genes in breast cancer have been identified. METHODS: Oncogenic lncRNAs associated with tumourigenesis and worse survival outcomes were examined and validated in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Then, the potential biological functions and expression regulation of these lncRNAs were studied via bioinformatics and genome data analysis. Moreover, progressive breast cancer subtype-specific lncRNAs were investigated via high-throughput sequencing in our cohort and TCGA validation...
July 24, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28734953/estimating-relative-mitochondrial-dna-copy-number-using-high-throughput-sequencing-data
#13
Pan Zhang, Brian D Lehmann, David C Samuels, Shilin Zhao, Ying-Yong Zhao, Yu Shyr, Yan Guo
We hypothesize that the relative mitochondria copy number (MTCN) can be estimated by comparing the abundance of mitochondrial DNA to nuclear DNA reads using high throughput sequencing data. To test this hypothesis, we examined relative MTCN across 13 breast cancer cell lines using the RT-PCR based NovaQUANT Human Mitochondrial to Nuclear DNA Ratio Kit as the gold standard. Six distinct computational approaches were used to estimate the relative MTCN in order to compare to the RT-PCR measurements. The results demonstrate that relative MTCN correlates well with the RT-PCR measurements using exome sequencing data, but not RNA-seq data...
July 19, 2017: Genomics
https://www.readbyqxmd.com/read/28717182/widespread-alternative-exon-usage-in-clinically-distinct-subtypes-of-invasive-ductal-carcinoma
#14
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/28701032/bcl2-regulation-according-to-molecular-subtype-of-breast-cancer-by-analysis-of-the-cancer-genome-atlas-database
#15
Ki-Tae Hwang, Kwangsoo Kim, Ji Hyun Chang, Sohee Oh, Young A Kim, Jong Yoon Lee, Se Hee Jung, In Sil Choi
Purpose: We investigated BCL2 regulation across DNA, RNA, protein, and methylation status according to molecular subtype of breast cancer using The Cancer Genome Atlas (TCGA) database. Materials and Methods: We analyzed clinical and biological data on 1,096 breast cancers from the TCGA database. Biological data included reverse phase protein array (RPPA), mRNA sequencing (mRNA seq), mRNA microarray, methylation, copy number alteration linear, copy number alteration nonlinear, and mutation data...
July 4, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28685435/hypoxia-related-tumor-acidosis-affects-microrna-expression-pattern-in-prostate-and-breast-tumor-cells
#16
A Riemann, S Reime, O Thews
MicroRNAs (miRNAs) are small non-coding RNA sequences which are able to modulate the expression of many functional proteins. The expression level of miRNAs can be modulated by parameters of the tumor microenvironment like hypoxia, nutrient deprivation or oxidative stress. Since miRNAs can act either as oncogenes or tumor suppressors, this may affect malignant progression or therapy resistance. In the present study it was analyzed whether extracellular acidosis can impact on miRNA expression. Therefore, tumor cells (R3327-AT-1 prostate and Walker-256 mammary carcinoma cells) were incubated at pH 6...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28684636/foxc1-regulates-fgfr1-isoform-switching-to-promote-invasion-following-tgf%C3%AE-induced-emt
#17
Alexander Hopkins, Mackenzie L Coatham, Fred B Berry
Epithelial-to-mesenchymal transition (EMT) is an important physiological process that drives tissue formation during development, but also contributes to disease pathogenesis including fibrosis and cancer metastasis. Elevated expression of the FOXC1 transcription factor has been detected in several metastatic cancers that have undergone EMT. Therefore, mechanistic insight into the role of FOXC1 in the initiation of the EMT process was sought. It was determined that although Foxc1 transcript expression was elevated following TGF-β1 induced EMT of NMuMG cells, FOXC1 was not required for this induction...
July 6, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28679691/metastatic-triple-negative-breast-cancer-patient-with-tp53-tumor-mutation-experienced-11-months-progression-free-survival-on-bortezomib-monotherapy-without-adverse-events-after-ending-standard-treatments-with-grade-3-adverse-events
#18
Tobias Meißner, Adam Mark, Casey Williams, Wolfgang E Berdel, Stephanie Wiebe, Andrea Kerkhoff, Eva Wardelmann, Timo Gaiser, Carsten Müller-Tidow, Philip Rosenstiel, Norbert Arnold, Brian Leyland-Jones, Andre Franke, Martin Stanulla, Michael Forster
A triple-negative breast cancer patient had no hereditary BRCA1, BRCA2, or TP53 risk variants. After exhaustion of standard treatments, she underwent experimental treatments and whole-exome sequencing of tumor, blood, and a metastasis. Well-tolerated experimental bortezomib monotherapy was administered for a progression-free period of 11 mo. After progression, treatments were changed and the exome data were evaluated, expanded with RNA and exome sequencing of a late-stage metastasis. In the final stage, eribulin alone and in combination with anthracyclines were administered...
July 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28673325/maternal-intake-of-high-n-6-polyunsaturated-fatty-acid-diet-during-pregnancy-causes-transgenerational-increase-in-mammary-cancer-risk-in-mice
#19
Nguyen M Nguyen, Fabia de Oliveira Andrade, Lu Jin, Xiyuan Zhang, Madisa Macon, M Idalia Cruz, Carlos Benitez, Bryan Wehrenberg, Chao Yin, Xiao Wang, Jianhua Xuan, Sonia de Assis, Leena Hilakivi-Clarke
BACKGROUND: Maternal and paternal high-fat (HF) diet intake before and/or during pregnancy increases mammary cancer risk in several preclinical models. We studied if maternal consumption of a HF diet that began at a time when the fetal primordial germ cells travel to the genital ridge and start differentiating into germ cells would result in a transgenerational inheritance of increased mammary cancer risk. METHODS: Pregnant C57BL/6NTac mouse dams were fed either a control AIN93G or isocaloric HF diet composed of corn oil high in n-6 polyunsaturated fatty acids between gestational days 10 and 20...
July 3, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28672935/next-generation-sequencing-reveals-lymph-node-metastasis-associated-genetic-markers-in-colorectal-cancer
#20
Ni Xie, Yujiang Yao, Lili Wan, Ting Zhu, Litao Liu, Jianhui Yuan
Colorectal cancer is the third most prevalent type of cancer in the United States. Early diagnosis of lymph node metastases is essential to improve the prognosis for patients with colorectal cancer. Therefore, the present study aimed to screen genetic markers, including single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and mRNA expression, associated with lymph node metastases in patients with colorectal cancer to enable an early diagnosis. Targeted next-generation sequencing was applied to capture SNPs and CNVs in tumor-related candidate genes within tumor tissues from 39 colorectal cancer patients; reverse transcription-quantitative polymerase chain reaction was used to detect the specific mRNA level of tumor-related candidate genes, including vascular endothelial growth factor C, cyclin-A2, Interleukin-2, ATP-binding cassette sub-family G member 2, epidermal growth factor (EGF) and nuclear factor kappa B subunit 1 (NFKB1) on chromosome 4...
July 2017: Experimental and Therapeutic Medicine
keyword
keyword
94101
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"