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RNA sequencing Breast Cancer

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https://www.readbyqxmd.com/read/28622687/identification-of-a-novel-p53-target-col17a1-that-inhibits-breast-cancer-cell-migration-and-invasion
#1
Varalee Yodsurang, Chizu Tanikawa, Takafumi Miyamoto, Paulisally Hau Yi Lo, Makoto Hirata, Koichi Matsuda
p53 mutation is a marker of poor prognosis in breast cancers. To identify downstream targets of p53, we screened two transcriptome datasets, including cDNA microarrays of MCF10A breast epithelial cells with wild-type p53 or p53-null background, and RNA sequence analysis of breast invasive carcinoma. Here, we unveil ten novel p53 target candidates that are up-regulated after the induction of p53 in wild-type cells. Their expressions are also high in breast invasive carcinoma tissues with wild-type p53. The GO analysis identified epidermis development and ectoderm development, which COL17A1 participates, as significantly up-regulated by wild-type p53...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28618162/zeb1-regulated-inflammatory-phenotype-in-breast-cancer-cells
#2
Akihiro Katsura, Yusuke Tamura, Satoshi Hokari, Mayumi Harada, Masato Morikawa, Tsubasa Sakurai, Kei Takahashi, Anna Mizutani, Jun Nishida, Yuichiro Yokoyama, Yasuyuki Morishita, Takashi Murakami, Shogo Ehata, Kohei Miyazono, Daizo Koinuma
Zinc finger E-box binding protein 1 (ZEB1) and ZEB2 induce epithelial-mesenchymal transition (EMT) and enhance cancer progression. However, the global view of transcriptional regulation by ZEB1 and ZEB2 is yet to be elucidated. Here, we identified a ZEB1-regulated inflammatory phenotype in breast cancer cells using chromatin immunoprecipitation-sequencing and RNA sequencing, followed by gene set enrichment analysis (GSEA) of ZEB1-bound genes. Knockdown of ZEB1 and/or ZEB2 resulted in the down-regulation of genes encoding inflammatory cytokines related to poor prognosis in cancer patients, including IL6 and IL8, therefore suggesting that ZEB1 and ZEB2 have similar functions in terms of the regulation of production of inflammatory cytokines...
June 15, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28608266/potentially-pathogenic-germline-chek2-c-319-2t-a-among-multiple-early-onset-cancer-families
#3
Mev Dominguez-Valentin, Sigve Nakken, Hélène Tubeuf, Daniel Vodak, Per Olaf Ekstrøm, Anke M Nissen, Monika Morak, Elke Holinski-Feder, Alexandra Martins, Pål Møller, Eivind Hovig
To study the potential contribution of genes other than BRCA1/2, PTEN, and TP53 to the biological and clinical characteristics of multiple early-onset cancers in Norwegian families, including early-onset breast cancer, Cowden-like and Li-Fraumeni-like syndromes (BC, CSL and LFL, respectively). The Hereditary Cancer Biobank from the Norwegian Radium Hospital was used to identify early-onset BC, CSL or LFL for whom no pathogenic variants in BRCA1/2, PTEN, or TP53 had been found in routine diagnostic DNA sequencing...
June 12, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28601889/rna-sequence-analysis-reveals-differentially-expressed-genes-degs-in-patients-exhibiting-different-risks-of-tumor-metastasis
#4
Li-Feng Dong, Shu-Ying Xu, Jing-Pei Long, Fang Wan, Yi-Ding Chen
BACKGROUND Breast cancer is one of the most common malignancies in women. In a previous study, we found that for two patients who had a high risk of lymphatic metastasis, lymphatic metastasis did not occur; whereas, for two patients who had a low risk of lymphatic metastasis, lymphatic metastasis did occur. MATERIAL AND METHODS We analyzed the differential gene expressions of these four patients by RNA-sequence. The data (HRNM_T versus HRNM_N, LRYM_T versus LRYM_N, and HRNM_T versus LRYM_T) was then processed using differentially expressed genes (DEGs) analysis, functional analysis for DEGs, and PPI network construct...
June 11, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28591870/transcriptome-profiling-reveals-bisphenol-a-alternatives-activate-estrogen-receptor-alpha-in-human-breast-cancer-cells
#5
Robin Mesnage, Alexia Phedonos, Matthew Arno, Sucharitha Balu, J Christopher Corton, Michael N Antoniou
Plasticizers with estrogenic activity, such as bisphenol A (BPA), have potential adverse health effects in humans. Due to mounting evidence of these health effects, BPA is being phased out and replaced by other bisphenol variants in "BPA-free" products. We have compared estrogenic activity of BPA to 6 bisphenol analogues (bisphenol S, BPS; bisphenol F, BPF; bisphenol AP, BPAP; bisphenol AF, BPAF; bisphenol Z, BPZ; bisphenol B, BPB) in three human breast cancer cell lines. Estrogenicity was assessed (10-11M to 10-4M) by cell growth in an estrogen receptor (ER)-mediated cell proliferation assay, and by the induction of estrogen response element-mediated transcription in a luciferase assay...
June 7, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28558830/lincin-a-novel-nf90-binding-long-non-coding-rna-is-overexpressed-in-advanced-breast-tumors-and-involved-in-metastasis
#6
Zhengyu Jiang, Carolyn M Slater, Yan Zhou, Karthik Devarajan, Karen J Ruth, Yueran Li, Kathy Q Cai, Mary Daly, Xiaowei Chen
BACKGROUND: Recent genome-wide profiling by sequencing and distinctive chromatin signatures has identified thousands of long non-coding RNA (lncRNA) species (>200 nt). LncRNAs have emerged as important regulators of gene expression, involving in both developmental and pathological processes. While altered expression of lncRNAs has been observed in breast cancer development, their roles in breast cancer progression and metastasis are still poorly understood. METHODS: To identify novel breast cancer-associated lncRNA candidates, we employed a high-density SNP array-based approach to uncover intergenic lncRNA genes that are aberrantly expressed in breast cancer...
May 30, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28545022/a-high-throughput-method-to-detect-rna-profiling-by-integration-of-rt-mlpa-with-next-generation-sequencing-technology
#7
Jing Wang, Xue Yang, Haofeng Chen, Xuewei Wang, Xiangyu Wang, Yi Fang, Zhenyu Jia, Jidong Gao
RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28541721/a-joint-bayesian-model-for-integrating-microarray-and-rna-sequencing-transcriptomic-data
#8
Tianzhou Ma, Faming Liang, Steffi Oesterreich, George C Tseng
As the sequencing cost continued to drop in the past decade, RNA sequencing (RNA-seq) has replaced microarray to become the standard high-throughput experimental tool to analyze transcriptomic profile. As more and more datasets are generated and accumulated in the public domain, meta-analysis to combine multiple transcriptomic studies to increase statistical power has received increasing popularity. In this article, we propose a Bayesian hierarchical model to jointly integrate microarray and RNA-seq studies...
May 25, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28536419/the-long-non-coding-rna-linc00152-is-essential-for-cell-cycle-progression-through-mitosis-in-hela-cells
#9
Linda Nötzold, Lukas Frank, Minakshi Gandhi, Maria Polycarpou-Schwarz, Matthias Groß, Manuel Gunkel, Nina Beil, Holger Erfle, Nathalie Harder, Karl Rohr, Jakob Trendel, Jeroen Krijgsveld, Thomas Longerich, Peter Schirmacher, Michael Boutros, Sylvia Erhardt, Sven Diederichs
In recent years, long non-coding RNA (lncRNA) research has identified essential roles of these transcripts in virtually all physiological cellular processes including tumorigenesis, but their functions and molecular mechanisms are poorly understood. In this study, we performed a high-throughput siRNA screen targeting 638 lncRNAs deregulated in cancer entities to analyse their impact on cell division by using time-lapse microscopy. We identified 26 lncRNAs affecting cell morphology and cell cycle including LINC00152...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28535794/mutation-site-and-context-dependent-effects-of-esr1-mutation-in-genome-edited-breast-cancer-cell-models
#10
Amir Bahreini, Zheqi Li, Peilu Wang, Kevin M Levine, Nilgun Tasdemir, Lan Cao, Hazel M Weir, Shannon L Puhalla, Nancy E Davidson, Andrew M Stern, David Chu, Ben Ho Park, Adrian V Lee, Steffi Oesterreich
BACKGROUND: Mutations in the estrogen receptor alpha (ERα) 1 gene (ESR1) are frequently detected in ER+ metastatic breast cancer, and there is increasing evidence that these mutations confer endocrine resistance in breast cancer patients with advanced disease. However, their functional role is not well-understood, at least in part due to a lack of ESR1 mutant models. Here, we describe the generation and characterization of genome-edited T47D and MCF7 breast cancer cell lines with the two most common ESR1 mutations, Y537S and D538G...
May 23, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28521398/effect-of-satb1-silencing-on-the-proliferation-invasion-and-apoptosis-of-te-1-esophageal-cancer-cells
#11
Bo Huang, Fei Xiong, Siwang Wang, Xianping Lang, Xiaodong Wang, Hongli Zhou
The aim of the present study was to investigate the effect of special AT-rich sequence-binding protein-1 (SATB1)-targeted small interfering RNA (siRNA) on the proliferation, invasion and apoptosis of TE-1 human esophageal cancer cells. SATB1 has been correlated with the metastasis and poor prognosis of colon and breast cancer, but the role of SATB1 in esophageal cancer remains unknown. Therefore, the present study constructed and transfected SATB1-siRNA into TE-1 cells in order to knockdown the expression of the SATB1 gene...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28488140/characterization-of-a-new-brca1-rearrangement-in-an-italian-woman-with-hereditary-breast-and-ovarian-cancer-syndrome
#12
Paola Concolino, Roberta Rizza, Karl Hackmann, Ida Paris, Angelo Minucci, Elisa De Paolis, Giovanni Scambia, Cecilia Zuppi, Evelin Schrock, Ettore Capoluongo
BACKGROUND: We report a novel BRCA1 LGR, involving the complete duplication of exon 3, in an Italian patient with a strong family history of breast and ovarian cancer. Our purpose is to provide an effective characterization of this LGR using a combination of different methods able to establish the exact breakpoints of the duplication. METHODS: MAQ assay was used as primary screening method in LGRs detection. Array CGH, RT-PCR, and Long-PCR were used for a careful characterization of rearrangement and breakpoint regions...
May 9, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28466845/genetic-variation-and-rna-structure-regulate-microrna-biogenesis
#13
Noemi Fernandez, Ross A Cordiner, Robert S Young, Nele Hug, Sara Macias, Javier F Cáceres
MiRNA biogenesis is highly regulated at the post-transcriptional level; however, the role of sequence and secondary RNA structure in this process has not been extensively studied. A single G to A substitution present in the terminal loop of pri-mir-30c-1 in breast and gastric cancer patients had been previously described to result in increased levels of mature miRNA. Here, we report that this genetic variant directly affects Drosha-mediated processing of pri-mir-30c-1 in vitro and in cultured cells. Structural analysis of this variant revealed an altered RNA structure that facilitates the interaction with SRSF3, an SR protein family member that promotes pri-miRNA processing...
May 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28459823/a-comparison-of-per-sample-global-scaling-and-per-gene-normalization-methods-for-differential-expression-analysis-of-rna-seq-data
#14
Xiaohong Li, Guy N Brock, Eric C Rouchka, Nigel G F Cooper, Dongfeng Wu, Timothy E O'Toole, Ryan S Gill, Abdallah M Eteleeb, Liz O'Brien, Shesh N Rai
Normalization is an essential step with considerable impact on high-throughput RNA sequencing (RNA-seq) data analysis. Although there are numerous methods for read count normalization, it remains a challenge to choose an optimal method due to multiple factors contributing to read count variability that affects the overall sensitivity and specificity. In order to properly determine the most appropriate normalization methods, it is critical to compare the performance and shortcomings of a representative set of normalization routines based on different dataset characteristics...
2017: PloS One
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
#15
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/28446533/prognostic-evaluation-of-epidermal-growth-factor-receptor-egfr-genotype-and-phenotype-parameters-in-triple-negative-breast-cancers
#16
Sofia Levva, Vassiliki Kotoula, Ioannis Kostopoulos, Kyriaki Manousou, Christos Papadimitriou, Kyriaki Papadopoulou, Sotiris Lakis, Kyriakos Koukoulias, Vasilios Karavasilis, George Pentheroudakis, Eufemia Balassi, Flora Zagouri, Ioannis G Kaklamanos, Dimitrios Pectasides, Evangelia Razis, Gerasimos Aravantinos, Pavlos Papakostas, Dimitrios Bafaloukos, Grigorios Rallis, Helen Gogas, George Fountzilas
BACKGROUND: Epidermal growth factor receptor (EGFR) aberrations have been implicated in the pathogenesis of triple-negative breast cancer (TNBC) but their impact on prognosis and, therefore, druggability, remain controversial. Herein, we studied EGFR aberrations at different molecular levels and assessed their prognostic impact in patients with operable TNBC treated with adjuvant anthracycline-based chemotherapy. MATERIALS AND METHODS: We evaluated the prognostic impact of EGFR gene status by fluorescent in situ hybridization (FISH), EGFR coding mutations by Sanger and next-generation sequencing, relative EGFR messenger RNA (mRNA) levels by qPCR (upper quartile) and EGFR and p53 protein expression by immunohistochemistry (IHC), in 352 centrally-assessed tumors from an equal number of TNBC patients...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28427202/clinical-implications-of-genomic-profiles-in-metastatic-breast-cancer-with-a-focus-on-tp53-and-pik3ca-the-most-frequently-mutated-genes
#17
Ji-Yeon Kim, Eunjin Lee, Kyunghee Park, Woong-Yang Park, Hae Hyun Jung, Jin Seok Ahn, Young-Hyuck Im, Yeon Hee Park
Breast cancer (BC) has been genetically profiled through large-scale genome analyses. However, the role and clinical implications of genetic alterations in metastatic BC (MBC) have not been evaluated. Therefore, we conducted whole-exome sequencing (WES) and RNA-Seq of 37 MBC samples and targeted deep sequencing of another 29 MBCs. We evaluated somatic mutations from WES and targeted sequencing and assessed gene expression and performed pathway analysis from RNA-Seq. In this analysis, PIK3CA was the most commonly mutated gene in estrogen receptor (ER)-positive BC, while in ER-negative BC, TP53 was the most commonly mutated gene (p = 0...
April 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420963/rna-seq-analysis-of-microglia-reveals-time-dependent-activation-of-specific-genetic-programs-following-spinal-cord-injury
#18
Harun N Noristani, Yannick N Gerber, Jean-Charles Sabourin, Marine Le Corre, Nicolas Lonjon, Nadine Mestre-Frances, Hélène E Hirbec, Florence E Perrin
Neurons have inherent competence to regrow following injury, although not spontaneously. Spinal cord injury (SCI) induces a pronounced neuroinflammation driven by resident microglia and infiltrating peripheral macrophages. Microglia are the first reactive glial population after SCI and participate in recruitment of monocyte-derived macrophages to the lesion site. Both positive and negative influence of microglia and macrophages on axonal regeneration had been reported after SCI, raising the issue whether their response depends on time post-lesion or different lesion severity...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28402752/the-microrna-mir-210-is-expressed-by-cancer-cells-but-also-by-the-tumor-microenvironment-in-triple-negative-breast-cancer
#19
Isabelle Bar, Ahmad Merhi, Fadi Abdel-Sater, Abduelhakem Ben Addi, Sara Sollennita, Jean-Luc Canon, Paul Delrée
The triple-negative breast cancer (TNBC) subtype occurs in about 15% of breast cancer and is an aggressive subtype of breast cancer with poor outcome. Furthermore, treatment of patients with TNBC is more challenging due to the heterogeneity of the disease and the absence of well-defined molecular targets. Microribonucleic acid (RNA) represents a new class of biomarkers that are frequently dysregulated in cancer. It has been described that the microRNA miR-210 is highly expressed in TNBC, and its overexpression had been linked to poor prognosis...
June 2017: Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society
https://www.readbyqxmd.com/read/28400268/genetic-evidence-supporting-the-taxonomic-separation-of-the-arabian-and-northwest-african-subspecies-of-the-desert-hedgehog-paraechinus-aethiopicus
#20
Louiza Derouiche, Paul Vercammen, Rachid Bouhadad, Carlos Fernandes
Traditional subspecies call attention to differences between geographic populations with research potential, but their value is often in need of revision. Genetic data can be useful for evaluating the taxonomic validity of historical species and subspecies designations or for identifying morphologically cryptic divergent lineages worthy of further in-depth taxonomic study. The desert hedgehog (Paraechinus aethiopicus) has a wide but fragmented distribution in arid and semi-arid habitats from the northwest to the northeast of Africa and southwestern Asia, and its taxonomy is still unclear...
July 15, 2017: Gene
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