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RNA sequencing Breast Cancer

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https://www.readbyqxmd.com/read/29772266/pten-pdz-binding-domain-suppresses-mammary-carcinogenesis-in-the-mmtv-pymt-breast-cancer-model
#1
Mingfei Yan, Yubing Wang, Chi Wai Wong, Penelope Mei-Yu Or, Kin Lok Wong, Lisha Li, Alexander M Many, Hong Guan, Ui Soon Khoo, Andrew M Chan
Phosphatase and tension homolog (PTEN) is a potent tumor suppressor that possesses a PDZ-binding domain (PDZ-BD) at the end of its carboxyl terminus, whose functions during tumorigenesis remains unclear. Here, we crossed a mouse strain with germline deletion of PTEN PDZ-BD with MMTV-PyMT breast cancer model, and found that knockout (KO) mice display normal development of mammary glands, but have both increased breast tumorigenicity and lung metastasis. Orthotopic allograft experiments suggest the loss of PTEN PDZ-BD in breast cancer cells rather than in tumor microenvironment plays a prominent role in increasing tumor burden...
May 14, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29739788/mapk-reliance-via-acquired-cdk4-6-inhibitor-resistance-in-cancer
#2
Renee de Leeuw, Christopher McNair, Matthew J Schiewer, Neermala P Neupane, Lucas J Brand, Michael A Augello, Zhen Li, Larry C Cheng, Akihiro Yoshida, Sean M Courtney, Starr Hazard, Gerald Hardiman, Maha Hussain, J Alan Diehl, Justin M Drake, William K Kelly, Karen E Knudsen
PURPOSE: Loss of cell cycle control is a hallmark of cancer, which can be targeted with agents, including Cyclin Dependent Kinase-4/6 (CDK4/6) kinase inhibitors that impinge upon the G1-S cell cycle checkpoint via maintaining activity of the retinoblastoma tumor suppressor (RB). This class of drugs is under clinical investigation for various solid tumor types, and has recently been FDA-approved for treatment of breast cancer. However, development of therapeutic resistance is not uncommon...
May 8, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29739401/limited-utility-of-tissue-micro-arrays-in-detecting-intra-tumoral-heterogeneity-in-stem-cell-characteristics-and-tumor-progression-markers-in-breast-cancer
#3
Pascale Kündig, Charlotte Giesen, Hartland Jackson, Bernd Bodenmiller, Bärbel Papassotirolopus, Sandra Nicole Freiberger, Catharine Aquino, Lennart Opitz, Zsuzsanna Varga
BACKGROUND: Intra-tumoral heterogeneity has been recently addressed in different types of cancer, including breast cancer. A concept describing the origin of intra-tumoral heterogeneity is the cancer stem-cell hypothesis, proposing the existence of cancer stem cells that can self-renew limitlessly and therefore lead to tumor progression. Clonal evolution in accumulated single cell genomic alterations is a further possible explanation in carcinogenesis. In this study, we addressed the question whether intra-tumoral heterogeneity can be reliably detected in tissue-micro-arrays in breast cancer by comparing expression levels of conventional predictive/prognostic tumor markers, tumor progression markers and stem cell markers between central and peripheral tumor areas...
May 8, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29728310/lncrna-dancr-a-valuable-cancer-related-long-non-coding-rna-for-human-cancers
#4
REVIEW
Khaing Zar Thin, Xuefang Liu, Xiaobo Feng, Sudheesh Raveendran, Jian Cheng Tu
OBJECTIVES: Long noncoding RNAs (lncRNA) are a type of noncoding RNA that comprise of longer than 200 nucleotides sequences. They can regulate chromosome structure, gene expression and play an essential role in the pathophysiology of human diseases, especially in tumorigenesis and progression. Nowadays, they are being targeted as potential biomarkers for various cancer types. And many research studies have proven that lncRNAs might bring a new era to cancer diagnosis and support treatment management...
April 24, 2018: Pathology, Research and Practice
https://www.readbyqxmd.com/read/29728077/neuropilin-1-promotes-the-oncogenic-tenascin-c-integrin-%C3%AE-3-pathway-and-modulates-chemoresistance-in-breast-cancer-cells
#5
Adviti Naik, Aida Al-Yahyaee, Nada Abdullah, Juda-El Sam, Noura Al-Zeheimi, Mahmoud W Yaish, Sirin A Adham
BACKGROUND: Neuropilin-1 (NRP-1), a non-tyrosine kinase glycoprotein receptor, is associated with poor prognosis breast cancer, however transcriptomic changes triggered by NRP-1 overexpression and its association with chemoresistance in breast cancer have not yet been explored. METHODS: BT-474 NRP-1 variant cells were generated by stable overexpression of NRP-1 in the BT-474 breast cancer cell line. RNA sequencing and qRT-PCR were conducted to identify differentially expressed genes...
May 5, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29719590/2-hydroxyflavanone-effectively-targets-rlip76-mediated-drug-transport-and-regulates-critical-signaling-networks-in-breast-cancer
#6
Lokesh Dalasanur Nagaprashantha, Jyotsana Singhal, Hongzhi Li, Charles Warden, Xueli Liu, David Horne, Sanjay Awasthi, Ravi Salgia, Sharad S Singhal
Breast cancer (BC) is the most common cancer in women. Estrogen, epidermal growth factor receptor 2 (ERBB2, HER2), and oxidative stress represent critical mechanistic nodes associated with BC. RLIP76 is a major mercapturic acid pathway transporter whose expression is increased in BC. In the quest of a novel molecule with chemopreventive and chemotherapeutic potential, we evaluated the effects of 2'-Hydroxyflavanone (2HF) in BC. 2HF enhanced the inhibitory effects of RLIP76 depletion and also inhibited RLIP76-mediated doxorubicin transport in BC cells...
April 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29716623/mir-221-stimulates-breast-cancer-cells-and-cancer-associated-fibroblasts-cafs-through-selective-interference-with-the-a20-c-rel-ctgf-signaling
#7
Maria Francesca Santolla, Rosamaria Lappano, Francesca Cirillo, Damiano Cosimo Rigiracciolo, Anna Sebastiani, Sergio Abonante, Pierfrancesco Tassone, Pierosandro Tagliaferri, Maria Teresa Di Martino, Marcello Maggiolini, Adele Vivacqua
BACKGROUND: MicroRNA (miRNAs) are non-coding small RNA molecules that regulate gene expression by inhibiting the translation of target mRNAs. Among several dysregulated miRNAs in human cancer, the up-regulation of miR-221 has been associated with development of a variety of hematologic and solid malignancies. In this study, we investigated the involvement of miR-221 in breast cancer. METHODS: TaqMan microRNA assay was used to detect the miR-221 levels in normal cells and in MDA-MB 231 and SkBr3 breast cancer cells as well as in main players of the tumor microenvironment, namely cancer-associated fibroblasts (CAFs)...
May 2, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29706454/a-to-i-rna-editing-contributes-to-proteomic-diversity-in-cancer
#8
Xinxin Peng, Xiaoyan Xu, Yumeng Wang, David H Hawke, Shuangxing Yu, Leng Han, Zhicheng Zhou, Kamalika Mojumdar, Kang Jin Jeong, Marilyne Labrie, Yiu Huen Tsang, Minying Zhang, Yiling Lu, Patrick Hwu, Kenneth L Scott, Han Liang, Gordon B Mills
Adenosine (A) to inosine (I) RNA editing introduces many nucleotide changes in cancer transcriptomes. However, due to the complexity of post-transcriptional regulation, the contribution of RNA editing to proteomic diversity in human cancers remains unclear. Here, we performed an integrated analysis of TCGA genomic data and CPTAC proteomic data. Despite limited site diversity, we demonstrate that A-to-I RNA editing contributes to proteomic diversity in breast cancer through changes in amino acid sequences. We validate the presence of editing events at both RNA and protein levels...
April 23, 2018: Cancer Cell
https://www.readbyqxmd.com/read/29697201/mir-1307-regulates-cisplatin-resistance-by-targeting-mdm4-in-breast-cancer-expressing-wild-type-p53
#9
Xinyan Wang, Jianwei Zhu
BACKGROUND: Many chemotherapy regimens are used to treat breast cancer; however, breast cancer cells often develop drug resistance that usually leads to relapse and poor prognosis. MicroRNAs (miRNAs) are short non-coding RNA molecules that post-transcriptionally regulate gene expression and play crucial roles in diverse biological processes, such as development, differentiation, apoptosis, and proliferation. We investigated the roles of miRNAs in the development of drug resistance in human breast cancer cells...
April 26, 2018: Thoracic Cancer
https://www.readbyqxmd.com/read/29696079/profiling-plasma-extracellular-vesicle-by-pluronic-block-copolymer-based-enrichment-method-unveils-features-associated-with-breast-cancer-aggression-metastasis-and-invasion
#10
Zhenyu Zhong, Matthew Rosenow, Nick Xiao, David Spetzler
Extracellular vesicle (EV)-based liquid biopsies have been proposed to be a readily obtainable biological substrate recently for both profiling and diagnostics purposes. Development of a fast and reliable preparation protocol to enrich such small particles could accelerate the discovery of informative, disease-related biomarkers. Though multiple EV enrichment protocols are available, in terms of efficiency, reproducibility and simplicity, precipitation-based methods are most amenable to studies with large numbers of subjects...
2018: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/29683229/stromal-immunoglobulin-%C3%AE%C2%BAc-expression-is-associated-with-initiation-of-breast-cancer-in-ta2-mice-and-human-breast-cancer
#11
Shiwu Zhang, Fei Fei, Hua Wang, Yanjun Gu, Chunyuan Li, Xinlu Wang, Yongjie Zhao, Yuwei Li
The initiation of spontaneous breast cancer (SBC) in Tientsin Albino 2 (TA2) mice is related to mouse mammary tumor virus (MMTV) infection, and MMTV amplification is hormonally regulated. To explore the insertion site of MMTVLTR in TA2 mouse genome, reverse PCR and nested PCR were used to amplify the unknown sequence on both sides of the MMTV-LTRSAG gene in SBC and normal breast tissue of TA2 mice. Furthermore, the clinicopathological significance of the insertion site was evaluated in 43 samples of normal breast tissue, 46 samples of breast cystic hyperplasia, 54 samples of ductal carcinoma in situ, 142 samples of primary breast cancer, and 47 samples of lymph node metastatic breast cancer by RNA in situ hybridization...
April 23, 2018: Cancer Science
https://www.readbyqxmd.com/read/29682089/large-scale-analysis-of-dfna5-methylation-reveals-its-potential-as-biomarker-for-breast-cancer
#12
Lieselot Croes, Matthias Beyens, Erik Fransen, Joe Ibrahim, Wim Vanden Berghe, Arvid Suls, Marc Peeters, Patrick Pauwels, Guy Van Camp, Ken Op de Beeck
Background: Breast cancer is the most frequent cancer among women worldwide. Biomarkers for early detection and prognosis of these patients are needed. We hypothesized that deafness , autosomal dominant 5 ( DFNA5 ) may be a valuable biomarker, based upon strong indications for its role as tumor suppressor gene and its function in regulated cell death. In this study, we aimed to analyze DFNA5 methylation and expression in the largest breast cancer cohort to date using publicly available data from TCGA, in order to further unravel the role of DFNA5 as detection and/or prognostic marker in breast cancer...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29681456/chemoresistance-evolution-in-triple-negative-breast-cancer-delineated-by-single-cell-sequencing
#13
Charissa Kim, Ruli Gao, Emi Sei, Rachel Brandt, Johan Hartman, Thomas Hatschek, Nicola Crosetto, Theodoros Foukakis, Nicholas E Navin
Triple-negative breast cancer (TNBC) is an aggressive subtype that frequently develops resistance to chemotherapy. An unresolved question is whether resistance is caused by the selection of rare pre-existing clones or alternatively through the acquisition of new genomic aberrations. To investigate this question, we applied single-cell DNA and RNA sequencing in addition to bulk exome sequencing to profile longitudinal samples from 20 TNBC patients during neoadjuvant chemotherapy (NAC). Deep-exome sequencing identified 10 patients in which NAC led to clonal extinction and 10 patients in which clones persisted after treatment...
April 13, 2018: Cell
https://www.readbyqxmd.com/read/29678492/hmga1a-induces-alternative-splicing-of-estrogen-receptor-alpha-in-mcf-7-human-breast-cancer-cells
#14
Kenji Ohe, Shinsuke Miyajima, Tomoko Tanaka, Yuriko Hamaguchi, Yoshihiro Harada, Yuta Horita, Yuki Beppu, Fumiaki Ito, Takafumi Yamasaki, Hiroki Terai, Masayoshi Mori, Yusuke Murata, Makito Tanabe, Kenji Ashida, Munechika Enjoji, Toshihiko Yanase, Nobuhiro Harada, Toshiaki Utsumi, Akila Mayeda
The high-mobility group A protein 1a (HMGA1a) protein is known as an oncogene whose expression level in cancer tissue correlates with the malignant potential, and known as a component of senescence-related structures connecting it to tumor suppressor networks in fibroblasts. HMGA1 protein binds to DNA, but recent studies have shown it exerts novel functions through RNA-binding. Our previous studies have shown that sequence-specific RNA-binding of HMGA1a induces exon-skipping of Presenilin-2 exon 5 in sporadic Alzheimer disease...
April 17, 2018: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29671673/cancer-specific-snps-originate-from-low-level-heteroplasmic-variants-in-human-mitochondrial-genomes-of-a-matched-cell-line-pair
#15
Annica Hedberg, Erik Knutsen, Anne Silje Løvhaugen, Tor Erik Jørgensen, Maria Perander, Steinar D Johansen
Low-level mitochondrial heteroplasmy is a common phenomenon in both normal and cancer cells. Here, we investigate the link between low-level heteroplasmy and mitogenome mutations in a human breast cancer matched cell line by high-throughput sequencing. We identified 23 heteroplasmic sites, of which 15 were common between normal cells (Hs578Bst) and cancer cells (Hs578T). Most sites were clustered within the highly conserved Complex IV and ribosomal RNA genes. Two heteroplasmic variants in normal cells were found as fixed mutations in cancer cells...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29669595/imp1-regulates-uca1-mediated-cell-invasion-through-facilitating-uca1-decay-and-decreasing-the-sponge-effect-of-uca1-for-mir-122-5p
#16
Yanchun Zhou, Xiuhua Meng, Shaoying Chen, Wei Li, Delin Li, Robert Singer, Wei Gu
BACKGROUND: Long noncoding RNAs (LncRNAs) represent a class of widespread and diverse endogenous RNAs that can posttranscriptionally regulate gene expression through the interaction with RNA-binding proteins and micro RNAs (miRNAs). Here, we report that in breast carcinoma cells, the insulin-like growth factor 2 messenger RNA binding protein (IMP1) binds to lncRNA urethral carcinoma-associated 1 (UCA1) and suppresses the UCA1-induced invasive phenotype. METHODS: RT-qPCR and RNA sequence assays were used to investigate the expression of UCA1 and miRNAs in breast cancer cells in response to IMP1 expression...
April 18, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29661777/interferon-stimulated-genes-are-involved-in-cross-resistance-to-radiotherapy-in-tamoxifen-resistant-breast-cancer
#17
Annemarie E M Post, Marcel Smid, Anika Nagelkerke, John W M Martens, Johan Bussink, Fred Cjg Sweep, Paul N Span
PURPOSE: Treatment resistance is a main cause of adverse disease outcome in breast cancer patients. Here we aimed to investigate common features in tamoxifen-resistant and radioresistant breast cancer, since tamoxifen-resistant breast cancer cells are cross-resistant to irradiation in vitro. EXPERIMENTAL DESIGN: RNA sequencing of tamoxifen-resistant and radioresistant breast cancer cells was performed and validated by quantitative PCR. Pathways were further investigated in vitro and in breast cancer patient cohorts to establish their relation with treatment resistance...
April 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29657297/long-non-coding-rna-tug1-expression-is-associated-with-different-subtypes-in-human-breast-cancer
#18
Daniela F Gradia, Carolina Mathias, Rodrigo Coutinho, Iglenir J Cavalli, Enilze M S F Ribeiro, Jaqueline C de Oliveira
Taurine upregulated 1 gene ( TUG1 ) is a long non-coding RNA associated with several types of cancer. Recently, differential expression of TUG1 was found in cancerous breast tissues and associated with breast cancer malignancy features. Although this is evidence of a potential role in breast cancer, TUG1 expression could not be associated with different subtypes, possibly due to the small number of samples analyzed. Breast cancer is a heterogeneous disease and, based on molecular signatures, may be classified into different subtypes with prognostic implications...
December 20, 2017: Non-Coding RNA
https://www.readbyqxmd.com/read/29642945/rna-sequencing-of-murine-mammary-epithelial-stem-like-cells-hc11-undergoing-lactogenic-differentiation-and-its-comparison-with-embryonic-stem-cells
#19
Trinadha Rao Sornapudi, Rakhee Nayak, Prashanth Kumar Guthikonda, Srinivas Kethavath, Sailu Yellaboina, Sreenivasulu Kurukuti
OBJECTIVES: Understanding of transcriptional networks specifying HC11 murine mammary epithelial stem cell-like cells (MEC) in comparison with embryonic stem cells (ESCs) and their rewiring, under the influence of glucocorticoids (GC) and prolactin (PRL) hormones, is critical for elucidating the mechanism of lactogenesis. In this data note, we provide RNA sequencing data from murine MECs and ESCs, MECs treated with steroid hormone alone and in combination with PRL. This data could help in understanding temporal dynamics of mRNA transcription that impact the process of lactogenesis associated with mammary gland development...
April 11, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29629343/identification-of-epithelial-mesenchymal-transition-related-target-genes-induced-by-the-mutation-of-smad3-linker-phosphorylation
#20
Sujin Park, Kyung-Min Yang, Yuna Park, Eunji Hong, Chang Pyo Hong, Jinah Park, Kyoungwha Pang, Jihee Lee, Bora Park, Siyoung Lee, Haein An, Mi-Kyung Kwak, Junil Kim, Jin Muk Kang, Pyunggang Kim, Yang Xiao, Guangjun Nie, Akira Ooshima, Seong-Jin Kim
Background: Smad3 linker phosphorylation plays essential roles in tumor progression and metastasis. We have previously reported that the mutation of Smad3 linker phosphorylation sites (Smad3-Erk/Pro-directed kinase site mutant constructs [EPSM]) markedly reduced the tumor progression while increasing the lung metastasis in breast cancer. Methods: We performed high-throughput RNA-Sequencing of the human prostate cancer cell lines infected with adenoviral Smad3-EPSM to identify the genes regulated by Smad3-EPSM...
March 2018: Journal of Cancer Prevention
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