Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method.

Abstract:

:Breast cancer (BC) is a leading cause of cancer-related mortality in females and is recognized as a molecularly heterogeneous disease. Previous studies have suggested that alternative messenger RNA (mRNA) processing, particularly alternative polyadenylation [poly(A)] (APA), can be a powerful molecular biomarker with prognostic potential. Therefore, in the present study, we profiled APA sites in the luminal B subtype of BC by sequencing APA sites (SAPAS) method, in order to assess the relation of these APA site-switching events to the recognized molecular subtypes of BC, and to discover novel candidate genes and pathways in BC. Through comprehensive analysis, the trend of APA site-switching events in the 3' untranslated regions (3'UTRs) in the luminal B subtype of BC were found to be the same as that in MCF7 cell lines. Among the genes involved in the events, a significantly greater number of genes was found with shortened 3'UTRs in the samples, which were samples of primary cancer with relatively low proliferation. These findings may provide novel information for the clinical diagnosis and prognosis on a molecular level. Several potential biomarkers with significantly differential tandem 3'UTRs and expression were found and validated. The related biological progresses and pathways involved were partly confirmed by other studies. In conclusion, this study provides new insight into the diagnosis and prognosis of BC from the APA site profile aspect.

journal_name

Int J Mol Med

authors

Wang X,Li M,Yin Y,Li L,Tao Y,Chen D,Li J,Han H,Hou Z,Zhang B,Wang X,Ding Y,Cui H,Zhang H

doi

10.3892/ijmm.2014.1973

subject

Has Abstract

pub_date

2015-01-01 00:00:00

pages

39-50

issue

1

eissn

1107-3756

issn

1791-244X

journal_volume

35

pub_type

杂志文章
  • CCN5 overexpression inhibits profibrotic phenotypes via the PI3K/Akt signaling pathway in lung fibroblasts isolated from patients with idiopathic pulmonary fibrosis and in an in vivo model of lung fibrosis.

    abstract::Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease with unknown etiology and undefined treatment modality. Fibroblasts are regarded as the major cell type that mediates the onset and progression of lung fibrosis by secreting large amounts of extracellular matrix (ECM) proteins, ...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2013.1565

    authors: Zhang L,Li Y,Liang C,Yang W

    更新日期:2014-02-01 00:00:00

  • TREK‑TRAAK two‑pore domain potassium channels protect human retinal pigment epithelium cells from oxidative stress.

    abstract::The aim of the current study was to explore the potential of TREK‑TRAAK two‑pore domain potassium (K2P) channels in protecting human retinal pigment epithelium (hRPE) cells against oxidative stress. hRPE cells were obtained from donors, and then cell identification and detection of the expression levels of TREK‑TRAAK ...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2018.3813

    authors: Huang H,Li H,Shi K,Wang L,Zhang X,Zhu X

    更新日期:2018-11-01 00:00:00

  • Expression of Hu-IFN-alphaR2 chain of type I interferon receptor in human hepatocellular carcinoma and non-cancerous tissues.

    abstract::Type I interferon (IFN) receptor consists of two chains (Hu-IFN-alphaR1 and Hu-IFN-alphaR2), and Hu-IFN-alphaR2 takes a soluble, short, or long form (Hu-IFN-alphaR2a, Hu-IFN-alphaR2b, or Hu-IFN-alphaR2c, respectively). We examined Hu-IFN-alphaR2 expression in hepatocellular carcinoma (HCC) tissues and their correspond...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.6.6.621

    authors: Takayama A,Yano H,Ogasawara S,Higaki K,Kojiro M

    更新日期:2000-12-01 00:00:00

  • Role of poly(ADP-ribosyl)ation in a 'two-hit' model of hypoxia and oxidative stress in human A549 epithelial cells in vitro.

    abstract::A preceding hypoxic insult can sensitize the cells or the organism to a subsequent, second insult. The aim of the present study was to investigate the molecular mechanism of this phenomenon (often termed 'two-hit' injury paradigm), in an in vitro model of hypoxia/oxidative stress injury in A549 epithelial cells, with ...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2013.1397

    authors: Erdélyi K,Pacher P,Virág L,Szabó C

    更新日期:2013-08-01 00:00:00

  • Abnormal expression of SIRTs in psoriasis: Decreased expression of SIRT 1-5 and increased expression of SIRT 6 and 7.

    abstract::The prevalence of psoriasis is increasing, and poses a serious risk to human health and quality of life. Psoriasis, a chronic immune‑mediated skin disease with epidermal hyperkeratosis and parakeratosis, is associated with numerous complications, including metabolic syndromes that are regulated by sirtuins (SIRTs) via...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2019.4173

    authors: Fan X,Yan K,Meng Q,Sun R,Yang X,Yuan D,Li F,Deng H

    更新日期:2019-07-01 00:00:00

  • Protective effects of CXCR3/HO‑1 gene‑modified BMMSCs on damaged intestinal epithelial cells: Role of the p38‑MAPK signaling pathway.

    abstract::The purpose of the present study was to investigate whether bone marrow mesenchymal stem cells (BMMSCs) modified by CXC‑chemokine receptor type 3 (CXCR3) and heme oxygenase‑1 (HO‑1) genes can repair damaged intestinal epithelial cells in vitro, and the role of the p38 mitogen‑activated protein kinase (p38‑MAPK) pathwa...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2019.4120

    authors: Yin M,Shen Z,Yang L,Zheng W,Song H

    更新日期:2019-05-01 00:00:00

  • Multiparametric analysis for the enumeration of CD34+ cells from bone marrow and stimulated peripheral blood.

    abstract::Determination of CD34+ cells was performed in bone marrow and G-CSF mobilised peripheral blood samples. We adopted three different protocols of analysis: the Milan/Mulhouse protocol, the ISHAGE guidelines for CD34+ cell determination and our own protocol based upon the use of PAINT-A-GATEPRO software analysis program....

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.1.1.67

    authors: Venditti A,Buccisano F,Del Poeta G,Battaglia A,Tamburini A,Bruno A,Adorno G,Caravita T,Santinelli S,Del Moro B,Epiceno AM,Ballatore G,Amadori S

    更新日期:1998-01-01 00:00:00

  • Vaccination with embryonic stem cells generates effective antitumor immunity against ovarian cancer.

    abstract::To date, only a few studies have suggested that human embryonic stem cells (hESCs) might effectively immunize against colon and lung cancer. The purpose of this study was to investigate the therapeutic potential of hESCs as a vaccine to induce widespread antitumor effects in differe...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2012.1195

    authors: Zhang Z,Chen X,Chang X,Ye X,Li Y,Cui H

    更新日期:2013-01-01 00:00:00

  • Alternative splicing of apoptosis-related genes in imatinib-treated K562 cells identified by exon array analysis.

    abstract::Imatinib is the therapeutic standard for newly diagnosed patients with chronic myeloid leukemia (CML). In these patients, imatinib has been shown to induce an apoptotic response specifically in cells expressing the oncogenic fusion protein BCR-ABL. Previous studies in our lab revealed that imatinib-induced apoptosis i...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2011.872

    authors: Liu J,Xiao Y,Xiong HM,Li J,Huang B,Zhang HB,Feng DQ,Chen XM,Wang XZ

    更新日期:2012-04-01 00:00:00

  • Alterations in gene expression during sexual differentiation in androgen receptor knockout mice induced by environmental endocrine disruptors.

    abstract::In the present study, we aimed to explore the effect of environmental endocrine disruptors (EEDs) on sexual differentiation in androgen receptor (AR)-/-, AR+/- and AR+/+ male mice. By using a Cre-loxP conditional knockout strategy, we generated AR knockout mice. By mating flox-AR female mice with AR-Cre male mice, the...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2014.2015

    authors: Liu D,Shen L,Tao Y,Kuang Y,Cai L,Wang D,He M,Tong X,Zhou S,Sun J,Shi C,Wang C,Wu Y

    更新日期:2015-02-01 00:00:00

  • XPD inhibits cell growth and invasion and enhances chemosensitivity in esophageal squamous cell carcinoma by regulating the PI3K/AKT signaling pathway.

    abstract::Esophageal squamous cell carcinoma (ESCC) is a lethal disease due to its high aggressiveness. The aim of the present study was to investigate the role of xeroderma pigmentosum complementation group D (XPD) in the growth and invasion of ESCC and to elucidate the potential underlying molecular mechanisms. Western blot a...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2020.4593

    authors: Jian J,Li S,Liu LZ,Zhen L,Yao L,Gan LH,Huang YQ,Fang N

    更新日期:2020-07-01 00:00:00

  • Cysteine induces longitudinal bone growth in mice by upregulating IGF-I.

    abstract::Cysteine (Cys) is known to exert various effects, such as antioxidant, antipancreatitic and antidiabetic effects. However, the effects of Cys on longitudinal bone growth have not been elucidate to date. Thus, the aim of the present study was to evaluate the effects of Cys on bone growth. Growth-plate thickness and bon...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2015.2257

    authors: Moon PD,Kim MH,Oh HA,Nam SY,Han NR,Jeong HJ,Kim HM

    更新日期:2015-08-01 00:00:00

  • HDAC inhibitor sodium butyrate prevents allergic rhinitis and alters lncRNA and mRNA expression profiles in the nasal mucosa of mice.

    abstract::Our previous study demonstrated that intranasal administration of histone deacetylase inhibitor sodium butyrate (NaB) exhibits therapeutic effects on a mouse model of allergic rhinitis (AR). However, whether NaB is effective on AR when administered orally and prophylactically, as well as its potential effects on gene ...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2020.4489

    authors: Wang J,Cui M,Sun F,Zhou K,Fan B,Qiu JH,Chen FQ

    更新日期:2020-04-01 00:00:00

  • Connective tissue growth factor induces osteogenic differentiation of vascular smooth muscle cells through ERK signaling.

    abstract::Connective tissue growth factor (CTGF) plays an important role in the pathogenesis of atherosclerosis by promoting vascular smooth muscle cell (VSMC) growth, migration, apoptosis, adhesion and the secretion of matrix components. The osteogenic differentiation of VSMCs is essential in the development of vascular calcif...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2013.1398

    authors: Huang J,Huang H,Wu M,Li J,Xie H,Zhou H,Liao E,Peng Y

    更新日期:2013-08-01 00:00:00

  • Comprehensive circular RNA profiling reveals the regulatory role of the hsa_circ_0137606/miR‑1231 pathway in bladder cancer progression.

    abstract::Bladder cancer (BC) is one of the most common malignant tumors in males globally. Its progression imposes a heavy burden on patients; however, the expression profile of circular (circ)RNAs in BC progression remains unclear. This study explored changes in circRNA expression during BC progression by sequencing different...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2019.4340

    authors: Li W,Li Y,Sun Z,Zhou J,Cao Y,Ma W,Xie K,Yan X

    更新日期:2019-11-01 00:00:00

  • Differential expression of peroxisomal proliferator activated receptors alpha and delta in skeletal muscle in response to changes in diet and exercise.

    abstract::Peroxisome proliferator-activated receptors (PPARs) alpha, delta and gamma are nuclear transcription factors that control key genes involved in fatty acid metabolism and energy homeostasis. Little is known about PPAR activation in vivo and the existence of overlapping functions between PPARalpha, -delta and -gamma. As...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:

    authors: Kannisto K,Chibalin A,Glinghammar B,Zierath JR,Hamsten A,Ehrenborg E

    更新日期:2006-01-01 00:00:00

  • Human chondrocytes differentially express matrix modulators during in vitro expansion for tissue engineering.

    abstract::Cartilage tissue engineering plays an important role in the generation of grafts for reconstructive surgery. In cultured chondrocytes, the dedifferentiation of cells seems unavoidable for multiplication. Dedifferentiated cells produce matrix of less quality, and the molecular basis is still not well understood. Theref...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:

    authors: Goessler UR,Bieback K,Bugert P,Naim R,Schafer C,Sadick H,Hormann K,Riedel F

    更新日期:2005-10-01 00:00:00

  • Molecular characterization of mesoderm-restricted basic helix-loop-helix protein, POD-1/Capsulin.

    abstract::Members of the basic helix-loop-helix (bHLH) family of transcription factors have been implicated in the regulation of cell proliferation and differentiation. Here we describe molecular characterization of mesoderm-specific bHLH protein, POD-1/Capsulin. Northern blot analysis showed that POD-1/Capsulin are preferentia...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.5.1.27

    authors: Miyagishi M,Nakajima T,Fukamizu A

    更新日期:2000-01-01 00:00:00

  • Significance of heme oxygenase in prolactin-mediated cell proliferation and angiogenesis in human endothelial cells.

    abstract::Our objectives were to determine whether heme oxygenase-1 is a second messenger for prolactin-mediated angiogenesis. Endothelial cell proliferation and angiogenesis assay demonstrated that cell number and capillary formation were increased by prolactin (10 and 25 ng/ml). Both protein synthesis and mRNA analysis confir...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:

    authors: Malaguarnera L,Pilastro MR,Quan S,Ghattas MH,Yang L,Mezentsev AV,Kushida T,Abraham NG,Kappas A

    更新日期:2002-10-01 00:00:00

  • Expression of thioredoxin in patients with Graves' disease.

    abstract::Thioredoxin (TRX), which is a stress-inducible protein with redox-active disulfide structures, has various biological activities by regulating DNA binding of transcription factors in cells. In Graves' disease that is among the common diseases of the thyroid, endogenous stresses that are induced by excess thyroid hormo...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:

    authors: Kihara M,Kontani K,Yamauchi A,Miyauchi A,Nakamura H,Yodoi J,Yokomise H

    更新日期:2005-05-01 00:00:00

  • The role of S100A4 gene encoding an S100-related calcium-binding protein in human bile duct adenocarcinoma cell lines: correlation of S100A4 expression and invasive growth in Matrigel Matrix.

    abstract::S100A4, one of the tandemly arranged S100 genes at chromosome 1q21, has been suggested to play a functional role in cell motility and invasiveness of tumor cell growth. We investigated the expression of S100A4 and the in vitro invasiveness of 4 human bile duct adenocarcinoma cell lines by the Matrigel assay. S100A4 wa...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.6.5.539

    authors: Katayama N,Murao S,Ajiki T,Kitazawa S,Onoyama H,Kuroda Y,Maeda S

    更新日期:2000-11-01 00:00:00

  • CDC25A inhibition suppresses the growth and invasion of human hepatocellular carcinoma cells.

    abstract::CDC25A is a cell cycle-activating phosphatase that promotes transition from the G1 to S phase. We previously reported that overexpression of CDC25A in human hepatocellular carcinoma (HCC) tissue samples was associated with poor prognosis. In this study, we attempted suppression of CDC25A in HCC cells to elucidate the ...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:

    authors: Xu X,Yamamoto H,Liu G,Ito Y,Ngan CY,Kondo M,Nagano H,Dono K,Sekimoto M,Monden M

    更新日期:2008-02-01 00:00:00

  • iTRAQ-based quantitative proteomic analysis of cerebrospinal fluid reveals NELL2 as a potential diagnostic biomarker of tuberculous meningitis.

    abstract::Tuberculous meningitis (TBM) is a serious complication of tuberculosis that affects the central nervous system. As TBM may result in permanent sequelae and death, rapid, accurate diagnostic tests using novel biomarkers are required for the early diagnosis and treatment of TBM. A quantitative proteomic study was theref...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2015.2131

    authors: Yang Y,Mu J,Chen G,Zhan Y,Zhong J,Wei Y,Cheng K,Qin B,You H,Xie P

    更新日期:2015-05-01 00:00:00

  • Roles of GINS2 in K562 human chronic myelogenous leukemia and NB4 acute promyelocytic leukemia cells.

    abstract::GINS2 has been found to be closely related to cell proliferation, survival and maintenance of genomic integrity in addition to the induction of polyploidy. However, the molecular mechanisms of GINS2-mediated tumor regression have not been fully elucidated. Our study showed that GINS2 interacted with PML-C (a structura...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2013.1339

    authors: Gao Y,Wang S,Liu B,Zhong L

    更新日期:2013-06-01 00:00:00

  • Acute in vivo effects of leptin and leptin fragments on corticosteroid hormone secretion and entero-insular axis in the rat.

    abstract::Leptin is a 147-amino acid adipose tissue-secreted hormone, which acts via several subtypes of receptors, the main and better known variants of which are named Ob-Ra and Ob-Rb. Structure-activity relationship studies pointed out the importance of the N-terminal and C-terminal amino-acid sequences 22-115 and 116-166, r...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:

    authors: Malendowicz LK,Gorska T,Tortorella C,Nowak M,Majchrzak M,Spinazzi R,Nussdorfer GG,Nowak KW

    更新日期:2004-06-01 00:00:00

  • Cold atmospheric plasma treatment selectively targets head and neck squamous cell carcinoma cells.

    abstract::The treatment of locoregional recurrence (LRR) of head and neck squamous cell carcinoma (HNSCC) often requires a combination of surgery, radiation therapy and/or chemotherapy. Survival outcomes are poor and the treatment outcomes are morbid. Cold atmospheric plasma (CAP) is an ionized gas produced at room temperature ...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2014.1849

    authors: Guerrero-Preston R,Ogawa T,Uemura M,Shumulinsky G,Valle BL,Pirini F,Ravi R,Sidransky D,Keidar M,Trink B

    更新日期:2014-10-01 00:00:00

  • The inhibitory effect and the molecular mechanism of glabridin on RANKL-induced osteoclastogenesis in RAW264.7 cells.

    abstract::Osteoblastic bone formation and osteoclastic bone resorption are in balance to maintain a constant, homeostatically controlled amount of bone. Excessive bone resorption by osteoclasts is involved in the pathogenesis of bone-related disorders. In the present study, we evaluated the i...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2011.822

    authors: Kim HS,Suh KS,Sul D,Kim BJ,Lee SK,Jung WW

    更新日期:2012-02-01 00:00:00

  • Characterization of the nuclear localization signal in the DNA helicase responsible for Bloom syndrome.

    abstract::Bloom syndrome (BS) is a rare genetic disorder characterized by small body size, photosensitivity, immunodeficiency and a high predisposition to various types of cancer. BLM was identified as the causative gene for BS. The BLM protein is homologous to DNA helicase and has two basic amino acid clusters in its C-termina...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.5.5.477

    authors: Hayakawa S,Kaneko H,Fukao T,Kasahara K,Matsumoto T,Furuichi Y,Kondo N

    更新日期:2000-05-01 00:00:00

  • Effects of apicidin, a histone deacetylase inhibitor, on the regulation of apoptosis in H-ras-transformed breast epithelial cells.

    abstract::The cellular susceptibility of cancer cells to histone deacetylase (HDAC) inhibitors is increased by the etopic expression of oncogenic Ras. However, the ability of HDAC inhibitors to regulate the apoptotic pathway in human breast cancer cells is still not completely understood. In this study, the anti-proliferative e...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:

    authors: Park H,Im JY,Kim J,Choi WS,Kim HS

    更新日期:2008-03-01 00:00:00

  • Immune activation and antitumor response of ar-turmerone on P388D1 lymphoblast cell implanted tumors.

    abstract::Aromatic turmerone (ar-turmerone) has been reported to have a cytotoxic effect on L-1210 and HL-60 cells. In the present study, we investigated the anticancer responses and immune activities in implanted tumor cells. Our study found that ar-turmerone inhibited the increase in the nu...

    journal_title:International journal of molecular medicine

    pub_type: 杂志文章

    doi:10.3892/ijmm.2012.1196

    authors: Kim D,Suh Y,Lee H,Lee Y

    更新日期:2013-02-01 00:00:00