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Recent advances in predicting lncRNA-disease associations based on computational methods. Drug Discov Today 2023; 28:103432. [PMID: 36370992 DOI: 10.1016/j.drudis.2022.103432] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/19/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022]
Abstract
Mutations in and dysregulation of long non-coding RNAs (lncRNAs) are closely associated with the development of various human complex diseases, but only a few lncRNAs have been experimentally confirmed to be associated with human diseases. Predicting new potential lncRNA-disease associations (LDAs) will help us to understand the pathogenesis of human diseases and to detect disease markers, as well as in disease diagnosis, prevention and treatment. Computational methods can effectively narrow down the screening scope of biological experiments, thereby reducing the duration and cost of such experiments. In this review, we outline recent advances in computational methods for predicting LDAs, focusing on LDA databases, lncRNA/disease similarity calculations, and advanced computational models. In addition, we analyze the limitations of various computational models and discuss future challenges and directions for development.
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Das S, Kulkarni S, Singh Y, Kumar P, Thareja S. Selective Estrogen Receptor Modulators (SERMs) for the Treatment of ER+ Breast Cancer: An Overview. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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High-Dose Toremifene as a Promising Candidate Therapy for Hormone Receptor-Positive Metastatic Breast Cancer with Secondary Resistance to Aromatase Inhibitors. Int J Breast Cancer 2020; 2020:7156574. [PMID: 32099680 PMCID: PMC7037483 DOI: 10.1155/2020/7156574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
There are currently no established second- and later-line therapies for postmenopausal women with hormone receptor-positive advanced or metastatic breast cancer. We examined the efficacy of high-dose toremifene (HD-TOR) for this patient group and whether aromatase inhibitor (AI) resistance influences HD-TOR treatment outcome. This retrospective analysis investigated the outcomes of 19 women with postmenopausal hormone-sensitive recurrent or metastatic breast cancer who received HD-TOR, defined as 120 mg daily from 2012 to 2016. The median follow-up duration was 9.67 months. The overall response rate (ORR) and clinical benefit rate (CBR) were compared between various clinical subgroups, including patients exhibiting primary or secondary AI resistance as defined by the timing of recurrence or progression. Time to treatment failure (TTF) was estimated by the Kaplan–Meier method and compared between subgroups by the log-rank test. The overall ORR was 21.1%, and the CBR was 31.6%. CBR was significantly higher for patients without liver metastasis (50% vs. 0%, p = 0.044). Nine cases exhibited primary and eight cases secondary AI resistance. Both ORR and CBR were higher in patients with secondary AI resistance (25% vs. 0%, p = 0.087; 38% vs. 11%, p = 0.29). The median TTF was 6.2 months in the entire AI-resistant group (n = 17) and was longer in the secondary resistance subgroup than in the primary resistance subgroup (8.40 vs. 4.87 months; log-rank: p = 0.159). High-dose TOR appears to be most effective for postmenopausal breast cancer cases with secondary resistance to AIs, cases without prior AI treatment, and cases without liver metastasis. The detailed mechanisms of AI resistance and the clinical features of responsive cases need to be further clarified to identify the best candidates for HD-TOR.
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Getter T, Suh S, Hoang T, Handa JT, Dong Z, Ma X, Chen Y, Blackshaw S, Palczewski K. The selective estrogen receptor modulator raloxifene mitigates the effect of all- trans-retinal toxicity in photoreceptor degeneration. J Biol Chem 2019; 294:9461-9475. [PMID: 31073029 DOI: 10.1074/jbc.ra119.008697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/08/2019] [Indexed: 12/19/2022] Open
Abstract
The retinoid cycle is a metabolic process in the vertebrate retina that continuously regenerates 11-cis-retinal (11-cisRAL) from the all-trans-retinal (atRAL) isomer. atRAL accumulation can cause photoreceptor degeneration and irreversible visual dysfunction associated with incurable blinding retinal diseases, such as Stargardt disease, retinitis pigmentosa (RP), and atrophic age-related macular degeneration (AMD). The underlying cellular mechanisms leading to retinal degeneration remain uncertain, although previous studies have shown that atRAL promotes calcium influx associated with cell apoptosis. To identify compounds that mitigate the effects of atRAL toxicity, here we developed an unbiased and robust image-based assay that can detect changes in intracellular calcium levels in U2OS cells. Using our assay in a high-throughput screen of 2,400 compounds, we noted that selective estrogen receptor modulators (SERMs) potently stabilize intracellular calcium and thereby counteract atRAL-induced toxicity. In a light-induced retinal degeneration mouse model (Abca4 -/- Rdh8 -/-), raloxifene (a benzothiophene-type scaffold SERM) prevented the onset of photoreceptor apoptosis and thus protected the retina from degeneration. The minor structural differences between raloxifene and one of its derivatives (Y 134) had a major impact on calcium homeostasis after atRAL exposure in vitro, and we verified this differential impact in vivo In summary, the SERM raloxifene has structural and functional neuroprotective effects in the retina. We propose that the highly sensitive image-based assay developed here could be applied for the discovery of additional drug candidates preventing photoreceptor degeneration.
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Affiliation(s)
- Tamar Getter
- From the Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697, .,the Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Susie Suh
- From the Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697.,the Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Thanh Hoang
- the Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - James T Handa
- the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | | | - Xiuli Ma
- Polgenix Inc., Irvine, California 92617
| | - Yuanyuan Chen
- the Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and.,the McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Seth Blackshaw
- the Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Krzysztof Palczewski
- From the Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697, .,the Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
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Takuwa H, Tsuji W, Shintaku M, Yotsumoto F. Hormone signaling via androgen receptor affects breast cancer and prostate cancer in a male patient: A case report. BMC Cancer 2018; 18:1282. [PMID: 30577860 PMCID: PMC6303965 DOI: 10.1186/s12885-018-5216-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 12/13/2018] [Indexed: 03/10/2023] Open
Abstract
Background Male breast cancer (MBC) is rare, accounting for only around 1% of all breast cancers. Most MBCs are hormone-driven. Not only the estrogen receptor (ER), but also other steroid hormone receptors, including the androgen receptor (AR) and progesterone receptor (PgR) are expressed in MBC. AR activation in breast cancer cells facilitates downstream gene expression that drives tumorigenesis in a similar manner to ER. AR-mediated signalling works paradoxically in breast cancer and prostate cancer, and cancer cells expressing the AR are endocrine-sensitive. Case presentation We describe a case of double cancer of MBC and prostate cancer. A 69-year-old man was referred to our hospital with a lump in his left breast in the 1990s. The patient had cT3N3M0, stage IIIC breast cancer, and underwent a mastectomy and axillary lymph node dissection. Though adjuvant chemotherapy was administered, he experienced pleural metastasis 2 months after the surgery. Two years after the recurrence during endocrine therapy with oral 5-fluorouracil, he complained of frequent urination. Radiological and histological examinations revealed that the patient had cT3N0M0, stage III primary prostate cancer with a prostate-specific antigen (PSA) level of 40.5 ng/mL. Germline mutations in the BRCA1 and BRCA2 genes were not tested. He received multidisciplinary, continuous therapy for both breast and prostate cancer; however, 5 and 3 years after each diagnosis, respectively, he experienced a deep vein thrombosis in his right leg related to the endocrine therapy. Liver metastasis progressed after he stopped breast cancer therapy. However, long-term disease control had been achieved with anti-estrogen therapy for breast cancer and estrogen replacement therapy for prostate cancer. Conclusions Several studies have shown that estrogen exposure after estrogen depletion likely causes apoptosis of ER-positive breast cancer cells. Our findings indicate that this also applies to the environment in male body. AR dominant signaling prevents breast cancer recurrence and metastasis, especially in MBC patients.
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Affiliation(s)
- Haruko Takuwa
- Department of Breast Surgery, Shiga General Hospital, 5-4-30, Moriyama, Moriyama-City, Shiga, 524-8524, Japan.
| | - Wakako Tsuji
- Department of Breast Surgery, Shiga General Hospital, 5-4-30, Moriyama, Moriyama-City, Shiga, 524-8524, Japan
| | - Masayuki Shintaku
- Department of Breast Surgery, Shiga General Hospital, 5-4-30, Moriyama, Moriyama-City, Shiga, 524-8524, Japan
| | - Fumiaki Yotsumoto
- Department of Breast Surgery, Shiga General Hospital, 5-4-30, Moriyama, Moriyama-City, Shiga, 524-8524, Japan
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Li M, Chang T, Wei D, Tang M, Yan S, Du C, Cui HL. Label-free detection of anti-estrogen receptor alpha and its binding with estrogen receptor peptide alpha by terahertz spectroscopy. RSC Adv 2017. [DOI: 10.1039/c6ra28754a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Terahertz (THz) spectroscopic techniques were employed to study the hydration shell formation around anti-estrogen receptor alpha (AER-α) and to detect the binding reaction between AER-α and estrogen receptor peptide alpha (ERP-α).
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Affiliation(s)
- Mingliang Li
- College of Instrumentation & Electrical Engineering
- Jilin University
- Changchun
- China
| | - Tianying Chang
- College of Instrumentation & Electrical Engineering
- Jilin University
- Changchun
- China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
| | - Dongshan Wei
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Mingjie Tang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Shihan Yan
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Chunlei Du
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
- Chongqing Institute of Green and Intelligent Technology
- Chinese Academy of Sciences
- Chongqing
- China
| | - Hong-Liang Cui
- College of Instrumentation & Electrical Engineering
- Jilin University
- Changchun
- China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology
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Ahirwar R, Vellarikkal SK, Sett A, Sivasubbu S, Scaria V, Bora U, Borthakur BB, Kataki AC, Sharma JD, Nahar P. Aptamer-Assisted Detection of the Altered Expression of Estrogen Receptor Alpha in Human Breast Cancer. PLoS One 2016; 11:e0153001. [PMID: 27043307 PMCID: PMC4820125 DOI: 10.1371/journal.pone.0153001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/22/2016] [Indexed: 12/21/2022] Open
Abstract
An increase in the expression of estrogen receptors (ER) and the expanded population of ER-positive cells are two common phenotypes of breast cancer. Detection of the aberrantly expressed ERα in breast cancer is carried out using ERα-antibodies and radiolabelled ligands to make decisions about cancer treatment and targeted therapy. Capitalizing on the beneficial advantages of aptamer over the conventional antibody or radiolabelled ligand, we have identified a DNA aptamer that selectively binds and facilitates the detection of ERα in human breast cancer tissue sections. The aptamer is identified using the high throughput sequencing assisted SELEX screening. Biophysical characterization confirms the binding and formation of a thermodynamically stable complex between the identified DNA aptamer (ERaptD4) and ERα (Ka = 1.55±0.298×108 M-1; ΔH = 4.32×104±801.1 cal/mol; ΔS = -108 cal/mol/deg). Interestingly, the specificity measurements suggest that the ERaptD4 internalizes into ERα-positive breast cancer cells in a target-selective manner and localizes specifically in the nuclear region. To harness these characteristics of ERaptD4 for detection of ERα expression in breast cancer samples, we performed the aptamer-assisted histochemical analysis of ERα in tissue samples from breast cancer patients. The results were validated by performing the immunohistochemistry on same samples with an ERα-antibody. We found that the two methods agree strongly in assay output (kappa value = 0.930, p-value <0.05 for strong ERα positive and the ERα negative samples; kappa value = 0.823, p-value <0.05 for the weak/moderate ER+ve samples, n = 20). Further, the aptamer stain the ERα-positive cells in breast tissues without cross-reacting to ERα-deficient fibroblasts, adipocytes, or the inflammatory cells. Our results demonstrate a significant consistency in the aptamer-assisted detection of ERα in strong ERα positive, moderate ERα positive and ERα negative breast cancer tissues. We anticipate that the ERaptD4 aptamer targeting ERα may potentially be used for an efficient grading of ERα expression in cancer tissues.
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Affiliation(s)
- Rajesh Ahirwar
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Shamsudheen Karuthedath Vellarikkal
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Arghya Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | - Sridhar Sivasubbu
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Utpal Bora
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | | | | | | | - Pradip Nahar
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail:
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In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules. Sci Rep 2016; 6:21285. [PMID: 26899418 PMCID: PMC4761961 DOI: 10.1038/srep21285] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/21/2016] [Indexed: 11/17/2022] Open
Abstract
Aptamers, the chemical-antibody substitute to conventional antibodies, are primarily discovered through SELEX technology involving multi-round selections and enrichment. Circumventing conventional methodology, here we report an in silico selection of aptamers to estrogen receptor alpha (ERα) using RNA analogs of human estrogen response elements (EREs). The inverted repeat nature of ERE and the ability to form stable hairpins were used as criteria to obtain aptamer-alike sequences. Near-native RNA analogs of selected single stranded EREs were modelled and their likelihood to emerge as ERα aptamer was examined using AutoDock Vina, HADDOCK and PatchDock docking. These in silico predictions were validated by measuring the thermodynamic parameters of ERα -RNA interactions using isothermal titration calorimetry. Based on the in silico and in vitro results, we selected a candidate RNA (ERaptR4; 5′-GGGGUCAAGGUGACCCC-3′) having a binding constant (Ka) of 1.02 ± 0.1 × 108 M−1 as an ERα-aptamer. Target-specificity of the selected ERaptR4 aptamer was confirmed through cytochemistry and solid-phase immunoassays. Furthermore, stability analyses identified ERaptR4 resistant to serum and RNase A degradation in presence of ERα. Taken together, an efficient ERα-RNA aptamer is identified using a non-SELEX procedure of aptamer selection. The high-affinity and specificity can be utilized in detection of ERα in breast cancer and related diseases.
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Ahirwar R, Nahar P. Development of a label-free gold nanoparticle-based colorimetric aptasensor for detection of human estrogen receptor alpha. Anal Bioanal Chem 2015; 408:327-32. [PMID: 26476919 DOI: 10.1007/s00216-015-9090-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/23/2015] [Accepted: 09/29/2015] [Indexed: 11/24/2022]
Abstract
The increasing demand for easily available and low-cost diagnostics has fuelled the development of aptasensors as platforms for rapid, sensitive, and point-of-care testing of target analytes. Recently, gold nanoparticle (AuNP)-based aptasensors have attracted wide recognition owing to their color transition properties which allow real-time rapid sensing of targets. In this study, we utilized the color transition property of aptamer-functionalized AuNPs to detect and quantify estrogen receptor alpha (ERα), a key biomarker protein in breast cancer. We found that the coating of AuNPs with unmodified ERα-RNA aptamer (GGGGUCAAGGUGACCCC) makes them resistant to salt-induced aggregation. However, addition of ERα to the aptamer-protected AuNPs results in their spontaneous aggregation as evident from a color transition from wine red to deep blue. On the basis of this, we developed an ERα aptasensor, with limits of detection and quantification of 0.64 and 2.16 ng/mL, respectively; the aptasensor can efficiently detect and quantify ERα in a working range of 10 ng/mL-5μg/mL protein. Validation of the aptasensor on cellular extracts of ERα-positive MCF-7 and ERα-deficient MDA-MB-231 breast cancer cells showed a target-selective response in ERα-positive samples but not in cellular extracts of ERα-deficient breast cancer cells. Further, the small size and simple fabrication chemistry of aptamers provide an additional benefit to make the ERα aptasensor a potentially useful and cost-effective tool in point-of-care analyses of ERα.
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Affiliation(s)
- Rajesh Ahirwar
- Department of Chemical and Systems Biology, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,CSIR-Institute of Genomics and Integrative Biology, Academy of Scientific and Innovative Research, Delhi, 110007, India
| | - Pradip Nahar
- Department of Chemical and Systems Biology, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India. .,CSIR-Institute of Genomics and Integrative Biology, Academy of Scientific and Innovative Research, Delhi, 110007, India.
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Mori R, Nagao Y. High-dose toremifene for fulvestrant-resistant metastatic breast cancer: a report of two cases. Case Rep Oncol 2014; 7:383-8. [PMID: 25028579 PMCID: PMC4086043 DOI: 10.1159/000363649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Hormone receptor (HR)-positive metastatic breast cancer (MBC) is usually treated with hormone therapy. In postmenopausal females, aromatase inhibitors (AIs) are usually used as first-line therapy, and fulvestrant is used subsequently. The optimal treatment beyond fulvestrant has not been established. We experienced two cases in which high-dose toremifene (hdTOR) was effective after the failure of AIs and fulvestrant. CASE 1 A 73-year-old female with HR-positive left breast cancer (T2N1M0) underwent preoperative chemotherapy and mastectomy with axillary dissection. Computed tomography (CT) revealed liver tumors in S7 (23 mm) and S8 (25 mm) during adjuvant letrozole therapy, so fulvestrant was started. The tumors initially decreased in size (23 and 22 mm), but then progressed (36 and 25 mm). Treatment was changed to hdTOR, and the tumors shrunk to 26 mm (S7) and 24 mm (S8), and she was stable for 6 months while receiving hdTOR. CASE 2 An 81-year-old female with HR-positive left breast cancer (T2N1M0) underwent left mastectomy and axillary dissection. CT revealed liver tumors in S7 (20 mm) and S8 (11 mm) during adjuvant letrozole therapy, so fulvestrant treatment was started. The tumor in S7 shrunk (13 mm), but the tumor in S8 slightly progressed (13 mm), and both tumors progressed (14 and 18 mm) after 6 months. Treatment was changed to hdTOR, and the tumors slightly shrunk (12 and 14 mm) after 6 months. hdTOR has been continued for 9 months. CONCLUSION hdTOR was effective for MBC after multiple hormone therapies, likely because it acts via a different mechanism of action.
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Affiliation(s)
- Ryutaro Mori
- Department of Breast Surgery, Gifu Prefectural General Medical Center, Gifu, Japan
| | - Yasuko Nagao
- Department of Breast Surgery, Gifu Prefectural General Medical Center, Gifu, Japan
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A computational framework to infer human disease-associated long noncoding RNAs. PLoS One 2014; 9:e84408. [PMID: 24392133 PMCID: PMC3879311 DOI: 10.1371/journal.pone.0084408] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 11/13/2013] [Indexed: 12/11/2022] Open
Abstract
As a major class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been implicated in various critical biological processes. Accumulating researches have linked dysregulations and mutations of lncRNAs to a variety of human disorders and diseases. However, to date, only a few human lncRNAs have been associated with diseases. Therefore, it is very important to develop a computational method to globally predict potential associated diseases for human lncRNAs. In this paper, we developed a computational framework to accomplish this by combining human lncRNA expression profiles, gene expression profiles, and human disease-associated gene data. Applying this framework to available human long intergenic noncoding RNAs (lincRNAs) expression data, we showed that the framework has reliable accuracy. As a result, for non-tissue-specific lincRNAs, the AUC of our algorithm is 0.7645, and the prediction accuracy is about 89%. This study will be helpful for identifying novel lncRNAs for human diseases, which will help in understanding the roles of lncRNAs in human diseases and facilitate treatment. The corresponding codes for our method and the predicted results are all available at http://asdcd.amss.ac.cn/MingXiLiu/lncRNA-disease.html.
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Vogel CL, Johnston MA, Capers C, Braccia D. Toremifene for breast cancer: a review of 20 years of data. Clin Breast Cancer 2013; 14:1-9. [PMID: 24439786 DOI: 10.1016/j.clbc.2013.10.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/02/2013] [Indexed: 01/08/2023]
Abstract
Endocrine therapy is a cornerstone of medical treatment for estrogen receptor-positive breast cancer. The discovery of selective estrogen receptor modulators (SERMs) > 40 years ago represented a revolutionary advance in the treatment of breast cancer. As a therapeutic class, SERMs have either estrogenic or antiestrogenic activity, depending on the target tissue and the hormonal environment. In breast tissue, SERMs are antiestrogenic, making them a major treatment option for women with hormone-sensitive breast cancer. Toremifene citrate was developed > 20 years ago with the goal of achieving efficacy similar to that of tamoxifen and with an improved safety profile. Although studies to date have not confirmed a clear safety advantage or disadvantage for toremifene, clinical data support the efficacy and safety of toremifene for the treatment of breast cancer in postmenopausal patients. Toremifene also has a pharmacokinetic profile and metabolic pathway different from that of tamoxifen, which may provide a therapeutic advantage in certain patients. In addition, because of the selective estrogenic effects of SERMs in bone and on lipid levels along with a different side effect profile compared with the aromatase inhibitors (AIs), toremifene is a viable option to the AIs for some patients. Despite a number of clinical trials and over 500,000 patient years of use, many oncologists have limited familiarity with toremifene data. This article will examine the rationale for the use of toremifene in the treatment of women with breast cancer and review data from 20 years of clinical experience with this agent.
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Affiliation(s)
- Charles L Vogel
- Sylvester Comprehensive Cancer Center at Deerfield Beach, Miller School of Medicine, University of Miami, Miami FL.
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Morad SAF, Levin JC, Tan SF, Fox TE, Feith DJ, Cabot MC. Novel off-target effect of tamoxifen--inhibition of acid ceramidase activity in cancer cells. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:1657-64. [PMID: 23939396 DOI: 10.1016/j.bbalip.2013.07.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/18/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
Acid ceramidase (AC), EC 3.5.1.23, a lysosomal enzyme, catalyzes the hydrolysis of ceramide to constituent sphingoid base, sphingosine, and fatty acid. Because AC regulates the levels of pro-apoptotic ceramide and mitogenic sphingosine-1-phosphate, it is considered an apt target in cancer therapy. The present study reveals, for the first time, that the prominent antiestrogen, tamoxifen, is a pan-effective AC inhibitor in the low, single digit micromolar range, as demonstrated in a wide spectrum of cancer cell types, prostate, pancreatic, colorectal, and breast. Prostate cancer cells were chosen for the detailed investigations. Treatment of intact PC-3 cells with tamoxifen produced time- and dose-dependent inhibition of AC activity. Tamoxifen did not impact cell viability nor did it inhibit AC activity in cell-free assays. In pursuit of mechanism of action, we demonstrate that tamoxifen induced time-, as early as 5min, and dose-dependent, as low as 5μM, increases in lysosomal membrane permeability (LMP), and time- and dose-dependent downregulation of AC protein expression. Assessing various protease inhibitors revealed that a cathepsin B inhibitor blocked tamoxifen-elicited downregulation of AC protein; however, this action failed to restore AC activity unless assayed in a cell-free system at pH4.5. In addition, pretreatment with tamoxifen inhibited PC-3 cell migration. Toremifene, an antiestrogen structurally similar to tamoxifen, was also a potent inhibitor of AC activity. This study reveals a new, off-target action of tamoxifen that may be of benefit to enhance anticancer therapies that either incorporate ceramide or target ceramide metabolism.
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Affiliation(s)
- Samy A F Morad
- John Wayne Cancer Institute at Saint John's Health Center, Department of Experimental Therapeutics, Santa Monica, CA 90404, USA
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Maximov PY, Lee TM, Jordan VC. The discovery and development of selective estrogen receptor modulators (SERMs) for clinical practice. CURRENT CLINICAL PHARMACOLOGY 2013; 8:135-55. [PMID: 23062036 PMCID: PMC3624793 DOI: 10.2174/1574884711308020006] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 07/11/2012] [Accepted: 10/03/2012] [Indexed: 01/13/2023]
Abstract
Selective estrogen receptor modulators (SERMs) are structurally different compounds that interact with intracellular estrogen receptors in target organs as estrogen receptor agonists or antagonists. These drugs have been intensively studied over the past decade and have proven to be a highly versatile group for the treatment of different conditions associated with postmenopausal women's health, including hormone responsive cancer and osteoporosis. Tamoxifen, a failed contraceptive is currently used to treat all stages of breast cancer, chemoprevention in women at high risk for breast cancer and also has beneficial effects on bone mineral density and serum lipids in postmenopausal women. Raloxifene, a failed breast cancer drug, is the only SERM approved internationally for the prevention and treatment of postmenopausal osteoporosis and vertebral fractures. However, although these SERMs have many benefits, they also have some potentially serious adverse effects, such as thromboembolic disorders and, in the case of tamoxifen, uterine cancer. These adverse effects represent a major concern given that long-term therapy is required to prevent osteoporosis or prevent and treat breast cancer. The search for the 'ideal' SERM, which would have estrogenic effects on bone and serum lipids, neutral effects on the uterus, and antiestrogenic effects on breast tissue, but none of the adverse effects associated with current therapies, is currently under way. Ospemifene, lasofoxifene, bazedoxifene and arzoxifene, which are new SERM molecules with potentially greater efficacy and potency than previous SERMs, have been investigated for use in the treatment and prevention of osteoporosis. These drugs have been shown to be comparably effective to conventional hormone replacement therapy in animal models, with potential indications for an improved safety profile. Clinical efficacy data from ongoing phase III trials are available or are awaited for each SERM so that a true understanding of the therapeutic potential of these compounds can be obtained. In this article, we describe the discovery and development of the group of medicines called SERMs. The newer SERMs in late development: ospemifene, lasofoxifene, bazedoxifene, are arzoxifene are described in detail.
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Affiliation(s)
- Philipp Y Maximov
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Rd NW, Research Building, Suite E204A, Washington, DC 20057, USA
| | - Theresa M Lee
- Division of Hematology and Oncology, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC 20057, USA
| | - V. Craig Jordan
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Rd NW, Research Building, Suite E204A, Washington, DC 20057, USA
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