1
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A Novel Mechanism Underlying the Inhibitory Effects of Trastuzumab on the Growth of HER2-Positive Breast Cancer Cells. Cells 2022; 11:cells11244093. [PMID: 36552857 PMCID: PMC9777316 DOI: 10.3390/cells11244093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
To improve the efficacy of trastuzumab, it is essential to understand its mechanism of action. One of the significant issues that makes it difficult to determine the precise mechanism of trastuzumab action is the formation of various HER receptor dimers in HER2-positive breast cancer cells. So far, studies have focused on the role of HER2-HER3 heterodimers, and little is known regarding EGFR-HER2 heterodimers. Here, we study the role of trastuzumab on the cell signaling and cell proliferation mediated by EGFR-HER2 heterodimers in BT474 and SRBR3 cells. EGF stimulates the formation of both EGFR homodimer and EGFR-HER2 heterodimer. Trastuzumab only binds to HER2, not EGFR. Therefore, any effects of trastuzumab on EGF-induced activation of EGFR, HER2, and downstream signaling proteins, as well as cell proliferation, are through its effects on EGFR-HER2 heterodimers. We show that trastuzumab inhibits EGF-induced cell proliferation and cell cycle progression in BT474 and SKBR3 cells. Interestingly trastuzumab strongly inhibits EGF-induced Akt phosphorylation and slightly inhibits EGF-induced Erk activation, in both BT474 and SKBR3 cells. These data suggest the presence of a novel mechanism that allows trastuzumab to inhibit EGR-induced Akt activation and cell proliferation, without blocking EGF-induced EGFR-HER2 heterodimerization and activation. We show that trastuzumab inhibits EGF-induced lipid raft localization of the EGFR-HER2 heterodimer. Disruption of the lipid raft with MβCD blocks HER2-mediated AKT activation in a similar way to trastuzumab. MβCD and trastuzumab synergically inhibit AKT activation. We conclude that trastuzumab inhibits EGF-induced lipid raft localization of EGFR-HER2 heterodimer, which leads to the inhibition of Akt phosphorylation and cell proliferation, without blocking the formation and phosphorylation of the EGFR-HER2 heterodimer.
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2
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Xu S, Liu H, Wan L, Zhang W, Wang Q, Zhang S, Shang S, Zhang Y, Pang D. The MS-lincRNA landscape reveals a novel lincRNA BCLIN25 that contributes to tumorigenesis by upregulating ERBB2 expression via epigenetic modification and RNA-RNA interactions in breast cancer. Cell Death Dis 2019; 10:920. [PMID: 31801944 PMCID: PMC6892920 DOI: 10.1038/s41419-019-2137-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/17/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022]
Abstract
The landscape of molecular subtype-specific long intergenic noncoding RNAs (MS-lincRNAs) in breast cancer has not been elucidated. No study has investigated the biological function of BCLIN25, serving as a novel HER2 subtype-specific lincRNA, in human disease, especially in malignancy. Moreover, the mechanism of BCLIN25 in the regulation of ERBB2 expression remains unknown. Our present study aimed to investigate the role and underlying mechanism of BCLIN25 in the regulation of ERBB2 expression. The transcriptional landscape across five subtypes of breast cancer was investigated using RNA sequencing. Integrative transcriptomic analysis was performed to identify the landscape of novel lincRNAs. Next, WEKA was used to identify lincRNA-based subtype classification and MS-lincRNAs for breast cancer. The MS-lincRNAs were validated in 250 breast cancer samples in our cohort and datasets from The Cancer Genome Atlas and Gene Expression Omnibus. Furthermore, BCLIN25 was selected, and its role in tumorigenesis was examined in vitro and in vivo. Finally, the mechanism by which BCLIN25 regulates ERBB2 expression was investigated in detail. A total of 715 novel lincRNAs were differentially expressed across five breast cancer subtypes. Next, lincRNA-based subtype classifications and MS-lincRNAs were identified and validated using our breast cancer samples and public datasets. BCLIN25 was found to contribute to tumorigenesis in vitro and in vivo. Mechanistically, BCLIN25 was shown to increase the expression of ERBB2 by enhancing promoter CpG methylation of miR-125b, leading to miR-125b downregulation. In turn, ERBB2 mRNA degradation was found to be abolished due to decreased binding of miR-125b to the 3'-untranslated region (UTR) of ERBB2. These findings reveal the role of novel lincRNAs in breast cancer and provide a comprehensive landscape of breast cancer MS-lincRNAs, which may complement the current molecular classification system in breast cancer.
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Affiliation(s)
- Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, HRB, 150040, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, HRB, 150081, China
| | - Lin Wan
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, HRB, 150040, China
| | - Weijia Zhang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, HRB, 150040, China
| | - Shumei Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, HRB, 150081, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, HRB, 150081, China
| | - Yan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, HRB, 150001, China.
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, HRB, 150040, China.
- Heilongjiang Academy of Medical Sciences, Harbin, HRB, 150086, China.
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3
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Ren X. Genome-wide analysis reveals the emerging roles of long non-coding RNAs in cancer. Oncol Lett 2019; 19:588-594. [PMID: 31897174 DOI: 10.3892/ol.2019.11141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022] Open
Abstract
Cancer is the most intractable human disease that is primarily caused by genetic alterations. Recently, the general application of microarrays and high-throughput sequencing technology has revealed various important roles of long noncoding RNAs (lncRNAs) in cancer. This review summarizes the function, mechanism, diagnostic and treatment potential of lncRNAs identified through genome-wide analysis in cancer. Cell-, tissue- and development stage-specific expression patterns are major characteristics of cancer-associated lncRNAs, and various genetic alterations are also implicated. Microarray and sequencing analyses serve important roles in mechanistic studies of either nuclear or cytoplasmic lncRNAs. Collectively, genome-wide analysis is the inexorable trend of future studies or clinical applications of lncRNAs and offers a novel perspective regarding the prognosis and treatment of cancer.
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Affiliation(s)
- Xiaoxia Ren
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, P.R. China
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4
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Keshavarz M, Asadi MH, Riahi-Madvar A. Upregulation of pluripotent long noncoding RNA ES3 in HER2-positive breast cancer. J Cell Biochem 2019; 120:18398-18405. [PMID: 31211468 DOI: 10.1002/jcb.29152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 01/16/2023]
Abstract
Breast cancer is the second most common cancer and estimates to be responsible for 20% of all cancer patients. Breast cancer has several subtypes including luminal A, luminal B, normal breast-like, basal-like, and human epidermal growth factor receptor 2 (HER2)-enriched. HER2-positive breast cancer cells have higher HER2 expression than other breast cancer subtypes. This subtype is the most aggressive breast cancer subtype and has more ability to metastasis than other breast cancer subtypes. HER2 is a growth-promoting protein that is overexpressed in approximately 20 to 30% of breast cancers and its overexpression is strongly related to poor prognosis. New studies suggested that HER2 expression is correlated with cancer stem cell (CSC) markers in breast cancer. ES3 transcript as a pluripotency long noncoding RNA (lncRNA) is linked to pluripotency transcriptional networks in human embryonic stem cells, but its function in breast cancer is not clarified. In the current research, we found ES3 upregulation in breast cancer and its diagnostic value in breast cancer diagnosis. Furthermore, our findings revealed that ES3 transcript has a high expression in high-grade and high-stage breast tumors. In addition, our data demonstrated that ES3 expression downregulated during neural differentiation. Therefore, its expression may be correlated to breast tumor differentiation status. Notably, a high expression level of ES3 in HER2-positive breast tumor tissues motivated us to investigate the effect of HER2 on ES3 expression by blocking HER2 activity with lapatinib. The results showed that ES3 expression suppressed when HER2 activity was blocked. In summary, for the first time, we found that lncRNA ES3 was significantly upregulated in HER2-positive breast tumors and may contribute to breast cancer proliferation as a downstream target of HER2.
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Affiliation(s)
- Mostafa Keshavarz
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Malek Hossein Asadi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Ali Riahi-Madvar
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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5
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Mathias C, Zambalde EP, Rask P, Gradia DF, de Oliveira JC. Long non-coding RNAs differential expression in breast cancer subtypes: What do we know? Clin Genet 2019; 95:558-568. [PMID: 30614523 DOI: 10.1111/cge.13502] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/28/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022]
Abstract
Breast Cancer (BC) is the most commonly diagnosed cancer and is the leading cause of cancer deaths in women. BC is a heterogeneous disease with different clinical and genetic features. According to immunohistochemical markers, BC is subdivided into four main subtypes: luminal A, luminal B, ERBB2 positive and triple negative. Long non-coding RNAs (lncRNAs) are transcripts with more than 200 nucleotides and deregulated lncRNAs are associated with human diseases, including BC. In order to improve BC molecular classification, non-coding RNAs (ncRNAs), including lncRNAs, have been used. In this review, we focus on lncRNAs with differential expression in BC subtypes and how these RNAs may act to contribute to BC heterogeneity. We also emphasize the potential of these lncRNAs as biomarkers.
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Affiliation(s)
- Carolina Mathias
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Erika P Zambalde
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Philip Rask
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniela F Gradia
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
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6
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Nami B, Maadi H, Wang Z. Mechanisms Underlying the Action and Synergism of Trastuzumab and Pertuzumab in Targeting HER2-Positive Breast Cancer. Cancers (Basel) 2018; 10:cancers10100342. [PMID: 30241301 PMCID: PMC6210751 DOI: 10.3390/cancers10100342] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 02/08/2023] Open
Abstract
Human epidermal growth factor receptor (HER) 2 (HER2) is overexpressed in 20⁻30% of breast cancers. HER2 is a preferred target for treating HER2-positive breast cancer. Trastuzumab and pertuzumab are two HER2-targeted monoclonal antibodies approved by the Food and Drug Administration (FDA) to use as adjuvant therapy in combination with docetaxel to treat metastatic HER2-positive breast cancer. Adding the monoclonal antibodies to treatment regimen has changed the paradigm for treatment of HER2-positive breast cancer. Despite improving outcomes, the percentage of the patients who benefit from the treatment is still low. Continued research and development of novel agents and strategies of drug combinations is needed. A thorough understanding of the molecular mechanisms underlying the action and synergism of trastuzumab and pertuzumab is essential for moving forward to achieve high efficacy in treating HER2-positive breast cancer. This review examined and analyzed findings and hypotheses regarding the action and synergism of trastuzumab and pertuzumab and proposed a model of synergism based on available information.
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Affiliation(s)
- Babak Nami
- Signal Transduction Research Group, Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Hamid Maadi
- Signal Transduction Research Group, Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Zhixiang Wang
- Signal Transduction Research Group, Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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7
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Rizzolio S, Cagnoni G, Battistini C, Bonelli S, Isella C, Van Ginderachter JA, Bernards R, Di Nicolantonio F, Giordano S, Tamagnone L. Neuropilin-1 upregulation elicits adaptive resistance to oncogene-targeted therapies. J Clin Invest 2018; 128:3976-3990. [PMID: 29953416 DOI: 10.1172/jci99257] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/22/2018] [Indexed: 12/14/2022] Open
Abstract
Cancer cell dependence on activated oncogenes is therapeutically targeted, but acquired resistance is virtually unavoidable. Here we show that the treatment of addicted melanoma cells with BRAF inhibitors, and of breast cancer cells with HER2-targeted drugs, led to an adaptive rise in neuropilin-1 (NRP1) expression, which is crucial for the onset of acquired resistance to therapy. Moreover, NRP1 levels dictated the efficacy of MET oncogene inhibitors in addicted stomach and lung carcinoma cells. Mechanistically, NRP1 induced a JNK-dependent signaling cascade leading to the upregulation of alternative effector kinases EGFR or IGF1R, which in turn sustained cancer cell growth and mediated acquired resistance to BRAF, HER2, or MET inhibitors. Notably, the combination with NRP1-interfering molecules improved the efficacy of oncogene-targeted drugs and prevented or even reversed the onset of resistance in cancer cells and tumor models. Our study provides the rationale for targeting the NRP1-dependent upregulation of tyrosine kinases, which are responsible for loss of responsiveness to oncogene-targeted therapies.
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Affiliation(s)
- Sabrina Rizzolio
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy.,Oncology Department, University of Torino, Turin, Italy
| | - Gabriella Cagnoni
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy.,Oncology Department, University of Torino, Turin, Italy
| | - Chiara Battistini
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy.,Oncology Department, University of Torino, Turin, Italy
| | - Stefano Bonelli
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Claudio Isella
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy.,Oncology Department, University of Torino, Turin, Italy
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy.,Oncology Department, University of Torino, Turin, Italy
| | - Silvia Giordano
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy.,Oncology Department, University of Torino, Turin, Italy
| | - Luca Tamagnone
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy.,Oncology Department, University of Torino, Turin, Italy
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8
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Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis. Sci Rep 2018; 8:7324. [PMID: 29743621 PMCID: PMC5943353 DOI: 10.1038/s41598-018-25530-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/24/2018] [Indexed: 12/05/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are frequently dysregulated in many human cancers. We sought to identify candidate oncogenic lncRNAs in human colon tumors by utilizing RNA sequencing data from 22 colon tumors and 22 adjacent normal colon samples from The Cancer Genome Atlas (TCGA). The analysis led to the identification of ~200 differentially expressed lncRNAs. Validation in an independent cohort of normal colon and patient-derived colon cancer cell lines identified a novel lncRNA, lincDUSP, as a potential candidate oncogene. Knockdown of lincDUSP in patient-derived colon tumor cell lines resulted in significantly decreased cell proliferation and clonogenic potential, and increased susceptibility to apoptosis. The knockdown of lincDUSP affects the expression of ~800 genes, and NCI pathway analysis showed enrichment of DNA damage response and cell cycle control pathways. Further, identification of lincDUSP chromatin occupancy sites by ChIRP-Seq demonstrated association with genes involved in the replication-associated DNA damage response and cell cycle control. Consistent with these findings, lincDUSP knockdown in colon tumor cell lines increased both the accumulation of cells in early S-phase and γH2AX foci formation, indicating increased DNA damage response induction. Taken together, these results demonstrate a key role of lincDUSP in the regulation of important pathways in colon cancer.
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9
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Merry CR, McMahon S, Forrest ME, Bartels CF, Saiakhova A, Bartel CA, Scacheri PC, Thompson CL, Jackson MW, Harris LN, Khalil AM. Transcriptome-wide identification of mRNAs and lincRNAs associated with trastuzumab-resistance in HER2-positive breast cancer. Oncotarget 2018; 7:53230-53244. [PMID: 27449296 PMCID: PMC5288181 DOI: 10.18632/oncotarget.10637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/09/2016] [Indexed: 01/03/2023] Open
Abstract
Approximately, 25–30% of early-stage breast tumors are classified at the molecular level as HER2-positive, which is an aggressive subtype of breast cancer. Amplification of the HER2 gene in these tumors results in a substantial increase in HER2 mRNA levels, and consequently, HER2 protein levels. HER2, a transmembrane receptor tyrosine kinase (RTK), is targeted therapeutically by a monoclonal antibody, trastuzumab (Tz), which has dramatically improved the prognosis of HER2-driven breast cancers. However, ~30% of patients develop resistance to trastuzumab and recur; and nearly all patients with advanced disease develop resistance over time and succumb to the disease. Mechanisms of trastuzumab resistance (TzR) are not well understood, although some studies suggest that growth factor signaling through other receptors may be responsible. However, these studies were based on cell culture models of the disease, and thus, it is not known which pathways are driving the resistance in vivo. Using an integrative transcriptomic approach of RNA isolated from trastuzumab-sensitive and trastuzumab-resistant HER2+ tumors, and isogenic cell culture models, we identified a small set of mRNAs and lincRNAs that are associated with trastuzumab-resistance (TzR). Functional analysis of a top candidate gene, S100P, demonstrated that inhibition of S100P results in reversing TzR. Mechanistically, S100P activates the RAS/MEK/MAPK pathway to compensate for HER2 inhibition by trastuzumab. Finally, we demonstrated that the upregulation of S100P appears to be driven by epigenomic changes at the enhancer level. Our current findings should pave the path toward new therapies for breast cancer patients.
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Affiliation(s)
- Callie R Merry
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sarah McMahon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Megan E Forrest
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Courtney A Bartel
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cheryl L Thompson
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mark W Jackson
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lyndsay N Harris
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Medicine and Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ahmad M Khalil
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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10
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Zhao T, Wu L, Li X, Dai H, Zhang Z. Large intergenic non-coding RNA-ROR as a potential biomarker for the diagnosis and dynamic monitoring of breast cancer. Cancer Biomark 2017; 20:165-173. [PMID: 28869448 DOI: 10.3233/cbm-170064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tianhe Zhao
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Lichun Wu
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
- Division of Clinical Laboratory, Sichuan Cancer Hospital, Chengdu, Sichuan, China
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Xinyang Li
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Huangmei Dai
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental Health and Occupational Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
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11
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Zhang Y, Li Y, Wang Q, Zhang X, Wang D, Tang HC, Meng X, Ding X. Identification of an lncRNA‑miRNA‑mRNA interaction mechanism in breast cancer based on bioinformatic analysis. Mol Med Rep 2017; 16:5113-5120. [PMID: 28849135 PMCID: PMC5647044 DOI: 10.3892/mmr.2017.7304] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 04/06/2017] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNAs serve important roles in regulating the expression of certain genes and are involved in the principal biological processes of breast cancer. The majority of studies have focused on defining the regulatory functions of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs/miRs), and few studies have investigated how lncRNAs and miRNAs are transcriptionally regulated. In the present study, based on the breast invasive carcinoma dataset from The Cancer Genome Atlas at cBioPortal, and using a bioinformatics computational approach, an lncRNA-miRNA-mRNA network was constructed. The network consisted of 601 nodes and 706 edges, which represented the complex web of regulatory effects between lncRNAs, miRNAs and target genes. The results of the present study demonstrated that miR-510 was the most potent miRNA controller and regulator of numerous target genes. In addition, it was observed that the lncRNAs PVT1, CCAT1 and linc00861 exhibited possible interactions with clinical biomarkers, including receptor tyrosine-protein kinase erbB-2, estrogen receptor and progesterone receptor, demonstrated using RNA-protein interaction prediction software. The network of lncRNA-miRNA-mRNA interactions will facilitate further experimental studies and may be used to refine biomarker predictions for developing novel therapeutic approaches in breast cancer.
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Affiliation(s)
- Yuhan Zhang
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Yongfeng Li
- Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Qing Wang
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Xiping Zhang
- Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Dajin Wang
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
| | - Hong Chao Tang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Xuli Meng
- Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xianfeng Ding
- College of Life Science, Zhejiang Sci‑Tech University, Hangzhou, Zhejiang 310018, P.R. China
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12
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Wichman L, Somasundaram S, Breindel C, Valerio DM, McCarrey JR, Hodges CA, Khalil AM. Dynamic expression of long noncoding RNAs reveals their potential roles in spermatogenesis and fertility†. Biol Reprod 2017; 97:313-323. [DOI: 10.1093/biolre/iox084] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/27/2017] [Indexed: 12/20/2022] Open
Abstract
Abstract
Mammalian reproduction requires that males and females produce functional haploid germ cells through complex cellular differentiation processes known as spermatogenesis and oogenesis, respectively. While numerous studies have functionally characterized protein-coding genes and small noncoding RNAs (microRNAs and piRNAs) that are essential for gametogenesis, the roles of regulatory long noncoding RNAs (lncRNAs) are yet to be fully characterized. Previously, we and others have demonstrated that intergenic regions of the mammalian genome encode thousands of long noncoding RNAs, and many studies have now demonstrated their critical roles in key biological processes. Thus, we postulated that some lncRNAs may also impact mammalian spermatogenesis and fertility. In this study, we identified a dynamic expression pattern of lncRNAs during murine spermatogenesis. Importantly, we identified a subset of lncRNAs and very few mRNAs that appear to escape meiotic sex chromosome inactivation, an epigenetic process that leads to the silencing of the X- and Y-chromosomes at the pachytene stage of meiosis. Further, some of these lncRNAs and mRNAs show a strong testis expression pattern suggesting that they may play key roles in spermatogenesis. Lastly, we generated a mouse knockout of one X-linked lncRNA, Tslrn1 (testis-specific long noncoding RNA 1), and found that males carrying a Tslrn1 deletion displayed normal fertility but a significant reduction in spermatozoa. Our findings demonstrate that dysregulation of specific mammalian lncRNAs is a novel mechanism of low sperm count or infertility, thus potentially providing new biomarkers and therapeutic strategies.
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Affiliation(s)
- Lauren Wichman
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Saigopal Somasundaram
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Christine Breindel
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dana M. Valerio
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - John R. McCarrey
- Department of Biology, The University of Texas at San Antonio, Texas, USA
| | - Craig A. Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ahmad M. Khalil
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
- Case Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, USA
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Review: Regulation of the cancer epigenome by long non-coding RNAs. Cancer Lett 2017; 407:106-112. [PMID: 28400335 DOI: 10.1016/j.canlet.2017.03.040] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
Long non-coding RNAs have emerged as highly versatile players in the regulation of gene expression in development and human disease, particularly cancer. Hundreds of lncRNAs become dysregulated across tumor types, and multiple lncRNAs have demonstrated functions as tumor-suppressors or oncogenes. Furthermore, studies have demonstrated that dysregulation of lncRNAs results in alterations of the epigenome in cancer cells, potentially providing a novel mechanism for the massive epigenomic alterations observed in many tumors. Here, we highlight and provide some illustrious examples of lncRNAs in various epigenetic regulatory processes, including coordination of chromatin dynamics, regulation of DNA methylation, modulation of other non-coding RNAs and mRNA stability, and control of epigenetic substrate availability through altered tumor metabolism. In light of all these known and emerging functions in epigenetic regulation of tumorigenesis and cancer progression, lncRNAs represent attractive targets for future therapeutic strategies in cancer.
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Merry CR, Forrest ME, Sabers JN, Beard L, Gao XH, Hatzoglou M, Jackson MW, Wang Z, Markowitz SD, Khalil AM. DNMT1-associated long non-coding RNAs regulate global gene expression and DNA methylation in colon cancer. Hum Mol Genet 2015; 24:6240-53. [PMID: 26307088 DOI: 10.1093/hmg/ddv343] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/17/2015] [Indexed: 12/14/2022] Open
Abstract
The cancer epigenome exhibits global loss of DNA methylation, which contributes to genomic instability and aberrant gene expression by mechanisms that are yet to be fully elucidated. We previously discovered over 3300 long non-coding (lnc)RNAs in human cells and demonstrated that specific lncRNAs regulate gene expression via interactions with chromatin-modifying complexes. Here, we tested whether lncRNAs could also associate with DNA methyltransferases to regulate DNA methylation and gene expression. Using RIP-seq, we identified a subset of lncRNAs that interact with the DNA methyltransferase DNMT1 in a colon cancer cell line, HCT116. One lncRNA, TCONS_00023265, which we named DACOR1 (DNMT1-associated Colon Cancer Repressed lncRNA 1), shows high, tissue-specific expression in the normal colon (including colon crypts) but was repressed in a panel of colon tumors and patient-derived colon cancer cell lines. We identified the genomic occupancy sites of DACOR1, which we found to significantly overlap with known differentially methylated regions (DMRs) in colon tumors. Induction of DACOR1 in colon cancer cell lines significantly reduced their ability to form colonies in vitro, suggesting a growth suppressor function. Consistent with the observed phenotype, induction of DACOR1 led to the activation of tumor-suppressor pathways and attenuation of cancer-associated metabolic pathways. Notably, DACOR1 induction resulted in down-regulation of Cystathionine β-synthase, which is known to lead to increased levels of S-adenosyl methionine-the key methyl donor for DNA methylation. Collectively, our results demonstrate that deregulation of DNMT1-associated lncRNAs contributes to aberrant DNA methylation and gene expression during colon tumorigenesis.
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Affiliation(s)
- Callie R Merry
- Department of Genetics and Genome Sciences, Department of Biochemistry
| | | | | | | | | | | | - Mark W Jackson
- Case Comprehensive Cancer Center and Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center and
| | - Sanford D Markowitz
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center and
| | - Ahmad M Khalil
- Department of Genetics and Genome Sciences, Department of Biochemistry, Case Comprehensive Cancer Center and
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