1
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Cabarcas-Petroski S, Olshefsky G, Schramm L. MAF1 is a predictive biomarker in HER2 positive breast cancer. PLoS One 2023; 18:e0291549. [PMID: 37801436 PMCID: PMC10558074 DOI: 10.1371/journal.pone.0291549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/01/2023] [Indexed: 10/08/2023] Open
Abstract
RNA polymerase III transcription is pivotal in regulating cellular growth and frequently deregulated in various cancers. MAF1 negatively regulates RNA polymerase III transcription. Currently, it is unclear if MAF1 is universally deregulated in human cancers. Recently, MAF1 expression has been demonstrated to be altered in colorectal and liver carcinomas and Luminal B breast cancers. In this study, we analyzed clinical breast cancer datasets to determine if MAF1 alterations correlate with clinical outcomes in HER2-positive breast cancer. Using various bioinformatics tools, we screened breast cancer datasets for alterations in MAF1 expression. We report that MAF1 is amplified in 39% of all breast cancer sub-types, and the observed amplification co-occurs with MYC. MAF1 amplification correlated with increased methylation of the MAF1 promoter and MAF1 protein expression is significantly decreased in luminal, HER2-positive, and TNBC breast cancer subtypes. MAF1 protein expression is also significantly reduced in stage 2 and 3 breast cancer compared to normal and significantly decreased in all breast cancer patients, regardless of race and age. In SKBR3 and BT474 breast cancer cell lines treated with anti-HER2 therapies, MAF1 mRNA expression is significantly increased. In HER2-positive breast cancer patients, MAF1 expression significantly increases and correlates with five years of relapse-free survival in response to trastuzumab treatment, suggesting MAF1 is a predictive biomarker in breast cancer. These data suggest a role for MAF1 alterations in HER2-positive breast cancer. More extensive studies are warranted to determine if MAF1 serves as a predictive and prognostic biomarker in breast cancer.
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Affiliation(s)
| | | | - Laura Schramm
- Department of Biology, St. John’s University, Queens, NY, United States of America
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2
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Avgoulas DI, Tasioulis KS, Papi RM, Pantazaki AA. Therapeutic and Diagnostic Potential of Exosomes as Drug Delivery Systems in Brain Cancer. Pharmaceutics 2023; 15:pharmaceutics15051439. [PMID: 37242681 DOI: 10.3390/pharmaceutics15051439] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Cancer is designated as one of the principal causes of mortality universally. Among different types of cancer, brain cancer remains the most challenging one due to its aggressiveness, the ineffective permeation ability of drugs through the blood-brain barrier (BBB), and drug resistance. To overcome the aforementioned issues in fighting brain cancer, there is an imperative need for designing novel therapeutic approaches. Exosomes have been proposed as prospective "Trojan horse" nanocarriers of anticancer theranostics owing to their biocompatibility, increased stability, permeability, negligible immunogenicity, prolonged circulation time, and high loading capacity. This review provides a comprehensive discussion on the biological properties, physicochemical characteristics, isolation methods, biogenesis and internalization of exosomes, while it emphasizes their therapeutic and diagnostic potential as drug vehicle systems in brain cancer, highlighting recent advances in the research field. A comparison of the biological activity and therapeutic effectiveness of several exosome-encapsulated cargo including drugs and biomacromolecules underlines their great supremacy over the non-exosomal encapsulated cargo in the delivery, accumulation, and biological potency. Various studies on cell lines and animals give prominence to exosome-based nanoparticles (NPs) as a promising and alternative approach in the management of brain cancer.
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Affiliation(s)
- Dimitrios I Avgoulas
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Konstantinos S Tasioulis
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Rigini M Papi
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia A Pantazaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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3
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Cabarcas-Petroski S, Olshefsky G, Schramm L. BDP1 as a biomarker in serous ovarian cancer. Cancer Med 2023; 12:6401-6418. [PMID: 36305848 PMCID: PMC10028122 DOI: 10.1002/cam4.5388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/19/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND TFIIIB, an RNA polymerase III specific transcription factor has been found to be deregulated in human cancers with much of the research focused on the TBP, BRF1, and BRF2 subunits. To date, the TFIIIB specific subunit BDP1 has not been investigated in ovarian cancer but has previously been shown to be deregulated in neuroblastoma, breast cancer, and Non-Hodgkins lymphoma. RESULTS Using in silico analysis of clinically derived platforms, we report a decreased BDP1 expression as a result of deletion in serous ovarian cancer and a correlation with higher and advanced ovarian stages. Further analysis in the context of TP53 mutations, a major contributor to ovarian tumorigenesis, suggests that high BDP1 expression is unfavorable for overall survival and high BDP1 expression occurs in stages 2, 3 and 4 serous ovarian cancer. Additionally, high BDP1 expression is disadvantageous and unfavorable for progression-free survival. Lastly, BDP1 expression significantly decreased in patients treated with first-line chemotherapy, platin and taxane, at twelve-month relapse-free survival. CONCLUSIONS Taken together with a ROC analysis, the data suggest BDP1 could be of clinical relevance as a predictive biomarker in serous ovarian cancer. Lastly, this study further demonstrates that both the over- and under expression of BDP1 warrants further investigation and suggests BDP1 may exhibit dual function in the context of tumorigenesis.
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Affiliation(s)
| | | | - Laura Schramm
- Biology Department, St. John's University, Queens, New York, USA
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4
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Cao L, Zhang M, Zhang Y, Ji B, Wang X, Wang X. Progress of radiological‑pathological workflows in the differential diagnosis between primary central nervous system lymphoma and high‑grade glioma (Review). Oncol Rep 2022; 49:20. [PMID: 36484403 PMCID: PMC9773014 DOI: 10.3892/or.2022.8457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/03/2022] [Indexed: 12/13/2022] Open
Abstract
Primary central nervous system lymphoma (PCNSL) and high‑grade glioma (HGG) are distinct entities of the CNS with completely distinct treatments. The treatment of PCNSL is chemotherapy‑based, while surgery is the first choice for HGG. However, the clinical features of the two entities often overlap, and a clear pathological diagnosis is important for subsequent management, especially for the management of PCNSL. Stereotactic biopsy is recognized as one of the minimally invasive alternatives for evaluating the involvement of the CNS. However, in the case of limited tissue materials, the differential diagnosis between the two entities is still difficult. In addition, some patients are too ill to tolerate a needle biopsy. Therefore, combining imaging, histopathology and laboratory examinations is essential in order to make a clear diagnosis as soon as possible. The present study reviews the progress of comparative research on both imaging and laboratory tests based on the pathophysiological changes of the two entities, and proposes an integrative and optimized diagnostic process, with the purpose of building a better understanding for neurologists, hematologists, radiologists and pathologists.
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Affiliation(s)
- Luming Cao
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Mengchao Zhang
- Department of Radiology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Ying Zhang
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bin Ji
- Department of Nuclear Medicine, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Xuemei Wang
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Xueju Wang
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China,Correspondence to: Dr Xueju Wang, Department of Pathology, China-Japan Union Hospital, Jilin University, 126 Xiantai Street, Changchun, Jilin 130033, P.R. China, E-mail:
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5
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BDP1 Alterations Correlate with Clinical Outcomes in Breast Cancer. Cancers (Basel) 2022; 14:cancers14071658. [PMID: 35406430 PMCID: PMC8996959 DOI: 10.3390/cancers14071658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Breast cancer accounts for 30% of all new cancer diagnoses in the United States. The most common type of breast cancer is invasive breast cancer. A hallmark trait of breast cancer is uncontrolled cell growth due to genetic alterations. TFIIIB-mediated RNA polymerase III transcription is specifically deregulated in human cancers. The TFIIIB BDP1 subunit is not well characterized in human cancer. The objective of this study was to analyze publicly available clinical cancer datasets to determine if BDP1 alterations correlate with clinical outcomes in available breast cancer datasets. BDP1 copy number and expression negatively correlate with breast cancer outcomes, including stage, grade, and mortality. Abstract TFIIIB is deregulated in a variety of cancers. However, few studies investigate the TFIIIB subunit BDP1 in cancer. BDP1 has not been studied in breast cancer patients. Herein, we analyzed clinical breast cancer datasets to determine if BDP1 alterations correlate with clinical outcomes. BDP1 copy number (n = 1602; p = 8.03 × 10−9) and mRNA expression (n = 130; p = 0.002) are specifically decreased in patients with invasive ductal carcinoma (IDC). In IDC, BDP1 copy number negatively correlates with high grade (n = 1992; p = 2.62 × 10−19) and advanced stage (n = 1992; p = 0.005). BDP1 mRNA expression also negatively correlated with high grade (n = 55; p = 6.81 × 10−4) and advanced stage (n = 593; p = 4.66 × 10−4) IDC. Decreased BDP1 expression correlated with poor clinical outcomes (n = 295 samples): a metastatic event at three years (p = 7.79 × 10−7) and cancer reoccurrence at three years (p = 4.81 × 10−7) in IDC. Decreased BDP1 mRNA correlates with patient death at three (p = 9.90 × 10−6) and five (p = 1.02 × 10−6) years. Both BDP1 copy number (n = 3785; p = 1.0 × 10−14) and mRNA expression (n = 2434; p = 5.23 × 10−6) are altered in triple-negative invasive breast cancer (TNBC). Together, these data suggest a role for BDP1 as potential biomarker in breast cancer and additional studies are warranted.
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6
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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7
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Cabarcas-Petroski S, Meneses PI, Schramm L. A meta-analysis of BRF2 as a prognostic biomarker in invasive breast carcinoma. BMC Cancer 2020; 20:1093. [PMID: 33176745 PMCID: PMC7659115 DOI: 10.1186/s12885-020-07569-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Deregulation of the RNA polymerase III specific TFIIIB subunit BRF2 occurs in subtypes of human cancers. However, correlations between BRF2 alterations and clinical outcomes in breast cancer are limited. We conducted this review to analyze BRF2 alterations in genomic data sets housed in Oncomine and cBioPortal to identify potential correlations between BRF2 alterations and clinical outcomes. METHODS The authors queried both Oncomine and cBioPortal for alterations in BRF2 in human cancers and performed meta-analyses identifying significant correlations between BRF2 and clinical outcomes in invasive breast cancer (IBC). RESULTS A meta cancer outlier profile analysis (COPA) of 715 data sets (86,733 samples) in Oncomine identified BRF2 as overexpressed in 60% of breast cancer data sets. COPA scores in IBC data sets (3594 patients) are comparable for HER2 (24.211, median gene rank 60) and BRF2 (29.656, median gene rank 36.5). Overall survival in IBC patients with BRF2 alterations (21%) is significantly decreased (p = 9.332e-3). IBC patients with BRF2 alterations aged 46 to 50 have a significantly poor survival outcome (p = 7.093e-3). Strikingly, in metastatic breast cancer, BRF2 is altered in 33% of women aged 45-50. BRF2 deletions are predominant in this age group. CONCLUSION This study suggests BRF2 may be an prognostic biomarker in invasive breast carcinoma.
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Affiliation(s)
| | | | - Laura Schramm
- Department of Biological Sciences, St. John's University, Queens, NY, USA.
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8
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Puigdelloses M, González-Huárriz M, García-Moure M, Martínez-Vélez N, Esparragosa Vázquez I, Bruna J, Zandio B, Agirre A, Marigil M, Petrirena G, Nuñez-Córdoba JM, Tejada-Solís S, Díez-Valle R, Gállego-Culleré J, Martínez-Vila E, Patiño-García A, Alonso MM, Gállego Pérez-Larraya J. RNU6-1 in circulating exosomes differentiates GBM from non-neoplastic brain lesions and PCNSL but not from brain metastases. Neurooncol Adv 2020; 2:vdaa010. [PMID: 32642678 PMCID: PMC7212908 DOI: 10.1093/noajnl/vdaa010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common malignant primary brain tumor in adults. Circulating biomarkers may assist in the processes of differential diagnosis and response assessment. GBM cells release extracellular vesicles containing a subset of proteins and nucleic acids. We previously demonstrated that exosomes isolated from the serum of GBM patients had an increased expression of RNU6-1 compared to healthy subjects. In this exploratory study, we investigated the role of this small noncoding RNA as a diagnostic biomarker for GBM versus other brain lesions with some potential radiological similarities. Methods We analyzed the expression of RNU6-1 in circulating exosomes of GBM patients (n = 18), healthy controls (n = 30), and patients with subacute stroke (n = 30), acute/subacute hemorrhage (n = 30), acute demyelinating lesions (n = 18), brain metastases (n = 21), and primary central nervous system lymphoma (PCNSL; n = 12) using digital droplet PCR. Results Expression of RNU6-1 was significantly higher in GBM patients than in healthy controls (P = .002). RNU6-1 levels were also significantly higher in exosomes from GBM patients than from patients with non-neoplastic lesions (stroke [P = .05], hemorrhage [P = .01], demyelinating lesions [P = .019]) and PCNSL (P = .004). In contrast, no significant differences were found between patients with GBM and brain metastases (P = .573). Receiver operator characteristic curve analyses supported the role of this biomarker in differentiating GBM from subacute stroke, acute/subacute hemorrhage, acute demyelinating lesions, and PCNSL (P < .05), but again not from brain metastases (P = .575). Conclusions Our data suggest that the expression of RNU6-1 in circulating exosomes could be useful for the differentiation of GBM from non-neoplastic brain lesions and PCNSL, but not from brain metastases.
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Affiliation(s)
- Montserrat Puigdelloses
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Neurology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Marisol González-Huárriz
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Marc García-Moure
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Naiara Martínez-Vélez
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Inés Esparragosa Vázquez
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Neurology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jordi Bruna
- Department of Neurology, Hospital de Bellvitge, Barcelona, Spain
| | - Beatriz Zandio
- Department of Neurology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Amaia Agirre
- POLYMAT, University of the Basque Country, San Sebastian, Spain
| | - Miguel Marigil
- Division of Neurosurgery, Lariboisière University Hospital, Paris, France
| | | | - Jorge M Nuñez-Córdoba
- Research Support Service, Central Clinical Trials Unit, Clínica Universidad de Navarra, Pamplona, Spain.,Department of Preventive Medicine and Public Health, Medical School, Universidad de Navarra, Pamplona, Spain
| | - Sonia Tejada-Solís
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Department of Neurosurgery, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ricardo Díez-Valle
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Department of Neurosurgery, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | | | - Eduardo Martínez-Vila
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Neurology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ana Patiño-García
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Marta M Alonso
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jaime Gállego Pérez-Larraya
- Health Research Institute of Navarra (IDISNA), Pamplona, Spain.,Program in Solid Tumors, Center for the Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.,Department of Neurology, Clínica Universidad de Navarra, Pamplona, Spain
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9
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Nalbantoglu S, Karadag A. Introductory Chapter: Insight into the OMICS Technologies and Molecular Medicine. Mol Med 2019. [DOI: 10.5772/intechopen.86450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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10
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Durrieu-Gaillard S, Dumay-Odelot H, Boldina G, Tourasse NJ, Allard D, André F, Macari F, Choquet A, Lagarde P, Drutel G, Leste-Lasserre T, Petitet M, Lesluyes T, Lartigue-Faustin L, Dupuy JW, Chibon F, Roeder RG, Joubert D, Vagner S, Teichmann M. Regulation of RNA polymerase III transcription during transformation of human IMR90 fibroblasts with defined genetic elements. Cell Cycle 2018; 17:605-615. [PMID: 29171785 DOI: 10.1080/15384101.2017.1405881] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs that are essential for cellular homeostasis and growth. Its activity is regulated by inactivation of tumor suppressor proteins and overexpression of the oncogene c-MYC, but the concerted action of these tumor-promoting factors on Pol III transcription has not yet been assessed. In order to comprehensively analyse the regulation of Pol III transcription during tumorigenesis we employ a model system that relies on the expression of five genetic elements to achieve cellular transformation. Expression of these elements in six distinct transformation intermediate cell lines leads to the inactivation of TP53, RB1, and protein phosphatase 2A, as well as the activation of RAS and the protection of telomeres by TERT, thereby conducting to full tumoral transformation of IMR90 fibroblasts. Transformation is accompanied by moderately enhanced levels of a subset of Pol III-transcribed RNAs (7SK; MRP; H1). In addition, mRNA and/or protein levels of several Pol III subunits and transcription factors are upregulated, including increased protein levels of TFIIIB and TFIIIC subunits, of SNAPC1 and of Pol III subunits. Strikingly, the expression of POLR3G and of SNAPC1 is strongly enhanced during transformation in this cellular transformation model. Collectively, our data indicate that increased expression of several components of the Pol III transcription system accompanied by a 2-fold increase in steady state levels of a subset of Pol III RNAs is sufficient for sustaining tumor formation.
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Affiliation(s)
- Stéphanie Durrieu-Gaillard
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
| | - Hélène Dumay-Odelot
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
| | - Galina Boldina
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France.,c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France
| | - Nicolas J Tourasse
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
| | - Delphine Allard
- c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France
| | - Fabrice André
- c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France
| | - Françoise Macari
- d Institut de Génomique Fonctionnelle , UMR 5203 CNRS , F-34000 Montpellier , France
| | - Armelle Choquet
- d Institut de Génomique Fonctionnelle , UMR 5203 CNRS , F-34000 Montpellier , France
| | - Pauline Lagarde
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France.,g Université de Bordeaux , F-33076 Bordeaux , France
| | - Guillaume Drutel
- h NeuroCentre François Magendie , INSERM U862 , F-33077 Bordeaux , France
| | | | - Marion Petitet
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France
| | - Tom Lesluyes
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France
| | - Lydia Lartigue-Faustin
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France
| | - Jean-William Dupuy
- i Université de Bordeaux , Plateforme Protéome - Centre Génomique Fonctionnelle Bordeaux , 33076 Bordeaux , France
| | - Frédéric Chibon
- e Department of Biopathology , Institut Bergonié , Molecular Pathology Unit , F-33000 Bordeaux , France.,f Génétique et Biologie des Sarcomes- INSERM U916 , F- 33000 Bordeaux , France
| | - Robert G Roeder
- j The Rockefeller University , 1230 York Avenue, New York , NY 10065 , USA
| | - Dominique Joubert
- d Institut de Génomique Fonctionnelle , UMR 5203 CNRS , F-34000 Montpellier , France
| | - Stéphan Vagner
- c Institut Gustave Roussy , INSERM U981 , F-94805 Villejuif , France.,k Institut Curie , CNRS UMR 3348, F-91405 Orsay , France
| | - Martin Teichmann
- a Université de Bordeaux , ARNA Laboratory , F-33076 Bordeaux , France.,b INSERM, U1212 - CNRS UMR 5320 , ARNA Laboratory , F-33000 Bordeaux , France
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11
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Diette N, Koo J, Cabarcas-Petroski S, Schramm L. Gender Specific Differences in RNA Polymerase III Transcription. ACTA ACUST UNITED AC 2016; 7. [PMID: 27158556 DOI: 10.4172/2157-2518.1000251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND RNA polymerase (pol) III transcribes a variety of untranslated RNAs responsible for regulating cellular growth and is deregulated in a variety of cancers. In this study, we examined gender differences in RNA pol III transcription in vitro and in vivo. METHODS Expression levels of U6 snRNA, tMet, and known modulators of RNA pol III transcription were assayed in male and female derived adenocarcinoma (AC) lung cancer cell lines and male and female C57BL/6J mice using real time quantitative PCR. Methylation status of the U6 snRNA promoter was determined for lung and liver tissue isolated from male and female C57BL/6J mice by digesting genomic DNA with methylation sensitive restriction enzymes and digestion profiles were analyzed by qPCR using primers spanning the U6 promoter. RESULTS Here, we demonstrate that RNA pol III transcription is differentially regulated by EGCG in male and female derived AC lung cancer cell lines. Basal RNA pol III transcript levels are significantly different in male and female derived AC lung cancer cell lines. These data prompted an investigation of gender specific differences in RNA pol III transcription in vivo in lung and liver tissue. Herein, we report that U6 snRNA RNA pol III transcription is significantly stimulated in the liver tissue of male C57BL/6J mice. Further, the increase in U6 transcription correlates with a significant inhibition in the expression of p53, a negative regulator of RNA pol III transcription, and demethylation of the U6 promoter in the liver tissue of male C57BL/6J mice. CONCLUSIONS To the best of our knowledge, this is the first study demonstrating gender specific differences in RNA pol III transcription both in vivo and in vitro and further highlights the need to include both male and female cell lines and animals in experimental design.
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Affiliation(s)
- N Diette
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - J Koo
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - S Cabarcas-Petroski
- Pennsylvania State University, Beaver Campus, Monaca, Pennsylvania, 15061 USA
| | - L Schramm
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
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Koo J, Cabarcas-Petroski S, Petrie JL, Diette N, White RJ, Schramm L. Induction of proto-oncogene BRF2 in breast cancer cells by the dietary soybean isoflavone daidzein. BMC Cancer 2015; 15:905. [PMID: 26573593 PMCID: PMC4647806 DOI: 10.1186/s12885-015-1914-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/06/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND BRF2 is a transcription factor required for synthesis of a small group of non-coding RNAs by RNA polymerase III. Overexpression of BRF2 can transform human mammary epithelial cells. In both breast and lung cancers, the BRF2 gene is amplified and overexpressed and may serve as an oncogenic driver. Furthermore, elevated BRF2 can be independently prognostic of unfavorable survival. Dietary soy isoflavones increase metastasis to lungs in a model of breast cancer and a recent study reported significantly increased cell proliferation in breast cancer patients who used soy supplementation. The soy isoflavone daidzein is a major food-derived phytoestrogen that is structurally similar to estrogen. The putative estrogenic effect of soy raises concern that high consumption of soy foods by breast cancer patients may increase tumor growth. METHODS Expression of BRF2 RNA and protein was assayed in ER-positive or -negative human breast cancer cells after exposure to daidzein. We also measured mRNA stability, promoter methylation and response to the demethylating agent 5-azacytidine. In addition, expression was compared between mice fed diets enriched or deprived of isoflavones. RESULTS We demonstrate that the soy isoflavone daidzein specifically stimulates expression of BRF2 in ER-positive breast cancer cells, as well as the related factor BRF1. Induction is accompanied by increased levels of non-coding RNAs that are regulated by BRF2 and BRF1. Daidzein treatment stabilizes BRF2 and BRF1 mRNAs and selectively decreases methylation of the BRF2 promoter. Functional significance of demethylation is supported by induction of BRF2 by the methyltransferase inhibitor 5-azacytidine. None of these effects are observed in an ER-negative breast cancer line, when tested in parallel with ER-positive breast cancer cells. In vivo relevance is suggested by the significantly elevated levels of BRF2 mRNA detected in female mice fed a high-isoflavone commercial diet. In striking contrast, BRF2 and BRF1 mRNA levels are suppressed in matched male mice fed the same isoflavone-enriched diet. CONCLUSIONS The BRF2 gene that is implicated in cancer can be induced in human breast cancer cells by the isoflavone daidzein, through promoter demethylation and/or mRNA stabilization. Dietary isoflavones may also induce BRF2 in female mice, whereas the converse occurs in males.
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Affiliation(s)
- Jana Koo
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | | | - John L Petrie
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Nicole Diette
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - Robert J White
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Laura Schramm
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA.
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Lou G, Ma N, Xu Y, Jiang L, Yang J, Wang C, Jiao Y, Gao X. Differential distribution of U6 (RNU6-1) expression in human carcinoma tissues demonstrates the requirement for caution in the internal control gene selection for microRNA quantification. Int J Mol Med 2015; 36:1400-8. [PMID: 26352225 DOI: 10.3892/ijmm.2015.2338] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 08/24/2015] [Indexed: 11/06/2022] Open
Abstract
Alterations in microRNA (miRNA) expression patterns have been associated with a number of human diseases. Accurate quantitation of miRNA levels is important for their use as biomarkers and in determining their functions. Although the issue of proper miRNA detection was solved with the introduction of standard reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) assays, numerous issues with the selection of appropriate internal control genes remain. U6 (RNU6‑1) snRNA, the most commonly used internal control gene in miRNA RT‑qPCR assays, was shown to be unstable in clinical samples, particularly cancer tissues. Identification of the distribution of U6 in different tissues is the premise of more accurate quantification of miRNAs. However, the distribution of U6 in human carcinoma tissues and corresponding normal tissues is unknown. In the present study, U6 levels were significantly higher in human breast carcinoma tissues compared with the corresponding normal tissues by RT‑qPCR. In the carcinoma or corresponding adjacent normal tissues, the expression levels of U6 in epithelial cells were higher than those in the mesenchymal cells. Furthermore, the expression levels of U6 in the carcinoma tissues of the liver and intrahepatic bile ducts were higher than those in the adjacent normal tissues. These results suggest that the expression and distribution of U6 exhibits a high degree of variability among several types of human cells. Therefore, caution is required when selecting U6 as an internal control gene for evaluating expression profiles of miRNAs in patients with carcinoma, particularly carcinoma of the liver and intrahepatic bile ducts.
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Affiliation(s)
- Ge Lou
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Ning Ma
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Ya Xu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Lei Jiang
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Jing Yang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Chuxuan Wang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Yufei Jiao
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
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Manterola L, Guruceaga E, Gállego Pérez-Larraya J, González-Huarriz M, Jauregui P, Tejada S, Diez-Valle R, Segura V, Samprón N, Barrena C, Ruiz I, Agirre A, Ayuso A, Rodríguez J, González A, Xipell E, Matheu A, López de Munain A, Tuñón T, Zazpe I, García-Foncillas J, Paris S, Delattre JY, Alonso MM. A small noncoding RNA signature found in exosomes of GBM patient serum as a diagnostic tool. Neuro Oncol 2014; 16:520-7. [PMID: 24435880 DOI: 10.1093/neuonc/not218] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is the most frequent malignant brain tumor in adults, and its prognosis remains dismal despite intensive research and therapeutic advances. Diagnostic biomarkers would be clinically meaningful to allow for early detection of the tumor and for those cases in which surgery is contraindicated or biopsy results are inconclusive. Recent findings show that GBM cells release microvesicles that contain a select subset of cellular proteins and RNA. The aim of this hypothesis-generating study was to assess the diagnostic potential of miRNAs found in microvesicles isolated from the serum of GBM patients. METHODS To control disease heterogeneity, we used patients with newly diagnosed GBM. In the discovery stage, PCR-based TaqMan Low Density Arrays followed by individual quantitative reverse transcriptase polymerase chain reaction were used to test the differences in the miRNA expression levels of serum microvesicles among 25 GBM patients and healthy controls paired by age and sex. The detected noncoding RNAs were then validated in another 50 GBM patients. RESULTS We found that the expression levels of 1 small noncoding RNA (RNU6-1) and 2 microRNAs (miR-320 and miR-574-3p) were significantly associated with a GBM diagnosis. In addition, RNU6-1 was consistently an independent predictor of a GBM diagnosis. CONCLUSIONS Altogether our results uncovered a small noncoding RNA signature in microvesicles isolated from GBM patient serum that could be used as a fast and reliable differential diagnostic biomarker.
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Affiliation(s)
- Lorea Manterola
- Instituto Biodonostia and Hospital Universitario Donostia, San Sebastian, Spain (L.M., N.S., C.B., I.R., A.M., A.L.-M.); Center for Applied Medical Research (CIMA), Pamplona, Spain (E.G., V.S.); Clínica Universidad de Navarra, Pamplona, Spain (J.G.P-L., M.G-H., P.J., S.T., R.D.-V., J.R., A.G., E.X., M.M.A.); Polymat, University of the Basque Country, San Sebastian, Spain (A.A.); IMMA-CIOCC, Fundación Hospital de Madrid, Madrid, Spain (A.A.); Fundación Jimenez-Díaz, Madrid, Spain (J.G.-F.); Complejo Hospitalario de Navarra, Pamplona, Spain (T.T., I.Z.); Pitié-Salpètriere, Paris, France (S.P., J.Y.D.)
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Mroczek S, Dziembowski A. U6 RNA biogenesis and disease association. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:581-92. [PMID: 23776162 DOI: 10.1002/wrna.1181] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 12/15/2022]
Abstract
U6 snRNA is one of five uridine-rich noncoding RNAs that form the major spliceosome complex. Unlike other U-snRNAs, it reveals many distinctive aspects of biogenesis such as transcription by RNA polymerase III, transcript nuclear retention and particular features of transcript ends: monomethylated 5'-guanosine triphosphate as cap structure and a 2',3'-cyclic phosphate moiety (>P) at the 3' termini. U6-snRNA plays a central role in splicing and thus its transcription, maturation, snRNP formation, and recycling are essential for cellular homeostasis. U6 snRNA enters the splicing cycle as part of the tri-U4/U6.U5snRNP complex, and after significant structural arrangements forms the catalytic site of the spliceosome together with U2 snRNA and Prp8. U6 snRNA also contributes to the splicing reaction by coordinating metal cations required for catalysis. Many human diseases are associated with altered splicing processes. Disruptions of the basal splicing machinery can be lethal or lead to severe diseases such as spinal muscular atrophy, amyotrophic lateral sclerosis, or retinitis pigmentosa. Recent studies have identified a new U6 snRNA biogenesis factor Usb1, the absence of which leads to poikiloderma with neutropenia (PN) (OMIM 604173), an autosomal recessive skin disease. Usb1 is an evolutionarily conserved 3'→5' exoribonuclease that is responsible for removing 3'-terminal uridines from U6 snRNA transcripts, which leads to the formation of a 2',3' cyclic phosphate moiety (>P). This maturation step is fundamental for U6 snRNP assembly and recycling. Usb1 represents the first example of a direct association between a spliceosomal U6 snRNA biogenesis factor and human genetic disease.
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Affiliation(s)
- Seweryn Mroczek
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Cell cycle arrest and apoptosis by expression of a novel TPIP (TPIP-C2) cDNA encoding a C2-domain in HEK-293 cells. Mol Biol Rep 2012; 39:7389-402. [PMID: 22311048 DOI: 10.1007/s11033-012-1571-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 01/25/2012] [Indexed: 12/15/2022]
Abstract
The human TPIP (TPTE and PTEN homologous Inositol lipid Phosphatase) belongs to the PTEN (Phosphatase and TENsin homologue deleted on chromosome 10) family of dual-specific phosphatases and is expressed from the human chromosome 13 as multiple splice-variants, e.g., TPIPα, β, γ mRNAs. PTEN is a well characterized tumor suppressor, which controls survival, adhesion, motility and migration of mammalian cells, its C2-domain plays crucial role in controlling these functions. However, role of isolated C2-domain protein in regulation of cell proliferation and apoptosis is not reported. We report sequence analysis and function of a novel human TPIP (TPIP-C2) cDNA encoding a 193 amino acid C2-domain in cell proliferation and apoptosis regulation. In silico analysis and homology modelling revealed that the C2-domain of TPIP-C2 is similar to that of PTEN but with short disorder sequences overlapping or adjacent to the post-translational modification sites. Overexpression of TPIP-C2 cDNA in human embryonic kidney (HEK-293) cells caused cell cycle arrest, inhibition of cell proliferation and induced apoptosis in an activated caspase 3 and PARP-dependent manner in comparison to overexpression of the full length human PTEN cDNA. TPIP-C2 overexpressed cells also showed S-phase cell cycle arrest. We suggest that C2-domain of TPIP-C2 may act as a dominant negative effector, which may bind to and arrest the cell proliferation signalling complex and isolated TPIP-C2-domain-like proteins expressed in mammalian cells/tissues may play important role in regulation of cell proliferation and apoptosis. The TPIP-C2 cDNA may be exploited for inducing cell cycle-inhibition and apoptosis in human cancer cells and tissues.
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Mishra RR, Chaudhary JK, Bajaj GD, Rath PC. A novel human TPIP splice-variant (TPIP-C2) mRNA, expressed in human and mouse tissues, strongly inhibits cell growth in HeLa cells. PLoS One 2011; 6:e28433. [PMID: 22164291 PMCID: PMC3229583 DOI: 10.1371/journal.pone.0028433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/08/2011] [Indexed: 11/23/2022] Open
Abstract
Alternative splicing of mRNAs is known to involve a major regulation of gene expression at RNA level in mammalian cells. The PTEN (Phosphatase and TENsin homologue deleted from the human chromosome 10), TPTE (Transmembrane Phosphatase with TEnsin homology) and TPIP (TPTE and PTEN homologous Inositol lipid Phosphatase) belong to a family of dual-specific lipid and protein phosphatases. PTEN is a well characterized tumor suppressor, which plays crucial role in cell survival, cell cycle regulation, cell proliferation as well as adhesion, motility and migration of cells. The C2-domain of PTEN is essential for PTEN-functions. We have isolated a novel 1019 bp human TPIP cDNA (TPIP-C2) from a human testis cDNA library. In silico analysis of the cDNA revealed that it is produced from the TPIP-locus on the human chromosome 13 by alternative RNA-splicing. It has a unique 5′-Alu sequence, a LINE sequence followed by a 582 bp Open Reading Frame (ORF) encoding a 193 aa polypeptide with a partial phosphatase domain and a C2-domain. TPIP-C2 mRNA is expressed in human testis and in mouse tissues. Mouse testis and brain showed higher levels of TPIP-C2 mRNA in comparison to the heart, liver and kidney under normal physiological conditions. TPIP-C2 mRNAs from human and mouse testes show extensive sequence identity. Over-expression of TPIP-C2 cDNA in HeLa cells strongly (up to 85%) inhibited cell growth/proliferation and caused apoptosis in a caspase 3-dependent manner. These findings suggest for the first time that a TPIP splice-variant mRNA with a partial phosphatase domain and a C2-domain is expressed in cells and tissues of human and murine origins under normal physiological conditions. Inhibition of cell growth/proliferation and induction of apoptosis by overexpression of TPIP-C2 mRNA in HeLa cells suggest that it may be involved in negative regulation of cell growth/proliferation.
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Affiliation(s)
- Rasmi Rekha Mishra
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jitendra Kumar Chaudhary
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gagan Deep Bajaj
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pramod C. Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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