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Dragonetti M, Turco C, Benedetti A, Goeman F, Forcato M, Scalera S, Allegretti M, Esposito G, Fazi F, Blandino G, Donzelli S, Fontemaggi G. The lncRNAMALAT1-WTAP axis: a novel layer of EMT regulation in hypoxic triple-negative breast cancer. Cell Death Discov 2024; 10:276. [PMID: 38862471 PMCID: PMC11166650 DOI: 10.1038/s41420-024-02058-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Early metastatic disease development is one characteristic that defines triple-negative breast cancer (TNBC) as the most aggressive breast cancer (BC) subtype. Numerous studies have identified long non-coding RNAs (lncRNA) as critical players in regulating tumor progression and metastasis formation. Here, we show that MALAT1, a long non-coding RNA known to promote various features of BC malignancy, such as migration and neo angiogenesis, regulates TNBC cell response to hypoxia. By profiling MALAT1-associated transcripts, we discovered that lncRNA MALAT1 interacts with the mRNA encoding WTAP protein, previously reported as a component of the N6-methyladenosine (m6A) modification writer complex. In hypoxic conditions, MALAT1 positively regulates WTAP protein expression, which influences the response to hypoxia by favoring the transcription of the master regulators HIF1α and HIF1β. Furthermore, WTAP stimulates BC cell migratory ability and the expression of N-Cadherin and Vimentin, hallmarks of epithelial-to-mesenchymal transition (EMT). In conclusion, this study highlights the functional axis comprising MALAT1 and WTAP as a novel prognostic marker of TNBC progression and as a potential target for the development of therapeutic approaches for TNBC treatment.
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Affiliation(s)
- Martina Dragonetti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Chiara Turco
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Anna Benedetti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Frauke Goeman
- SAFU Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Scalera
- Biostatistics and Bioinformatics Unit, Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Matteo Allegretti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Gabriella Esposito
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 16, 00161, Rome, Italy
| | - Giovanni Blandino
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Sara Donzelli
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - Giulia Fontemaggi
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
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Yadav G, Kulshreshtha R. Pan-cancer analyses identify MIR210HG overexpression, epigenetic regulation and oncogenic role in human tumors and its interaction with the tumor microenvironment. Life Sci 2024; 339:122438. [PMID: 38242493 DOI: 10.1016/j.lfs.2024.122438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND Molecular entities showing dysregulation in multiple cancers may hold great biomarker or therapeutic potential. There is accumulating evidence that highlights the dysregulation of a long non-coding RNA, MIR210HG, in various cancers and its oncogenic role. However, a comprehensive analysis of MIR210HG expression pattern, molecular mechanisms, diagnostic or prognostic significance or evaluation of its interaction with tumor microenvironment across various cancers remains unstudied. METHODS A systematic pan-cancer analysis was done using multiple public databases and bioinformatic tools to study the molecular role and clinical significance of MIR210HG. We have analyzed expression patterns, genome alteration, transcriptional and epigenetic regulation, correlation with patient survival, immune infiltrates, co-expressed genes, interacting proteins, and pathways associated with MIR210HG. RESULTS The Pan cancer expression analysis of MIR210HG through various tumor datasets demonstrated that MIR210HG is significantly upregulated in most cancers and increased with the tumor stage in a subset of them. Furthermore, prognostic analysis revealed high MIR210HG expression is associated with poor overall and disease-free survival in specific cancer types. Genetic alteration analysis showed minimal alterations in the MIR210HG locus, indicating that overexpression in cancers is not due to gene amplification. The exploration of SNPs on MIR210HG suggested possible structural changes that may affect its interactions with the miRNAs. The correlation of MIR210HG with promoter methylation was found to be significantly negative in nature in majority of cancers depicting the possible epigenetic regulation of expression of MIR210HG. Additionally, MIR210HG showed negative correlations with immune cells and thus may have strong impact on the tumor microenvironment. Functional analysis indicates its association with hypoxia, angiogenesis, metastasis, and DNA damage repair processes. MIR210HG was found to interact with several proteins and potentially regulate chromatin modifications and transcriptional regulation. CONCLUSIONS A first pan-can cancer analysis of MIR210HG highlights its transcriptional and epigenetic deregulation and oncogenic role in the majority of cancers, its correlation with tumor microenvironment factors such as hypoxia and immune infiltration, and its potential as a prognostic biomarker and therapeutic target in several cancers.
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Affiliation(s)
- Garima Yadav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
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3
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Marret G, Temam S, Kamal M, Even C, Delord JP, Hoffmann C, Dolivet G, Malard O, Fayette J, Capitain O, Vergez S, Geoffrois L, Rolland F, Zrounba P, Laccourreye L, Saada-Bouzid E, Aide N, Bénavent V, Klijianenko J, Lamy C, Girard E, Vacher S, Masliah-Planchon J, de Koning L, Puard V, Borcoman E, Jimenez M, Bièche I, Gal J, Le Tourneau C. Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity. Sci Rep 2023; 13:22524. [PMID: 38110561 PMCID: PMC10728082 DOI: 10.1038/s41598-023-49887-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023] Open
Abstract
There is no strong and reliable predictive biomarker in head and neck squamous cell carcinoma (HNSCC) for EGFR inhibitors. We aimed to identify predictive and pharmacodynamic biomarkers of efficacy of afatinib, a pan-HER tyrosine kinase inhibitor, in a window-of-opportunity trial (NCT01415674). Multi-omics analyses were carried out on pre-treatment biopsy and surgical specimen for biological assessment of afatinib activity. Sixty-one treatment-naïve and operable HNSCC patients were randomised to afatinib 40 mg/day for 21-28 days versus no treatment. Afatinib produced a high rate of metabolic response. Responders had a higher expression of pERK1/2 (P = 0.02) and lower expressions of pHER4 (P = 0.03) and pRB1 (P = 0.002) in pre-treatment biopsy compared to non-responders. At the cellular level, responders displayed an enrichment of tumor-infiltrating B cells under afatinib (P = 0.02). At the molecular level, NF-kappa B signaling was over-represented among upregulated genes in non-responders (P < 0.001; FDR = 0.01). Although exploratory, phosphoproteomics-based biomarkers deserve further investigations as predictors of afatinib efficacy.
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Affiliation(s)
- Grégoire Marret
- Department of Drug Development and Innovation (D3i), Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Stéphane Temam
- Department of Head and Neck Surgery, Gustave Roussy, Villejuif, France
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Caroline Even
- Head and Neck Oncology Department, Gustave Roussy, Villejuif, France
| | - Jean-Pierre Delord
- Department of Medical Oncology, Centre Claudius Régaud, Toulouse, France
| | | | - Gilles Dolivet
- Department of Head and Neck Surgery, Institut de Cancérologie de Lorraine, Nancy, France
| | - Olivier Malard
- Department of Head and Neck Surgery, Centre Hospitalier Universitaire, Nantes, France
| | - Jérôme Fayette
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Olivier Capitain
- Department of Medical Oncology, Centre Paul Papin, Angers, France
| | - Sébastien Vergez
- Department of Head and Neck Surgery, Institut Claudius Regaud, Toulouse, France
| | - Lionel Geoffrois
- Department of Medical Oncology, Institut de Cancérologie de Lorraine, Nancy, France
| | - Frédéric Rolland
- Department of Medical Oncology, Centre René Gauducheau, Nantes, France
| | - Philippe Zrounba
- Department of Head and Neck Surgery, Centre Léon Bérard, Lyon, France
| | - Laurent Laccourreye
- Department of Head and Neck Surgery, Centre Hospitalier Universitaire, Angers, France
| | - Esma Saada-Bouzid
- Department of Medical Oncology, Centre Antoine Lacassagne, Nice, France
| | - Nicolas Aide
- Department of Nuclear Medicine, Centre François Baclesse, Caen, France
| | | | | | - Constance Lamy
- Department of Drug Development and Innovation (D3i), Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Elodie Girard
- Bioinformatics Core Facility, INSERM U900, Mines Paris Tech, Institut Curie, Paris, France
| | | | | | - Leanne de Koning
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Vincent Puard
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Edith Borcoman
- Department of Drug Development and Innovation (D3i), Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | | | - Ivan Bièche
- Genetics Department, Institut Curie, Paris, France
| | - Jocelyn Gal
- Department of Biostatistics, Centre Antoine Lacassagne, Nice, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, 26 Rue d'Ulm, 75005, Paris, France.
- INSERM U900, Institut Curie, Paris-Saclay University, Paris, France.
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Ghosh A, Pandey SP, Joshi DC, Rana P, Ansari AH, Sundar JS, Singh P, Khan Y, Ekka MK, Chakraborty D, Maiti S. Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin. Nucleic Acids Res 2023; 51:9415-9431. [PMID: 37558241 DOI: 10.1093/nar/gkad639] [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: 07/24/2022] [Accepted: 07/13/2023] [Indexed: 08/11/2023] Open
Abstract
Nuclear-retained long non-coding RNAs (lncRNAs) including MALAT1 have emerged as critical regulators of many molecular processes including transcription, alternative splicing and chromatin organization. Here, we report the presence of three conserved and thermodynamically stable RNA G-quadruplexes (rG4s) located in the 3' region of MALAT1. Using rG4 domain-specific RNA pull-down followed by mass spectrometry and RNA immunoprecipitation, we demonstrated that the MALAT1 rG4 structures are specifically bound by two nucleolar proteins, Nucleolin (NCL) and Nucleophosmin (NPM). Using imaging, we found that the MALAT1 rG4s facilitate the localization of both NCL and NPM to nuclear speckles, and specific G-to-A mutations that disrupt the rG4 structures compromised the localization of both NCL and NPM in speckles. In vitro biophysical studies established that a truncated version of NCL (ΔNCL) binds tightly to all three rG4s. Overall, our study revealed new rG4s within MALAT1, established that they are specifically recognized by NCL and NPM, and showed that disrupting the rG4s abolished localization of these proteins to nuclear speckles.
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Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Satya Prakash Pandey
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Dheeraj Chandra Joshi
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Priya Rana
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | | | - Praveen Singh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
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5
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Perisset S, Potilinski MC, Gallo JE. Role of Lnc-RNAs in the Pathogenesis and Development of Diabetic Retinopathy. Int J Mol Sci 2023; 24:13947. [PMID: 37762249 PMCID: PMC10531058 DOI: 10.3390/ijms241813947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Important advances in diabetic retinopathy (DR) research and management have occurred in the last few years. Neurodegenerative changes before the onset of microvascular alterations have been well established. So, new strategies are required for earlier and more effective treatment of DR, which still is the first cause of blindness in working age. We describe herein gene regulation through Lnc-RNAs as an interesting subject related to DR. Long non-coding RNAs (Lnc-RNAs) are non-protein-coding transcripts larger than 200 nucleotides. Lnc-RNAs regulate gene expression and protein formation at the epigenetic, transcriptional, and translational levels and can impact cell proliferation, apoptosis, immune response, and oxidative stress. These changes are known to take part in the mechanism of DR. Recent investigations pointed out that Lnc-RNAs might play a role in retinopathy development as Metastasis-Associated Lung Adenocarcinoma Transcript (Lnc-MALAT1), Maternally expressed gene 3 (Lnc-MEG3), myocardial-infarction-associated transcript (Lnc-MIAT), Lnc-RNA H19, Lnc-RNA HOTAIR, Lnc-RNA ANRIL B-Raf proto-oncogene (Lnc-RNA BANCR), small nucleolar RNA host gene 16 (Lnc-RNA SNHG16) and others. Several molecular pathways are impacted. Some of them play a role in DR pathophysiology, including the PI3K-Akt signaling axis, NAD-dependent deacetylase sirtuin-1 (Sirti1), p38 mitogen-activated protein kinase (P38/mapk), transforming growth factor beta signaling (TGF-β) and nuclear factor erythroid 2-related factor 2 (Nrf2). The way Lnc-RNAs affect diabetic retinopathy is a question of great relevance. Performing a more in-depth analysis seems to be crucial for researchers if they want to target Lnc-RNAs. New knowledge on gene regulation and biomarkers will enable investigators to develop more specialized therapies for diabetic retinopathy, particularly in the current growing context of precision medicine.
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Affiliation(s)
- Sofia Perisset
- Instituto de Investigaciones en Medicina Traslacional (IIMT), Facultad de Ciencias Biomédicas, Universidad Austral—CONICET, Pilar B1629, Buenos Aires, Argentina; (S.P.); (M.C.P.)
| | - M. Constanza Potilinski
- Instituto de Investigaciones en Medicina Traslacional (IIMT), Facultad de Ciencias Biomédicas, Universidad Austral—CONICET, Pilar B1629, Buenos Aires, Argentina; (S.P.); (M.C.P.)
| | - Juan E. Gallo
- Instituto de Investigaciones en Medicina Traslacional (IIMT), Facultad de Ciencias Biomédicas, Universidad Austral—CONICET, Pilar B1629, Buenos Aires, Argentina; (S.P.); (M.C.P.)
- Departamento de Oftalmología, Hospital Universitario Austral, Pilar B1629, Buenos Aires, Argentina
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Tsyganov MM, Ibragimova MK. MALAT1 Long Non-coding RNA and Its Role in Breast Carcinogenesis. Acta Naturae 2023; 15:32-41. [PMID: 37538803 PMCID: PMC10395780 DOI: 10.32607/actanaturae.11905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/02/2023] [Indexed: 08/05/2023] Open
Abstract
Our genome consists not only of protein-coding DNA, but also of the non-coding part that plays a very important role in the regulation of all cellular processes. A part of the non-coding genome comes with non-coding RNAs (ncRNAs), and disruption of the functional activity of these RNAs may be associated with oncogenesis in various cancer types. There exist two types of ncRNAs: small and long non-coding RNAs, which are classified according to their transcript length. Long non-coding metastasis-associated lung adenocarcinoma transcript 1, MALAT1 RNA (NEAT2), is a long non-coding RNA of particular interest. The aforementioned transcript takes part in the regulation of numerous cellular processes and pathogenesis of different malignant tumors, including breast tumors. This review focuses on experimental and clinical studies into the role of MALAT1 in carcinogenesis and the progression of breast cancer.
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Affiliation(s)
- M. M. Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050 Russian Federation
- Siberian State Medical University, Tomsk, 634050 Russian Federation
| | - M. K. Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050 Russian Federation
- Siberian State Medical University, Tomsk, 634050 Russian Federation
- National Research Tomsk State University, Tomsk, 634050 Russian Federation
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7
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Fouani Y, Gholipour A, Oveisee M, Shahryari A, Saberi H, Mowla SJ, Malakootian M. Distinct gene expression patterns of SOX2 and SOX2OT variants in different types of brain tumours. J Genet 2023. [DOI: 10.1007/s12041-023-01423-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Chen J, Ling C. Construction of a predictive model for breast cancer metastasis based on lncRNAs. Transl Cancer Res 2023; 12:387-397. [PMID: 36915588 PMCID: PMC10007891 DOI: 10.21037/tcr-23-129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/29/2022] [Indexed: 03/16/2023]
Abstract
Background There is currently a lack of biological markers to determine the risk of lymph node metastasis in breast cancer. A single long non-coding RNA (lncRNA) cannot accurately describe the heterogeneity of tumors. Thus, more accurate algorithms are needed to screen key pathogenic lncRNAs, and quantitative models are needed to describe the heterogeneity of breast cancer. Methods A whole transcriptome sequencing data set of breast cancer tissue samples was downloaded from The Cancer Genome Atlas database (n=1,091). A weighted correlation network analysis was conducted to identify the hub lncRNAs associated with lymph node metastasis. A logistic regression analysis was conducted to construct the risk score model. The relationship between the risk scores and the key lncRNAs and the infiltration of the immune cell subtypes was also explored. Results A total of 3 common lncRNAs were identified between the differentially expressed lncRNA set and the hub lncRNA set; that is, zinc finger protein 582-antisense RNA 1 (ZNF582-AS1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), and actin filament associated protein 1-antisense RNA 1 (AFAP1-AS1). The following formula was used to calculate the risk score: risk score =1.31 + 0.51 * ZNF582-AS1 - 0.66 * MALAT1 - 0.50 * AFAP1-AS1. The receiver operating characteristic curve showed that the areas under the curve for the risk score, ZNF582-AS1, MALAT1, and AFAP1-AS1 were 0.975, 0.793, 0.685, and 0764, respectively (P<0.05). The risk score was positively correlated with immune cell subtype infiltration. Conclusions ZNF582-AS1, MALAT1, and AFAP1-AS1 are the key lncRNAs involved in the lymph node metastasis of breast cancer. Our risk score model, which was based on ZNF582-AS1, MALAT1 and AFAP1-AS1, can accurately predict the risk of breast cancer lymph node metastasis. ZNF582-AS1, MALAT1, and AFAP1-AS1 are potential biomarkers for the lymph node metastasis of breast cancer.
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Affiliation(s)
- Jing Chen
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Chen Ling
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
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Mirzadeh Azad F, Taheri Bajgan E, Naeli P, Rudov A, Bagheri Moghadam M, Sadat Akhtar M, Gholipour A, Mowla SJ, Malakootian M. Differential Expression Pattern of linc-ROR Spliced Variants in Pluripotent and Non-Pluripotent Cell Lines. CELL JOURNAL 2022; 24:569-576. [PMID: 36259474 PMCID: PMC9617025 DOI: 10.22074/cellj.2022.8205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Indexed: 01/25/2023]
Abstract
OBJECTIVE The human large intergenic non-coding RNA-regulator of reprogramming program (linc-ROR) is known as a stem cell specific linc-RNA. linc-ROR counteracts differentiation via sequestering microRNA-145 (miR-145) that targets OCT4 transcript. Despite the research on the expression and function, the exact structure of linc-ROR transcripts is not clear. Considering the contribution of alternative splicing in transcripts structures and function, identifying different spliced variants of linc-ROR is necessary for further functional analyses. We aimed to find the alternatively spliced transcripts of linc-ROR and investigate their expression pattern in stem and cancer cell lines and during neural differentiation of NT2 cells as a model for understanding linc-ROR role in stem cell and differentiation. MATERIALS AND METHODS In this experimental study, linc-ROR locus was scanned for identifying novel exons. Different primer sets were used to detect new spliced variants by reverse transcription polymerase chain reaction (RT-PCR) and direct sequencing. Quantitative PCR (qPCR) and RT-PCR were employed to profile expression of linc-ROR transcripts in different cell lines and during neural differentiation of stem cells. RESULTS We could discover 13 novel spliced variants of linc-ROR harboring unique array of exons. Our work uncovered six novel exons, some of which were the product of exonized transposable elements. Monitoring expression profile of the linc-ROR spliced variants in a panel of pluripotent and non-pluripotent cells exhibited that all transcripts were primarily expressed in pluripotent cells. Moreover, the examined linc-ROR spliced variants showed a similar downregulation during neural differentiation of NT2 cells. CONCLUSION Altogether, our data showed despite the difference in the structure and composition of exons, various spliced variants of linc-ROR showed similar expression pattern in stem cells and through differentiation.
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Affiliation(s)
- Fatemeh Mirzadeh Azad
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran,Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Elham Taheri Bajgan
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parisa Naeli
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran,Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Alexander Rudov
- Department of Biomolecular Sciences, University of Urbino, Via Saffi Urbino, Italy
| | - Mahrokh Bagheri Moghadam
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mozhgan Sadat Akhtar
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Akram Gholipour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Javad Mowla
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran,Cardiogenetic Research CenterRajaie Cardiovascular Medical and Research CenterIran University
of Medical SciencesTehranIran
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10
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The Long and the Short of It: NEAT1 and Cancer Cell Metabolism. Cancers (Basel) 2022; 14:cancers14184388. [PMID: 36139550 PMCID: PMC9497099 DOI: 10.3390/cancers14184388] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Altered metabolism is a hallmark of most cancers. The way that cancer cells regulate their energy production to fuel constant proliferation has been of interest with the hope that it may be exploited therapeutically. The long noncoding RNA, NEAT1, is often dysregulated in tumours. NEAT1 RNA can be transcribed as two isoforms with different lengths, with each variant responsible for different functions. This review explores how the isoforms contribute to cancer metabolism. Abstract The long noncoding RNA NEAT1 is known to be heavily dysregulated in many cancers. A single exon gene produces two isoforms, NEAT1_1 and NEAT1_2, through alternative 3′-end processing. As the longer isoform, NEAT1_2 is an essential scaffold for nuclear paraspeckle formation. It was previously thought that the short NEAT1_1 isoform only exists to keep the NEAT1 locus active for rapid paraspeckle formation. However, a recent glycolysis-enhancing function for NEAT1_1, contributing to cancer cell proliferation and the Warburg effect, has been demonstrated. Previous studies have mainly focused on quantifying total NEAT1 and NEAT1_2 expression levels. However, in light of the NEAT1_1 role in cancer cell metabolism, the contribution from specific NEAT1 isoforms is no longer clear. Here, the roles of NEAT1_1 and NEAT1_2 in metabolism and cancer progression are discussed.
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Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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12
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Discovery of Long Non-Coding RNA MALAT1 Amplification in Precancerous Colorectal Lesions. Int J Mol Sci 2022; 23:ijms23147656. [PMID: 35887000 PMCID: PMC9318831 DOI: 10.3390/ijms23147656] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/12/2022] Open
Abstract
A colorectal adenoma, an aberrantly growing tissue, arises from the intestinal epithelium and is considered as precursor of colorectal cancer (CRC). In this study, we investigated structural and numerical chromosomal aberrations in adenomas, hypothesizing that chromosomal instability (CIN) occurs early in adenomas. We applied array comparative genomic hybridization (aCGH) to fresh frozen colorectal adenomas and their adjacent mucosa from 16 patients who underwent colonoscopy examination. In our study, histologically similar colorectal adenomas showed wide variability in chromosomal instability. Based on the obtained results, we further stratified patients into four distinct groups. The first group showed the gain of MALAT1 and TALAM1, long non-coding RNAs (lncRNAs). The second group involved patients with numerous microdeletions. The third group consisted of patients with a disrupted karyotype. The fourth group of patients did not show any CIN in adenomas. Overall, we identified frequent losses in genes, such as TSC2, COL1A1, NOTCH1, MIR4673, and GNAS, and gene gain containing MALAT1 and TALAM1. Since long non-coding RNA MALAT1 is associated with cancer cell metastasis and migration, its gene amplification represents an important event for adenoma development.
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13
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Faber GP, Nadav-Eliyahu S, Shav-Tal Y. Nuclear speckles - a driving force in gene expression. J Cell Sci 2022; 135:275909. [PMID: 35788677 DOI: 10.1242/jcs.259594] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nuclear speckles are dynamic membraneless bodies located in the cell nucleus. They harbor RNAs and proteins, many of which are splicing factors, that together display complex biophysical properties dictating nuclear speckle formation and maintenance. Although these nuclear bodies were discovered decades ago, only recently has in-depth genomic analysis begun to unravel their essential functions in modulation of gene activity. Major advancements in genomic mapping techniques combined with microscopy approaches have enabled insights into the roles nuclear speckles may play in enhancing gene expression, and how gene positioning to specific nuclear landmarks can regulate gene expression and RNA processing. Some studies have drawn a link between nuclear speckles and disease. Certain maladies either involve nuclear speckles directly or dictate the localization and reorganization of many nuclear speckle factors. This is most striking during viral infection, as viruses alter the entire nuclear architecture and highjack host machinery. As discussed in this Review, nuclear speckles represent a fascinating target of study not only to reveal the links between gene positioning, genome subcompartments and gene activity, but also as a potential target for therapeutics.
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Affiliation(s)
- Gabriel P Faber
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shani Nadav-Eliyahu
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
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14
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Predictive and Prognostic Value of Non-Coding RNA in Breast Cancer. Cancers (Basel) 2022; 14:cancers14122952. [PMID: 35740618 PMCID: PMC9221286 DOI: 10.3390/cancers14122952] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 12/21/2022] Open
Abstract
For decades since the central dogma, cancer biology research has been focusing on the involvement of genes encoding proteins. It has been not until more recent times that a new molecular class has been discovered, named non-coding RNA (ncRNA), which has been shown to play crucial roles in shaping the activity of cells. An extraordinary number of studies has shown that ncRNAs represent an extensive and prevalent group of RNAs, including both oncogenic or tumor suppressive molecules. Henceforth, various clinical trials involving ncRNAs as extraordinary biomarkers or therapies have started to emerge. In this review, we will focus on the prognostic and diagnostic role of ncRNAs for breast cancer.
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15
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KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:536-540. [PMID: 34990803 PMCID: PMC9801026 DOI: 10.1016/j.gpb.2021.12.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 01/26/2023]
Abstract
KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.
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16
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Karimi P, Bakhtiarizadeh MR, Salehi A, Izadnia HR. Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken. Sci Rep 2022; 12:2558. [PMID: 35169237 PMCID: PMC8847365 DOI: 10.1038/s41598-022-06528-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.
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Affiliation(s)
- Parastoo Karimi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
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17
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Ghosh A, Pandey SP, Ansari AH, Sundar J, Singh P, Khan Y, Ekka MK, Chakraborty D, Maiti S. Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA. Nucleic Acids Res 2022; 50:378-396. [PMID: 34761272 PMCID: PMC8754661 DOI: 10.1093/nar/gkab1066] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA-G-quadruplexes (rG4s) present in the 3' region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre-mRNA splicing of endogenous genes. These results reveal a central role of rG4s within the 3' region of MALAT1 orchestrating AS.
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Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Satya Prakash Pandey
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | | | - Praveen Singh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
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18
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Hu D, Lou X, Meng N, Li Z, Teng Y, Zou Y, Wang F. Peripheral Blood-Based DNA Methylation of Long Non-Coding RNA H19 and Metastasis-Associated Lung Adenocarcinoma Transcript 1 Promoters are Potential Non-Invasive Biomarkers for Gastric Cancer Detection. Cancer Control 2021; 28:10732748211043667. [PMID: 34615385 PMCID: PMC8504648 DOI: 10.1177/10732748211043667] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Introduction The early diagnosis and detection could greatly improve the clinical outcome of gastric cancer (GC) patients. However, the non-invasive biomarkers for GC detection remain to be identified. Method We used online databases (GEPIA, UALCAN, Kaplan-Meier plotter, TIMER, and MEXPRESS) to explore the association between H19 or metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) expression in tissues and the occurrence, development, prognosis, the levels of immune cell infiltration, and methylation of GC; the correlation between mRNA expression and DNA methylation levels of genes were also examined. Methylation levels of H19 or MALAT1 in peripheral blood were compared between 150 GC patients and 100 healthy controls (HCs). Predictive nomograms were constructed among female and male groups for GC diagnosis. The calibration curves, Hosmer–Lemeshow test, and decision curve analysis were also used to examine the nomograms’ predictive ability and clinical values. Results Using multiple online databases, we found that the mRNA expressions of H19 and MALAT1 in tissues were related to the occurrence of GC, and such expressions were associated with immune cell infiltration of GC and negatively correlated with DNA methylation levels of H19 and MALAT1. H19 gene, H19C island, and MALAT1B island, as well as 20 CpG sites were hypermethylated in peripheral blood of GC patients compared with HCs; similar results were also found in female and male groups (P < .05 for all). The combination of H19c3, H19c4, MALAT1b12, and age, as well as the combination of H19b7, H19c1, H19c5, and age in the nomograms could distinguish GC patients from HCs in the female group and male group, respectively. Conclusion We found statistically significant hypermethylation of H19 and MALAT1 promoters in GC patients, and meaningful sensitivity and specificity of MALAT1 and H19 methylation in discriminating GC and HCs were observed in both female and male groups, which indicates that the peripheral blood-based DNA methylation of H19 and MALAT1 could act as potential non-invasive biomarkers for the diagnosis of GC.
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Affiliation(s)
- Dingtao Hu
- Department of Oncology, 36639The First Affiliated Hospital of Anhui Medical University, China
| | - Xiaoqi Lou
- Department of Oncology, 36639The First Affiliated Hospital of Anhui Medical University, China
| | - Nana Meng
- Department of Quality Management Office, 533251The Second Affiliated Hospital of Anhui Medical University, China
| | - Zhen Li
- Department of Epidemiology and Biostatistics, School of Public Health of Anhui Medical University, China
| | - Ying Teng
- Department of Epidemiology and Biostatistics, School of Public Health of Anhui Medical University, China
| | - Yanfeng Zou
- Department of Epidemiology and Biostatistics, School of Public Health of Anhui Medical University, China
| | - Fang Wang
- Department of Oncology, 36639The First Affiliated Hospital of Anhui Medical University, China
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19
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Wozniak M, Czyz M. The Functional Role of Long Non-Coding RNAs in Melanoma. Cancers (Basel) 2021; 13:cancers13194848. [PMID: 34638331 PMCID: PMC8508152 DOI: 10.3390/cancers13194848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/15/2022] Open
Abstract
Melanoma is the most lethal skin cancer, with increasing incidence worldwide. The molecular events that drive melanoma development and progression have been extensively studied, resulting in significant improvements in diagnostics and therapeutic approaches. However, a high drug resistance to targeted therapies and adverse effects of immunotherapies are still a major challenge in melanoma treatment. Therefore, the elucidation of molecular mechanisms of melanomagenesis and cancer response to treatment is of great importance. Recently, many studies have revealed the close association of long noncoding RNAs (lncRNAs) with the development of many cancers, including melanoma. These RNA molecules are able to regulate a plethora of crucial cellular processes including proliferation, differentiation, migration, invasion and apoptosis through diverse mechanisms, and even slight dysregulation of their expression may lead to tumorigenesis. lncRNAs are able to bind to protein complexes, DNA and RNAs, affecting their stability, activity, and localization. They can also regulate gene expression in the nucleus. Several functions of lncRNAs are context-dependent. This review summarizes current knowledge regarding the involvement of lncRNAs in melanoma. Their possible role as prognostic markers of melanoma response to treatment and in resistance to therapy is also discussed.
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20
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PARP inhibitors and radiation potentiate liver cell death in vitro. Do hepatocellular carcinomas have an achilles' heel? Clin Res Hepatol Gastroenterol 2021; 45:101553. [PMID: 33183998 DOI: 10.1016/j.clinre.2020.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/10/2020] [Accepted: 09/30/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND A promising avenue for cancer treatment is exacerbating the deregulation of the DNA repair machinery that would normally protect the genome. To address the applicability of poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) combined with radiotherapy for the treatment of hepatocellular carcinoma (HCC) two approaches were used: firstly, the in vitro sensitivity to the PARPi Veliparib and Talazoparib +/- radiation exposure was determined in liver cell lines and the impact of the HBV X protein (HBx) that deregulates cellular DNA damage repair via SMC5/6 degradation was investigated. Secondly, PARP expression profiles and DNA damage levels using the surrogate marker gammaH2AX were assessed in a panel of control liver vs HCC tissues. METHODS Cell cytotoxicity was measured by clonogenic survival or relative cell growth and the DNA damage response using immunological-based techniques in Hep3B, PLC/PRF/5, HepG2- and HepaRG-derived models. Transcriptome changes due to HBx expression vs SMC6 loss were assessed by RNA sequencing in HepaRG-derived models. PARP and PARG transcripts (qPCR) and PARP1, H2AX and gammaH2AX protein levels (RPPA) were compared in control liver vs HBV-, HCV-, alcohol- and non-alcoholic steatohepatitis-associated HCC (tumor/peritumor) tissues. RESULTS PARPi cytotoxicity was significantly enhanced when combined with X-rays (2Gy) with Talazoparib having a greater impact than Veliparib in most in vitro models. HBx expression significantly lowered survival, probably driven by SMC5/6 loss based on the transcriptome analysis and higher DNA damage levels. PARP1 and PARP2 transcript levels were significantly higher in tumor than peritumor and control tissues. The HBV/HCV/alcohol-associated tumor tissues studied had reduced H2AX but higher gammaH2AX protein levels compared to peritumor and control tissues providing evidence of increased DNA damage during liver disease progression. CONCLUSIONS These proof-of-concept experiments support PARPi alone or combined with radiotherapy for HCC treatment, particularly for HBV-associated tumors, that warrant further investigation.
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21
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Dimitrakopoulos FI, Kottorou A, Tzezou A. Endocrine resistance and epigenetic reprogramming in estrogen receptor positive breast cancer. Cancer Lett 2021; 517:55-65. [PMID: 34077785 DOI: 10.1016/j.canlet.2021.05.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/08/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023]
Abstract
Despite the enormous advances during the last three decades, breast cancer continues to be the most frequent type of cancer as well as one of the most frequent cancer-related causes of death in women. Therapeutic management of patients with hormone receptor-positive breast cancer becomes very often a challenge, since de novo or acquired resistance deprives a significant percentage of the patients from the clinical benefit of the well-tolerated hormone therapy. Several molecular mechanisms are implicated in resistance to endocrine therapy, including changes in hormone receptor signaling, activation of parallel signaling pathways, modifications of cell cycle regulators, activation of different transcription factors as well as changes in stem cells activity. In addition, a growing number of studies supports the pivotal role of epigenetic changes not only in the initiation and progression of breast cancer, but also in resistance to endocrine therapy. These changes refer to DNA methylation, histone post-translational modifications as well as to ncRNAs alterations. In this review, we provide an overview of epigenetic mechanisms underlying the endocrine resistance focusing exclusively on breast cancer patients.
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Affiliation(s)
- Foteinos-Ioannis Dimitrakopoulos
- Molecular Oncology Laboratory, Medical School of Patras, University of Patras, 26500, Patras, Greece; Division of Oncology, University Hospital of Patras, 26500, Patras, Greece
| | - Anastasia Kottorou
- Molecular Oncology Laboratory, Medical School of Patras, University of Patras, 26500, Patras, Greece; Division of Oncology, University Hospital of Patras, 26500, Patras, Greece
| | - Aspasia Tzezou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece; Laboratory of Cytogenetics and Molecular Genetics, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece.
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22
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Cisneros-Villanueva M, Hidalgo-Pérez L, Cedro-Tanda A, Peña-Luna M, Mancera-Rodríguez MA, Hurtado-Cordova E, Rivera-Salgado I, Martínez-Aguirre A, Jiménez-Morales S, Alfaro-Ruiz LA, Arellano-Llamas R, Tenorio-Torres A, Domínguez-Reyes C, Villegas-Carlos F, Ríos-Romero M, Hidalgo-Miranda A. LINC00460 Is a Dual Biomarker That Acts as a Predictor for Increased Prognosis in Basal-Like Breast Cancer and Potentially Regulates Immunogenic and Differentiation-Related Genes. Front Oncol 2021; 11:628027. [PMID: 33912452 PMCID: PMC8074675 DOI: 10.3389/fonc.2021.628027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/23/2022] Open
Abstract
Breast cancer (BRCA) is a serious public health problem, as it is the most frequent malignant tumor in women worldwide. BRCA is a molecularly heterogeneous disease, particularly at gene expression (mRNAs) level. Recent evidence shows that coding RNAs represent only 34% of the total transcriptome in a human cell. The rest of the 66% of RNAs are non−coding, so we might be missing relevant biological, clinical or regulatory information. In this report, we identified two novel tumor types from TCGA with LINC00460 deregulation. We used survival analysis to demonstrate that LINC00460 expression is a marker for poor overall (OS), relapse-free (RFS) and distant metastasis-free survival (DMFS) in basal-like BRCA patients. LINC00460 expression is a potential marker for aggressive phenotypes in distinct tumors, including HPV-negative HNSC, stage IV KIRC, locally advanced lung cancer and basal-like BRCA. We show that the LINC00460 prognostic expression effect is tissue-specific, since its upregulation can predict poor OS in some tumors, but also predicts an improved clinical course in BRCA patients. We found that the LINC00460 expression is significantly enriched in the Basal-like 2 (BL2) TNBC subtype and potentially regulates the WNT differentiation pathway. LINC00460 can also modulate a plethora of immunogenic related genes in BRCA, such as SFRP5, FOSL1, IFNK, CSF2, DUSP7 and IL1A and interacts with miR-103-a-1, in-silico, which, in turn, can no longer target WNT7A. Finally, LINC00460:WNT7A ratio constitutes a composite marker for decreased OS and DMFS in Basal-like BRCA, and can predict anthracycline therapy response in ER-BRCA patients. This evidence confirms that LINC00460 is a master regulator in BRCA molecular circuits and influences clinical outcome.
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Affiliation(s)
- Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Mexico
| | - Lizbett Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Alberto Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Mónica Peña-Luna
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | | | - Eduardo Hurtado-Cordova
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Irene Rivera-Salgado
- Departamento de Anatomía Patológica, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos, Ciudad de México, México
| | - Alejandro Martínez-Aguirre
- Departamento de Anatomía Patológica, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos, Ciudad de México, México
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Luis Alberto Alfaro-Ruiz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Rocío Arellano-Llamas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | | | | | | | - Magdalena Ríos-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
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23
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Falahati Z, Mohseni-Dargah M, Mirfakhraie R. Emerging Roles of Long Non-coding RNAs in Uterine Leiomyoma Pathogenesis: a Review. Reprod Sci 2021; 29:1086-1101. [PMID: 33844188 DOI: 10.1007/s43032-021-00571-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/01/2021] [Indexed: 01/19/2023]
Abstract
Uterine leiomyoma (UL), as the most prevalent type of women's health disorders, is a benign tumor that originates from the smooth muscle cell layer of the uterus. A great number of associated complications are observed including infertility, miscarriage, bleeding, pain, dysmenorrhea, menorrhagia, and dyspareunia. Although the etiology of UL is largely undefined, environmental and genetic factors are witnessed to engage in the UL development. As long non-coding RNAs (lncRNAs) are involved in various types of cellular functions, in recent years, a great deal of attention has been drawn to them and their possible roles in UL pathogenesis. Moreover, they have illustrated their potential to be promising candidates for UL treatment. In this review paper, firstly, an overview of UL pathogenesis is presented. Then, the regulation of lncRNAs in UL and their possible mechanisms in cancer development are reviewed. Eventually, therapeutic approaches targeting lncRNAs in various cancers and UL are explored.
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Affiliation(s)
- Zahra Falahati
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Masoud Mohseni-Dargah
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Koodakyar St., Velenjak Ave, Chamran Highway, Tehran, Iran.
- Genomic Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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24
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Shuai T, Khan MR, Zhang XD, Li J, Thorne RF, Wu M, Shao F. lncRNA TRMP-S directs dual mechanisms to regulate p27-mediated cellular senescence. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:971-985. [PMID: 34094715 PMCID: PMC8141606 DOI: 10.1016/j.omtn.2021.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) undergo extensive alternative splicing, but little is known about isoform functions. A prior investigation of lncRNA RP11-369C8.1 reported that its splice variant TRMP suppressed p27 translation through PTBP1. Here we characterize a second major splice variant, TRMP-S (short variant), whose enforced loss promotes cancer cell-cycle arrest and p27-dependent entry into cellular senescence. Remarkably, despite sharing a single common exon with TRMP, TRMP-S restrains p27 expression through distinct mechanisms. First, TRMP-S stabilizes UHRF1 protein levels, an epigenetic inhibitor of p27, by promoting interactions between UHRF1 and its deubiquitinating enzyme USP7. Alternatively, binding interactions between TRMP-S and FUBP3 prevent p53 mRNA interactions with RPL26 ribosomal protein, the latter essential for promoting p53 translation with ensuing suppression of p53 translation limiting p27 expression. Significantly, as TRMP-S is itself transactivated by p53, this identifies negative feedback regulation between p53 and TRMP-S. Different splicing variants of the RP11-369C8.1 gene thereby exert distinct roles that converge on the homeostatic control of p27 expression, providing an important precedent for understanding the actions of alternatively spliced lncRNAs.
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Affiliation(s)
- Tian Shuai
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
| | - Muhammad Riaz Khan
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China.,School of Biomedical Sciences & Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jingmin Li
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China.,School of Environmental & Life Sciences, The University of Newcastle, Callaghan, NSW 2258, Australia
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China.,CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Centre for Excellence in Molecular Cell Science, the First Affiliated Hospital of University of Science and Technology of China, Hefei 230027, China
| | - Fengmin Shao
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
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25
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Elevated long noncoding RNA MALAT-1 expression is predictive of poor prognosis in patients with breast cancer: a meta-analysis. Biosci Rep 2021; 40:225866. [PMID: 32700729 PMCID: PMC7419804 DOI: 10.1042/bsr20200215] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 07/08/2020] [Accepted: 07/21/2020] [Indexed: 12/29/2022] Open
Abstract
Accumulating evidence indicates that aberrant regulation of metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1), a long noncoding RNA (lncRNA), plays a vital role in tumorigenesis. However, its association with breast cancer has not been systematically evaluated. In the current study, a meta-analysis was conducted to clarify the association between MALAT-1 and the prognosis and clinicopathological features of breast cancer. Relevant literature published in several databases was searched. Hazard ratio (HR) and odds ratio (OR) with 95% confidence interval (CI) were calculated to evaluate the effect of MALAT-1 expression on the survival outcomes and clinicopathological features of breast cancer. A total of 12 studies involving 4106 patients were identified. Pooled HR demonstrated that elevated MALAT-1 expression significantly predicted unfavorable overall survival (HR = 2.06, 95% CI: 1.66–2.56, P<0.0001) in patients with breast cancer. Subgroup analysis stratified by cancer type, sample size, and method of variance analysis also showed statistically significant associations. Additionally, the HR of patients with up-regulated MALAT-1 expression concerning disease-free survival (DFS), recurrence-free survival (RFS), and disease-specific survival (DSS) was 1.91 (95% CI: 1.53–2.39, P<0.0001). Further, elevated MALAT-1 expression was positively correlated with the progesterone receptor (PR) status (OR = 1.47, 95% CI: 1.18–1.82). Thus, MALAT-1 is a promising biomarker for predicting survival outcomes in patients with breast cancer.
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26
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Mishra R, Patel H, Alanazi S, Kilroy MK, Garrett JT. PI3K Inhibitors in Cancer: Clinical Implications and Adverse Effects. Int J Mol Sci 2021; 22:3464. [PMID: 33801659 PMCID: PMC8037248 DOI: 10.3390/ijms22073464] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
The phospatidylinositol-3 kinase (PI3K) pathway is a crucial intracellular signaling pathway which is mutated or amplified in a wide variety of cancers including breast, gastric, ovarian, colorectal, prostate, glioblastoma and endometrial cancers. PI3K signaling plays an important role in cancer cell survival, angiogenesis and metastasis, making it a promising therapeutic target. There are several ongoing and completed clinical trials involving PI3K inhibitors (pan, isoform-specific and dual PI3K/mTOR) with the goal to find efficient PI3K inhibitors that could overcome resistance to current therapies. This review focuses on the current landscape of various PI3K inhibitors either as monotherapy or in combination therapies and the treatment outcomes involved in various phases of clinical trials in different cancer types. There is a discussion of the drug-related toxicities, challenges associated with these PI3K inhibitors and the adverse events leading to treatment failure. In addition, novel PI3K drugs that have potential to be translated in the clinic are highlighted.
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Affiliation(s)
| | | | | | | | - Joan T. Garrett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati, Cincinnati, OH 45267-0514, USA; (R.M.); (H.P.); (S.A.); (M.K.K.)
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27
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Chen J, Liu Y, Min J, Wang H, Li F, Xu C, Gong A, Xu M. Alternative splicing of lncRNAs in human diseases. Am J Cancer Res 2021; 11:624-639. [PMID: 33791145 PMCID: PMC7994174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023] Open
Abstract
Alternative splicing (AS), a vital post-transcription process for eukaryote gene expression regulating, can efficiently improve gene utilization and increase the variety of RNA transcripts and proteins. However, AS of non-coding RNAs (ncRNAs) has not been paid enough attention to compared with that of protein-coding RNAs (mRNAs) for a long time. In fact, AS of ncRNAs, especially long noncoding RNAs (lncRNAs), also plays a significant regulatory role in the human disease. Recently, some bifunctional genes transcribed into both mRNA and lncRNA transcripts by AS have been observed. Here, we focus on the AS of lncRNAs and bifunctional genes producing lncRNA transcripts and propose a strategy for the future research of lncRNA AS.
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Affiliation(s)
- Jiaxi Chen
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Yawen Liu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Jingyu Min
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Huizhi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Feifan Li
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Chunhui Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Aihua Gong
- Department of Cell Biology, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversityZhenjiang 212001, Jiangsu, China
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28
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Assis RIF, Feltran GDS, Silva MES, Palma ICDR, Rovai ES, Miranda TBD, Ferreira MR, Zambuzzi WF, Birbrair A, Andia DC, da Silva RA. Non-coding RNAs repressive role in post-transcriptional processing of RUNX2 during the acquisition of the osteogenic phenotype of periodontal ligament mesenchymal stem cells. Dev Biol 2021; 470:37-48. [PMID: 33152274 DOI: 10.1016/j.ydbio.2020.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 02/08/2023]
Abstract
Mesenchymal stem cells are candidates for therapeutic strategies in periodontal repair due to their osteogenic potential. In this study, we identified epigenetic markers during osteogenic differentiation, taking advantage of the individual pattern of mesenchymal cells of the periodontal ligament with high (h-PDLCs) and low (l-PDLCs) osteogenic capacity. We found that the involvement of non-coding RNAs in the regulation of the RUNX2 gene is strongly associated with high osteogenic potential. Moreover, we evaluated miRs and genes that encode enzymes to process miRs and their biogenesis. Our data show the high expression of the XPO5 gene, and miRs 7 and 22 observed in the l-PDLCs might be involved in acquiring osteogenic potential, suppressing RUNX2 gene expression. Further, an inversely proportional correlation between lncRNAs (HOTAIR and HOTTIP) and RUNX2 gene expression was observed in both l- and h-PDLCs, and it was also related to the distinct osteogenic phenotypes. Thus, our results indicate the low expression of XPO5 in h-PDLC might be the limiting point for blocking the miRs biogenesis, allowing the high gene expression of RUNX2. In accordance, the low expression of miRs, HOTAIR, and HOTTIP could be a prerequisite for increased osteogenic potential in h-PDLCs. These results will help us to better understand the underlying mechanisms of osteogenesis, considering the heterogeneity in the osteogenic potential of PDLCs that might be related to a distinct transcriptional profile of lncRNAs and the biogenesis machinery.
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Affiliation(s)
- Rahyza I F Assis
- Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Geórgia da S Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, 18618-970, Botucatu, São Paulo, Brazil
| | | | | | - Emanuel Silva Rovai
- Faculty of Dentistry, University of Taubaté, 12020-340, Taubaté, São Paulo, Brazil
| | | | - Marcel Rodrigues Ferreira
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, 18618-970, Botucatu, São Paulo, Brazil
| | - Willian F Zambuzzi
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, 18618-970, Botucatu, São Paulo, Brazil
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Denise C Andia
- School of Dentistry, Health Science Institute, Paulista University, 04026-002, São Paulo, Brazil.
| | - Rodrigo A da Silva
- Faculty of Dentistry, University of Taubaté, 12020-340, Taubaté, São Paulo, Brazil; Program in Environmental and Experimental Pathology, Paulista University, São Paulo, 04026-002, São Paulo, Brazil.
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29
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Nielsen BS, Larsen J, Høffding J, Nhat SL, Madsen NH, Møller T, Holst B, Holmstrøm K. Detection of lncRNA by LNA-Based In Situ Hybridization in Paraffin-Embedded Cancer Cell Spheroids. Methods Mol Biol 2021; 2348:123-137. [PMID: 34160803 DOI: 10.1007/978-1-0716-1581-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cancer cell spheroids are considered important preclinical tools to evaluate the efficacy of new drugs. In cancer cell spheroids, the cells assemble and grow in 3D structures with cell contact interactions that are partly impermeable, which leads to central hypoxia and necrosis. The cell spheroids thus possess several features identified in clinical tumors. Not only will the effect and behavior of therapeutic drugs in 3D cell spheroids be affected more similarly than in cells grown on culture plates, but molecular interactions and signaling pathways in cells are also more likely to mimic the in vivo situation. The monitoring of various biomarkers including lncRNAs in 3D cell spheroids is important to assess a potentially induced phenotype in the cells and the effects of drugs. Specifically, for lncRNAs, in situ localization can be done using locked nucleic acid (LNA) probe technology. Here we present a protocol for preparation of cell spheroids for use in LNA probe-based in situ hybridization to study lncRNA expression in paraffin embedded 3D cancer cell spheroids.
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Affiliation(s)
| | | | - Jakob Høffding
- Bioneer A/S, Hørsholm, Denmark.,Københavns Professionshøjskole, København, Denmark
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30
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Liao H, Chen Q, Xiao J. Reflections on the Role of Malat1 in Gynecological Cancer. Cancer Manag Res 2020; 12:13489-13500. [PMID: 33408521 PMCID: PMC7779295 DOI: 10.2147/cmar.s286804] [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: 10/14/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have received significant attention over the last few years. Malat1, as one of the most extensively studied ncRNAs, is believed to be not only a potential biomarker for disease diagnosis and prognosis, but also a candidate drug target for gynecological cancers. This potential is supported by a growing body of experimental evidence demonstrating that Malat1 participates in the occurrence, progression, and metastasis of tumors. Research has also shown that Malat1 can influence patient survival by regulating a range of target genes and signaling pathways. However, previous review articles have generally failed to consider the role of Malat1 in gynecological cancer in detail. In the present review, we summarize recent progress in research relating to the clinical relevance of Malat1 and the molecular mechanisms underlying the action of this ncRNA. Besides, we put forward some action points for further research after taking into consideration the sub-location and other essential properties of Malat1, which might enable us to have a better understanding of the potential of this molecule regarding clinical diagnosis and treatment.
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Affiliation(s)
- Huiyan Liao
- The 2nd Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, People's Republic of China
| | - Qi Chen
- The 6th Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, People's Republic of China
| | - Jing Xiao
- Department of Gynecology, the University Town Branch, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510120, People's Republic of China
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31
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Scholl SM, Beal J, de Koning L, Girard E, Popovic M, de la Rochefordière A, Lecuru F, Fourchotte V, Ngo C, Floquet A, Berns EM, Kenter G, Gestraud P, von der Leyen H, Lecerf C, Puard V, Roman SR, Latouche A, Kereszt A, Balint B, Rouzier R, Kamal M. Genetic markers and phosphoprotein forms of beta-catenin pβ-Cat552 and pβ-Cat675 are prognostic biomarkers of cervical cancer. EBioMedicine 2020; 61:103049. [PMID: 33096476 PMCID: PMC7581879 DOI: 10.1016/j.ebiom.2020.103049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 09/21/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality world wide and constitutes the third most common malignancy in women. The RAIDs consortium (http://www.raids-fp7.eu/) conducted a prospective European study [BioRAIDs (NCT02428842)] with the objective to stratify CC patients for innovative treatments. A "metagene" of genomic markers in the PI3K pathway and epigenetic regulators had been previously associated with poor outcome [2]. METHODS To detect new, more specific, targets for treatment of patients who resist standard chemo-radiation, a high-dimensional Cox model was applied to define dominant molecular variants, copy number variations, and reverse phase protein arrays (RPPA). FINDINGS Survival analysis on 89 patients with all omics data available, suggested loss-of-function (LOF) or activating molecular alterations in nine genes to be candidate biomarkers for worse prognosis in patients treated by chemo-radiation while LOF of ATRX, MED13 as well as CASP8 were associated with better prognosis. When protein expression data by RPPA were factored in, the supposedly low molecular weight and nuclear form, of beta-catenin, phosphorylated in Ser552 (pβ-Cat552), ranked highest for good prognosis, while pβ-Cat675 was associated with worse prognosis. INTERPRETATION These findings call for molecularly targeted treatments involving p53, Wnt pathway, PI3K pathway, and epigenetic regulator genes. Pβ-Cat552 and pβ-Cat675 may be useful biomarkers to predict outcome to chemo-radiation, which targets the DNA repair axis. FUNDING European Union's Seventh Program for research, technological development and demonstration (agreement N°304,810), the Fondation ARC pour la recherche contre le cancer.
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Affiliation(s)
- Suzy M Scholl
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France.
| | - Jonas Beal
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Leanne de Koning
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Elodie Girard
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Marina Popovic
- Oncology Institute of Vojvodina, Put doktora Goldmana, 421204 Sremska Kamenica, Serbia
| | | | - Fabrice Lecuru
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Virginie Fourchotte
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Charlotte Ngo
- Service de chirurgie cancérologique gynécologique et du sein, Hôpital Européen Georges Pompidou, APHP et faculté de médecine, Université Paris Descartes, France
| | - Anne Floquet
- Chirurgie onco-gynécologique and Oncology, Institut Bergonié, Centre Régional de Lutte contre le Cancer Bordeaux-Aquitaine, France
| | - Els Mjj Berns
- Dept Medical Oncology, Erasmus MC, 3000 CA Rotterdam, Netherlands
| | - Gemma Kenter
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Department of Gynaecologic Oncology Amsterdam, Amsterdam UMC and The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Pierre Gestraud
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Heiko von der Leyen
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Hannover Clinical Trial Center, Hannover Medical School Germany
| | - Charlotte Lecerf
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Vincent Puard
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Sergio Roman Roman
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Aurelien Latouche
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France; Conservatoire national des arts et métiers, Paris, France
| | - Attila Kereszt
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; SeqOmics Biotechnology Ltd, Vallalkozok utja 7, Morahalom, Hungary
| | - Balazs Balint
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Roman Rouzier
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
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32
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Biopathological Significance of PIWI-piRNA Pathway Deregulation in Invasive Breast Carcinomas. Cancers (Basel) 2020; 12:cancers12102833. [PMID: 33008024 PMCID: PMC7600338 DOI: 10.3390/cancers12102833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The PIWI-piRNA ribonucleoproteic complexes are pivotal regulators of genome integrity, differentiation and homeostasis and their dysregulation has recently been implicated in carcinogenesis. The aim of this study was to analyze the four PIWILs gene expression in invasive breast carcinomas (IBC) at RNA level using quantitative RT-PCR and protein level using immunohistochemistry. In normal breast tissue, PIWILs 2 and 4 were solely expressed, whereas an abnormal emergence of PIWIL1 and 3 was observed in respectively 30% and 6% of IBCs. Conversely, PIWIL2 was underexpressed in 48.3% and PIWIL4 downregulated in 43.3% of IBCs. Similar patterns of PIWIL deregulation were observed in a multitumoral panel, suggesting a generic mechanism in most cancers. PIWIL2 underexpression was significantly associated with DNA methylation and strong cytotoxic immune response. Characterization of the newly recognized PIWIL-piRNA pathway in IBCs opens interesting therapeutic perspectives using piRNAs, hypomethylating drugs, checkpoints immunotherapies and anti-PIWIL 1–3 antibodies. Abstract The PIWI proteins emerging in the development of human cancers, edify PIWI-piRNA ribonucleoproteic complexes acting as pivotal regulators of genome integrity, differentiation and homeostasis. The aim of this study is to analyze the four PIWILs gene expression in invasive breast carcinomas (IBCs): at RNA level using quantitative RT-PCR (n = 526) and protein level using immunohistochemistry (n = 150). In normal breast tissue, PIWILs 2 and 4 were solely expressed, whereas an abnormal emergence of PIWIL1 and 3 was observed in respectively 30% and 6% of IBCs. Conversely, PIWIL2 was underexpressed in 48.3% and PIWIL4 downregulated in 43.3% of IBCs. Significant positive associations were observed between PIWIL4 underexpression, HR+ status and HR+ ERBB2+ molecular subtype and PIWIL2 underexpression, PR- status, ERBB2- status and molecular subtype. Similar patterns of PIWIL deregulation were observed in a multitumoral panel, suggesting a generic mechanism in most cancers. PIWIL2-4 underexpression was mainly regulated at epigenetic or post-transcriptional levels. PIWIL2 underexpression was significantly associated with DNA methylation and strong cytotoxic immune response. PIWIL2-4 were mainly associated with genes implicated in cell proliferation. As a result of this study, characterization of the PIWIL-piRNA pathway in IBCs opens interesting therapeutic perspectives using piRNAs, hypomethylating drugs, checkpoints immunotherapies and anti-PIWIL 1–3 antibodies.
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33
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Hlaváč V, Holý P, Souček P. Pharmacogenomics to Predict Tumor Therapy Response: A Focus on ATP-Binding Cassette Transporters and Cytochromes P450. J Pers Med 2020; 10:jpm10030108. [PMID: 32872162 PMCID: PMC7565825 DOI: 10.3390/jpm10030108] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Pharmacogenomics is an evolving tool of precision medicine. Recently, due to the introduction of next-generation sequencing and projects generating "Big Data", a plethora of new genetic variants in pharmacogenes have been discovered. Cancer resistance is a major complication often preventing successful anticancer treatments. Pharmacogenomics of both somatic mutations in tumor cells and germline variants may help optimize targeted treatments and improve the response to conventional oncological therapy. In addition, integrative approaches combining copy number variations and long noncoding RNA profiling with germline and somatic variations seem to be a promising approach as well. In pharmacology, expression and enzyme activity are traditionally the more studied aspects of ATP-binding cassette transporters and cytochromes P450. In this review, we briefly introduce the field of pharmacogenomics and the advancements driven by next-generation sequencing and outline the possible roles of genetic variation in the two large pharmacogene superfamilies. Although the evidence needs further substantiation, somatic and copy number variants as well as rare variants and common polymorphisms in these genes could all affect response to cancer therapy. Regulation by long noncoding RNAs has also been shown to play a role. However, in all these areas, more comprehensive studies on larger sets of patients are needed.
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Affiliation(s)
- Viktor Hlaváč
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague, Czech Republic; (P.H.); (P.S.)
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
- Correspondence: ; Tel.: +420-267082681; Fax: +420-267311236
| | - Petr Holý
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague, Czech Republic; (P.H.); (P.S.)
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
- Third Faculty of Medicine, Charles University, 100 00 Prague, Czech Republic
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague, Czech Republic; (P.H.); (P.S.)
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
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Deng Y, Luo H, Yang Z, Liu L. LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers. Brief Bioinform 2020; 22:5895039. [PMID: 32820322 DOI: 10.1093/bib/bbaa179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023] Open
Abstract
Accumulating studies demonstrated that the roles of lncRNAs for tumorigenesis were isoform-dependent and their aberrant splicing patterns in cancers contributed to function specificity. However, there is no existing database focusing on cancer-related alternative splicing of lncRNAs. Here, we developed a comprehensive database called LncAS2Cancer, which collected 5335 bulk RNA sequencing and 1826 single-cell RNA sequencing samples, covering over 30 cancer types. By applying six state-of-the-art splicing algorithms, 50 859 alternative splicing events for 8 splicing types were identified and deposited in the database. In addition, the database contained the following information: (i) splicing patterns of lncRNAs under seven different conditions, such as gene interference, which facilitated to infer potential regulators; (ii) annotation information derived from eight sources and manual curation, to understand the functional impact of affected sequences; (iii) survival analysis to explore potential biomarkers; as well as (iv) a suite of tools to browse, search, visualize and download interesting information. LncAS2Cancer could not only confirm the known cancer-associated lncRNA isoforms but also indicate novel ones. Using the data deposited in LncAS2Cancer, we compared gene model and transcript overlap between lncRNAs and protein-coding genes and discusses how these factors, along with sequencing depth, affected the interpretation of splicing signals. Based on recurrent signals and potential confounders, we proposed a reliable score to prioritize splicing events for further elucidation. Together, with the broad collection of lncRNA splicing patterns and annotation, LncAS2Cancer will provide important new insights into the diverse functional roles of lncRNA isoforms in human cancers. LncAS2Cancer is freely available at https://lncrna2as.cd120.com/.
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Affiliation(s)
- Yulan Deng
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Hao Luo
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Zhenyu Yang
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University
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Peng L, Jiang J, Tang B, Nice EC, Zhang YY, Xie N. Managing therapeutic resistance in breast cancer: from the lncRNAs perspective. Theranostics 2020; 10:10360-10377. [PMID: 32929354 PMCID: PMC7482807 DOI: 10.7150/thno.49922] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is the most common female malignancy and the second leading cause of cancer-related death worldwide. In spite of significant advances in clinical management, the mortality of BC continues to increase due to the frequent occurrence of treatment resistance. Intensive studies have been conducted to elucidate the molecular mechanisms underlying BC therapeutic resistance, including increased drug efflux, altered drug targets, activated bypass signaling pathways, maintenance of cancer stemness, and deregulated immune response. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are intimately involved in BC therapy resistance through multiple modes of action. Therefore, an in-depth understanding of the implication of lncRNAs in resistance to clinical therapies may improve the clinical outcome of BC patients. Here, we highlight the role and underlying mechanisms of lncRNAs in regulating BC treatment resistance with an emphasis on lncRNAs-mediated resistance in different clinical scenarios, and discuss the potential of lncRNAs as novel biomarkers or therapeutic targets to improve BC therapy response.
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Affiliation(s)
- Liyuan Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Bo Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, P.R. China
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
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Arun G, Aggarwal D, Spector DL. MALAT1 Long Non-Coding RNA: Functional Implications. Noncoding RNA 2020; 6:E22. [PMID: 32503170 PMCID: PMC7344863 DOI: 10.3390/ncrna6020022] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
The mammalian genome is pervasively transcribed and the functional significance of many long non-coding RNA (lncRNA) transcripts are gradually being elucidated. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is one of the most well-studied lncRNAs. MALAT1 is a highly conserved nuclear retained lncRNA that is abundantly expressed in cells and tissues and has been shown to play a role in regulating genes at both the transcriptional and post-transcriptional levels in a context-dependent manner. However, Malat1 has been shown to be dispensable for normal development and viability in mice. Interestingly, accumulating evidence suggests that MALAT1 plays an important role in numerous diseases including cancer. Here, we discuss the current state-of-knowledge in regard to MALAT1 with respect to its function, role in diseases, and the potential therapeutic opportunities for targeting MALAT1 using antisense oligonucleotides and small molecules.
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Affiliation(s)
- Gayatri Arun
- Envisagenics, 101 Avenue of the Americas, New York, NY 10013, USA;
| | - Disha Aggarwal
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
| | - David L. Spector
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
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Prabhu KS, Raza A, Karedath T, Raza SS, Fathima H, Ahmed EI, Kuttikrishnan S, Therachiyil L, Kulinski M, Dermime S, Junejo K, Steinhoff M, Uddin S. Non-Coding RNAs as Regulators and Markers for Targeting of Breast Cancer and Cancer Stem Cells. Cancers (Basel) 2020; 12:cancers12020351. [PMID: 32033146 PMCID: PMC7072613 DOI: 10.3390/cancers12020351] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/27/2020] [Accepted: 02/02/2020] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is regarded as a heterogeneous and complicated disease that remains the prime focus in the domain of public health concern. Next-generation sequencing technologies provided a new perspective dimension to non-coding RNAs, which were initially considered to be transcriptional noise or a product generated from erroneous transcription. Even though understanding of biological and molecular functions of noncoding RNA remains enigmatic, researchers have established the pivotal role of these RNAs in governing a plethora of biological phenomena that includes cancer-associated cellular processes such as proliferation, invasion, migration, apoptosis, and stemness. In addition to this, the transmission of microRNAs and long non-coding RNAs was identified as a source of communication to breast cancer cells either locally or systemically. The present review provides in-depth information with an aim at discovering the fundamental potential of non-coding RNAs, by providing knowledge of biogenesis and functional roles of micro RNA and long non-coding RNAs in breast cancer and breast cancer stem cells, as either oncogenic drivers or tumor suppressors. Furthermore, non-coding RNAs and their potential role as diagnostic and therapeutic moieties have also been summarized.
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Affiliation(s)
- Kirti S. Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
- Correspondence: ; Tel.: +974-4439-0966
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha 3050, Qatar; (A.R.); (S.D.)
| | | | - Syed Shadab Raza
- Department of Stem Cell Biology and Regenerative Medicine, Era University, Lucknow 226003, India;
| | - Hamna Fathima
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
| | - Eiman I. Ahmed
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
- Qatar College of Pharmacy, Qatar University, Doha 3050, Qatar
| | - Lubna Therachiyil
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
- Qatar College of Pharmacy, Qatar University, Doha 3050, Qatar
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha 3050, Qatar; (A.R.); (S.D.)
| | - Kulsoom Junejo
- General Surgery Department, Hamad General Hospital, Hamad Medical Corporation, Doha 3050, Qatar;
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
- Department of Dermatology Venereology, Hamad Medical Corporation, Doha 3050, Qatar
- Department of Dermatology, Weill Cornell Medicine, Qatar Foundation, Education City, Doha 24144, Qatar
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; (H.F.); (E.I.A.); (S.K.); (L.T.); (M.K.); (M.S.); (S.U.)
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Abolghasemi M, Tehrani SS, Yousefi T, Karimian A, Mahmoodpoor A, Ghamari A, Jadidi-Niaragh F, Yousefi M, Kafil HS, Bastami M, Edalati M, Eyvazi S, Naghizadeh M, Targhazeh N, Mihanfar A, Yousefi B, Safa A, Majidinia M, Rameshknia V. Critical roles of long noncoding RNAs in breast cancer. J Cell Physiol 2020; 235:5059-5071. [PMID: 31951025 DOI: 10.1002/jcp.29442] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 08/26/2019] [Indexed: 12/22/2022]
Abstract
Breast cancer is a major clinical challenge that affects a wide range of the female population and heavily burdens the health system. In the past few decades, attempts have been made to understand the etiology of breast cancer, possible environmental risk factors, and the genetic predispositions, pathogenesis, and molecular aberrations involved in the process. Studies have shown that breast cancer is a heterogeneous entity; each subtype has its specific set of aberrations in different cell signaling pathways, such as Notch, Wnt/β-catenin, transforming growth factor-β, and mitogen-activated protein kinase pathways. One novel group of molecules that have been shown to be inducted in the regulation of multiple cell signaling pathways is the long noncoding RNAs (lncRNAs). These molecules have important implications in the regulation of multiple signaling pathways by interacting with various genes, affecting the transcription process, and finally, playing roles in posttranslational control of these genes. There is growing evidence that lncRNAs are involved in the process of breast cancer formation by effecting the aforementioned signaling pathways, and that this involvement can have significant diagnostic and prognostic values in clinical contexts. The present review aims to elicit the significance of lncRNAs in the regulation of cell signaling pathways, and the resulting changes in cell survival, proliferation, and invasion, which are the hallmarks of breast cancer.
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Affiliation(s)
- Maryam Abolghasemi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.,Student Research Committee, Babol University of medical sciences, Babol, Iran
| | - Sadra S Tehrani
- Department of Clinical Biochemistry, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tooba Yousefi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.,Student Research Committee, Babol University of medical sciences, Babol, Iran
| | - Ansar Karimian
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.,Student Research Committee, Babol University of medical sciences, Babol, Iran
| | - Ata Mahmoodpoor
- Anesthesiology Research Team, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aliakbar Ghamari
- Anesthesiology Research Team, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mehdi Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein S Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Bastami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Edalati
- Department of Laboratory Sciences, Paramedical Faculty, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shirin Eyvazi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Naghizadeh
- Department of Clinical Biochemistry, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Niloufar Targhazeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ainaz Mihanfar
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amin Safa
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Vahid Rameshknia
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Faculty of Medicine, Islamic Azad University, Tabriz, Iran
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DGCR8/ZFAT-AS1 Promotes CDX2 Transcription in a PRC2 Complex-Dependent Manner to Facilitate the Malignant Biological Behavior of Glioma Cells. Mol Ther 2019; 28:613-630. [PMID: 31813799 DOI: 10.1016/j.ymthe.2019.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 11/24/2022] Open
Abstract
Studies have found that RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are dysregulated and play an important regulatory role in the development of tumors. Based on The Cancer Genome Atlas (TCGA) database, our findings from experiments, and the evidence of previous studies, we screened DiGeorge syndrome critical region gene 8 (DGCR8), ZFAT antisense RNA 1 (ZFAT-AS1), and caudal type homeobox 2 (CDX2) as research candidates. In the present study, DGCR8 and CDX2 were highly expressed and ZFAT-AS1 was markedly downregulated in glioma tissues and cells. DGCR8 or CDX2 knockdown or ZFAT-AS1 overexpression suppressed glioma cell proliferation, migration, and invasion and facilitated apoptosis. DGCR8 might decrease ZFAT-AS1 expression by attenuating its stability in a manner of inducing its cleavage. Importantly, ZFAT-AS1 could inhibit CDX2 transcription by mediating the methylation of histone H3 on lysine 27 (H3K27me3) modification induced by PRC2 in the CDX2 promoter region. In addition, CDX2 transcriptionally activated DGCR8 expression by binding to its promoter regions, forming a positive feedback loop of DGCR8/ZFAT-AS1/CDX2. In conclusion, DGCR8/ZFAT-AS1 promotes CDX2 transcription in a PRC2 complex-dependent manner to facilitate the malignant biological behavior of glioma cells.
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Metastasis Associated Lung Adenocarcinoma Transcript 1: An update on expression pattern and functions in carcinogenesis. Exp Mol Pathol 2019; 112:104330. [PMID: 31712117 DOI: 10.1016/j.yexmp.2019.104330] [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: 10/15/2019] [Accepted: 11/03/2019] [Indexed: 12/28/2022]
Abstract
The Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is among long non-coding RNAs (lncRNAs) which has disapproved the old term of "junk DNA" which was used for majority of human genome which are not transcribed to proteins. An extensive portion of literature points to the fundamental role of this lncRNA in tumorigenesis process of diverse cancers ranging from solid tumors to leukemia. Being firstly identified in lung cancer, it has prognostic and diagnostic values in several cancer types. Consistent with the proposed oncogenic roles for this lncRNA, most of studies have shown up-regulation of MALAT1 in malignant tissues compared with non-malignant/normal tissues of the same source. However, few studies have shown down-regulation of MALAT1 in breast cancer, endometrial cancer, colorectal cancer and glioma. In the current study, we have conducted a comprehensive literature search and provided an up-date on the role of MALAT1 in cancer biology. Our investigation underscores a potential role as a diagnostic/prognostic marker and a putative therapeutic target for MALAT1.
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Drak Alsibai K, Vacher S, Meseure D, Nicolas A, Lae M, Schnitzler A, Chemlali W, Cros J, Longchampt E, Cacheux W, Pignot G, Callens C, Pasmant E, Allory Y, Bieche I. High Positive Correlations between ANRIL and p16- CDKN2A/ p15- CDKN2B/ p14- ARF Gene Cluster Overexpression in Multi-Tumor Types Suggest Deregulated Activation of an ANRIL-ARF Bidirectional Promoter. Noncoding RNA 2019; 5:ncrna5030044. [PMID: 31438464 PMCID: PMC6789474 DOI: 10.3390/ncrna5030044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/08/2019] [Accepted: 08/15/2019] [Indexed: 01/10/2023] Open
Abstract
The CDKN2B-AS1 gene, also called ANRIL, is located at the human CDKN2A/B locus at 9p21.3 and transcribed by RNA polymerase II into a long non-coding RNA of 3834 bp. The CDKN2B-AS1 gene overlaps a critical region of 125 kb covering the CDKN2B gene. The CDKN2A/B locus encompasses three major tumor suppressors juxtaposed and joined into a p16-CDKN2A/p15-CDKN2B/p14-ARF gene cluster. CDKN2A encodes splice variants p16-CDKN2A and p14-ARF, and CDKN2B encodes p15-CDKN2B. ANRIL shares a bidirectional promoter with the p14-ARF gene and is transcribed from the opposite strand to the cluster. We performed an analysis of the expression level of ANRIL and tumor suppressor p16-CDKN2A, p15-CDKN2B, and p14-ARF genes using quantitative RT-PCR in a multitumor panel. We observed the overexpression of the four genes ANRIL, p16-CDKN2A, p15-CDKN2B, and p14-ARF in the great majority of the 17 different cancer types. ANRIL was upregulated in 13/17 tumors compared to normal tissues, ranging from 5% (prostate cancer) to 91% (cervix cancer), with variable expression of p16-CDKN2A, p15-CDKN2B, and p14-ARF genes. A high positive correlation was identified between levels of expression of ANRIL and the three tumor suppressors. The strongest positive association was observed with p14-ARF (p < 0.001) in all but one (lung squamous cell carcinoma) of the examined tumor types. This correlation suggests coordinated deregulated mechanisms in all cancer types through aberrant activation of a bidirectional p14-ARF/ANRIL promoter. Furthermore, significant positive correlation was unexpectedly established in prostatic carcinomas, in contradiction with previous data.
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Affiliation(s)
| | - Sophie Vacher
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Didier Meseure
- Platform of Experimental Pathology, Institut Curie, 75248 Paris, France.
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France.
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France.
| | - Andre Nicolas
- Platform of Experimental Pathology, Institut Curie, 75248 Paris, France
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
| | - Marick Lae
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
| | - Anne Schnitzler
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Walid Chemlali
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Jerome Cros
- Department of Pathology, Beaujon Hospital, APHP Nord, 92110 Clichy, France
| | | | - Wulfran Cacheux
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Geraldine Pignot
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Celine Callens
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Eric Pasmant
- Department of Genetics, Cochin Hospital, APHP, 75014 Paris, France
- Cochin Institute, Inserm U1016, Paris Descartes University, 75014 Paris, France
| | - Yves Allory
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
| | - Ivan Bieche
- Platform of Experimental Pathology, Institut Curie, 75248 Paris, France
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
- Department of Genetics, Cochin Hospital, APHP, 75014 Paris, France
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Induction of Acquired Resistance towards EGFR Inhibitor Gefitinib in a Patient-Derived Xenograft Model of Non-Small Cell Lung Cancer and Subsequent Molecular Characterization. Cells 2019; 8:cells8070740. [PMID: 31323891 PMCID: PMC6678194 DOI: 10.3390/cells8070740] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/04/2019] [Accepted: 07/17/2019] [Indexed: 02/08/2023] Open
Abstract
In up to 30% of non-small cell lung cancer (NSCLC) patients, the oncogenic driver of tumor growth is a constitutively activated epidermal growth factor receptor (EGFR). Although these patients gain great benefit from treatment with EGFR tyrosine kinase inhibitors, the development of resistance is inevitable. To model the emergence of drug resistance, an EGFR-driven, patient-derived xenograft (PDX) NSCLC model was treated continuously with Gefitinib in vivo. Over a period of more than three months, three separate clones developed and were subsequently analyzed: Whole exome sequencing and reverse phase protein arrays (RPPAs) were performed to identify the mechanism of resistance. In total, 13 genes were identified, which were mutated in all three resistant lines. Amongst them the mutations in NOMO2, ARHGEF5 and SMTNL2 were predicted as deleterious. The 53 mutated genes specific for at least two of the resistant lines were mainly involved in cell cycle activities or the Fanconi anemia pathway. On a protein level, total EGFR, total Axl, phospho-NFκB, and phospho-Stat1 were upregulated. Stat1, Stat3, MEK1/2, and NFκB displayed enhanced activation in the resistant clones determined by the phosphorylated vs. total protein ratio. In summary, we developed an NSCLC PDX line modelling possible escape mechanism under EGFR treatment. We identified three genes that have not been described before to be involved in an acquired EGFR resistance. Further functional studies are needed to decipher the underlying pathway regulation.
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Epigenetic Reprogramming of TGF-β Signaling in Breast Cancer. Cancers (Basel) 2019; 11:cancers11050726. [PMID: 31137748 PMCID: PMC6563130 DOI: 10.3390/cancers11050726] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022] Open
Abstract
The Transforming Growth Factor-β (TGF-β) signaling pathway has a well-documented, context-dependent role in breast cancer development. In normal and premalignant cells, it acts as a tumor suppressor. By contrast, during the malignant phases of breast cancer progression, the TGF-β signaling pathway elicits tumor promoting effects particularly by driving the epithelial to mesenchymal transition (EMT), which enhances tumor cell migration, invasion and ultimately metastasis to distant organs. The molecular and cellular mechanisms that govern this dual capacity are being uncovered at multiple molecular levels. This review will focus on recent advances relating to how epigenetic changes such as acetylation and methylation control the outcome of TGF-β signaling and alter the fate of breast cancer cells. In addition, we will highlight how this knowledge can be further exploited to curb tumorigenesis by selective targeting of the TGF-β signaling pathway.
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Abstract
Over the past decade, the amount of research and the number of publications on associations between circulating small and long non-coding RNAs (ncRNAs) and cancer have grown exponentially. Particular focus has been placed on the development of diagnostic and prognostic biomarkers to enable efficient patient management - from early detection of cancer to monitoring for disease recurrence or progression after treatment. Owing to their high abundance and stability, circulating ncRNAs have potential utility as non-invasive, blood-based biomarkers that can provide information on tumour biology and the effects of treatments, such as targeted therapies and immunotherapies. Increasing evidence highlights the roles of ncRNAs in cell-to-cell communication, with a number of ncRNAs having the capacity to regulate gene expression outside of the cell of origin through extracellular vesicle-mediated transfer to recipient cells, with implications for cancer progression and therapy resistance. Moreover, 'foreign' microRNAs (miRNAs) encoded by non-human genomes (so-called xeno-miRNAs), such as viral miRNAs, have been shown to be present in human body fluids and can be used as biomarkers. Herein, we review the latest developments in the use of circulating ncRNAs as diagnostic and prognostic biomarkers and discuss their roles in cell-to-cell communication in the context of cancer. We provide a compendium of miRNAs and long ncRNAs that have been reported in the literature to be present in human body fluids and that have the potential to be used as diagnostic and prognostic cancer biomarkers.
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45
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Li F, Li X, Qiao L, Liu W, Xu C, Wang X. MALAT1 regulates miR-34a expression in melanoma cells. Cell Death Dis 2019; 10:389. [PMID: 31101802 PMCID: PMC6525244 DOI: 10.1038/s41419-019-1620-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/16/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022]
Abstract
Melanoma is one of the most common skin malignancies. Both microRNAs and long non-coding RNAs (lncRNAs) have critical roles in the progression of cancers, including melanoma. However, the underlying molecular mechanism has not been fully characterized. We demonstrated that miR-34a is negatively correlated with MALAT1 in melanoma cells and tumor specimens. Interestingly, MALAT1, which contains functional sequence-specific miR-34a-binding sites, regulates miR-34a stability in melanoma cells and in vivo. Importantly, MALAT1 was significantly enriched in the Ago2 complex, but not when the MALAT1-binding site of miR-34a was mutated. Furthermore, MALAT1 could be shown to regulate c-Myc and Met expression by functioning as a miR-34a sponge. Our results reveal an unexpected mode of action for MALAT1 as an important regulator of miR-34a.
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Affiliation(s)
- Fei Li
- Department of Dermatology, Air Force Medical Center, PLA, Beijing, China.
| | - Xinji Li
- Department of Radiation Oncology, Air Force Medical Center, PLA, Beijing, China
| | - Li Qiao
- Department of Dermatology, Air Force Medical Center, PLA, Beijing, China
| | - Wen Liu
- Department of Dermatology, Air Force Medical Center, PLA, Beijing, China
| | - Chengshan Xu
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Xiaogang Wang
- Beijing Advanced Innovation Center for Big Data-based Precision Medicine, Beihang University, Beijing, China.
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Yang J, Nie J, Ma X, Wei Y, Peng Y, Wei X. Targeting PI3K in cancer: mechanisms and advances in clinical trials. Mol Cancer 2019; 18:26. [PMID: 30782187 PMCID: PMC6379961 DOI: 10.1186/s12943-019-0954-x] [Citation(s) in RCA: 871] [Impact Index Per Article: 174.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/06/2019] [Indexed: 02/07/2023] Open
Abstract
Phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling is one of the most important intracellular pathways, which can be considered as a master regulator for cancer. Enormous efforts have been dedicated to the development of drugs targeting PI3K signaling, many of which are currently employed in clinical trials evaluation, and it is becoming increasingly clear that PI3K inhibitors are effective in inhibiting tumor progression. PI3K inhibitors are subdivided into dual PI3K/mTOR inhibitors, pan-PI3K inhibitors and isoform-specific inhibitors. In this review, we performed a critical review to summarize the role of the PI3K pathway in tumor development, recent PI3K inhibitors development based on clinical trials, and the mechanisms of resistance to PI3K inhibition.
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Affiliation(s)
- Jing Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ji Nie
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xuelei Ma
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yong Peng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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Fallah H, Ganji M, Arsang-Jang S, Sayad A, Taheri M. Consideration of the role of MALAT1 long noncoding RNA and catalytic component of RNA-induced silencing complex (Argonaute 2, AGO2) in autism spectrum disorders: Yes, or no? Meta Gene 2019. [DOI: 10.1016/j.mgene.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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48
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Li RH, Chen M, Liu J, Shao CC, Guo CP, Wei XL, Li YC, Huang WH, Zhang GJ. Long noncoding RNA ATB promotes the epithelial-mesenchymal transition by upregulating the miR-200c/Twist1 axe and predicts poor prognosis in breast cancer. Cell Death Dis 2018; 9:1171. [PMID: 30518916 PMCID: PMC6281614 DOI: 10.1038/s41419-018-1210-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/27/2018] [Accepted: 11/05/2018] [Indexed: 02/05/2023]
Abstract
Recent studies indicate that the long noncoding RNA ATB (lncATB) can induce the epithelial−mesenchymal transition (EMT) in cancer cells, but the specific cellular targets of lncATB require further investigation. In the present study, the upregulation of lncATB in breast cancer cells was validated in a TGF-β-induced EMT model. Gain- and loss-of-function studies demonstrated that lncATB enhanced cell migration, invasion and clonogenicity in vitro and in vivo. LncATB promoted the EMT by acting as a sponge for the miR-200 family and restoring Twist1 expression. Subsequently, the clinical significance of lncATB was investigated in a cohort of breast cancer patients (N = 131). Higher lncATB expression was correlated with increased nodal metastasis (P = 0.036) and advanced clinical stage (P = 0.011) as well as shorter disease-free survival (P = 0.043) and overall survival (P = 0.046). These findings define Twist1 as a major target of lncATB in the induction of the EMT and highlight lncATB as a biomarker in breast cancer patients.
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Affiliation(s)
- Rong-Hui Li
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Min Chen
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China.,The Cancer Center, Xiang'an Hospital of Xiamen University, 2000 East Xiang'an Rd., Xiang'an, Xiamen, China
| | - Jing Liu
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Chang-Chun Shao
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Cui-Ping Guo
- The Breast Center, The Cancer Hospital of SUMC, 515041, Shantou, Guangdong, China
| | - Xiao-Long Wei
- Department of Pathology, The Cancer Hospital of SUMC, Shantou, Guangdong, China
| | - Yao-Chen Li
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China
| | - Wen-He Huang
- The Breast Center, The Cancer Hospital of SUMC, 515041, Shantou, Guangdong, China
| | - Guo-Jun Zhang
- ChangJiang Scholar's Laboratory, Shantou University Medical College (SUMC), 515041, Shantou, Guangdong, China. .,The Cancer Center, Xiang'an Hospital of Xiamen University, 2000 East Xiang'an Rd., Xiang'an, Xiamen, China.
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Pecero ML, Salvador-Bofill J, Molina-Pinelo S. Long non-coding RNAs as monitoring tools and therapeutic targets in breast cancer. Cell Oncol (Dordr) 2018; 42:1-12. [DOI: 10.1007/s13402-018-0412-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2018] [Indexed: 12/31/2022] Open
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50
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Li J, Cui Z, Li H, Lv X, Gao M, Yang Z, Bi Y, Zhang Z, Wang S, Zhou B, Yin Z. Clinicopathological and prognostic significance of long noncoding RNA MALAT1 in human cancers: a review and meta-analysis. Cancer Cell Int 2018; 18:109. [PMID: 30093838 PMCID: PMC6080354 DOI: 10.1186/s12935-018-0606-z] [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: 05/28/2018] [Accepted: 07/31/2018] [Indexed: 12/11/2022] Open
Abstract
Background The aberrant regulation of MALAT1 has been indicated to be involved in various carcinogenic pathways contributing to the tumourigenesis and progression of cancers. The current meta-analysis summarized the research advances of MALAT1 functions and analyzed its prognostic value among multiple types of cancers. Methods Eligible studies were identified through retrieving the PubMed, Web of Science, and CNKI databases, up to Mar 1, 2018. 28 studies of 5436 patients and 36 studies of 3325 patients were enrolled in the meta-analysis to evaluate the association of MALAT1 expression with survival outcomes and clinical parameters. Results The results demonstrated that over-expression of MALAT1 may predict lymph node metastasis (pooled OR = 2.335, 95% CI 1.606–3.395, P = 0.000) and distant metastasis (pooled OR = 2.456, 95% CI 1.407–4.286, P = 0.002). Moreover, MALAT1 was also related with tumour size (pooled OR = 1.875, 95% CI 1.257–2.795, P = 0.002) and TNM stage (pooled OR = 2.034, 95% CI 1.111–3.724, P = 0.021). Additionally, elevated MALAT1 expression could predict poor OS (pooled HR = 2.298, 95% CI 1.953–2.704, P = 0.000), DFS (pooled HR = 2.036, 95% CI 1.240–3.342, P = 0.005), RFS (pooled HR = 2.491, 95% CI 1.505–4.123, P = 0.000), DSS (pooled HR = 2.098, 95% CI 1.372–3.211, P = 0.001) and PFS (pooled HR = 1.842, 95% CI 1.138–2.983, P = 0.013) in multivariate model. Importantly, subgroup analyses disclosed that increased MALAT1 expression had a poor OS among different cancer types (Estrogen-dependent cancer: pooled HR = 2.656, 95% CI 1.560–4.523; urological cancer: pooled HR = 1.952, 95% CI 1.189–3.204; glioma: pooled HR = 2.315, 95% CI 1.643–3.263; digestive cancer: pooled HR = 2.451, 95% CI 1.862–3.227). Conclusions The present findings demonstrated that MALAT1 may be a novel biomarker for predicting survival outcome, lymph node metastasis and distant metastasis. Electronic supplementary material The online version of this article (10.1186/s12935-018-0606-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Li
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Zhigang Cui
- 3School of Nursing, China Medical University, Shenyang, 110122 China
| | - Hang Li
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Xiaoting Lv
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Min Gao
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Zitai Yang
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Yanhong Bi
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Ziwei Zhang
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Shengli Wang
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Baosen Zhou
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
| | - Zhihua Yin
- 1Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, 110122 People's Republic of China
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