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Krsek A, Baticic L, Sotosek V, Braut T. The Role of Biomarkers in HPV-Positive Head and Neck Squamous Cell Carcinoma: Towards Precision Medicine. Diagnostics (Basel) 2024; 14:1448. [PMID: 39001338 PMCID: PMC11241541 DOI: 10.3390/diagnostics14131448] [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: 06/10/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
Head and neck cancer (HNC) represents a significant global health challenge, with squamous cell carcinomas (SCCs) accounting for approximately 90% of all HNC cases. These malignancies, collectively referred to as head and neck squamous cell carcinoma (HNSCC), originate from the mucosal epithelium lining the larynx, pharynx, and oral cavity. The primary risk factors associated with HNSCC in economically disadvantaged nations have been chronic alcohol consumption and tobacco use. However, in more affluent countries, the landscape of HNSCC has shifted with the identification of human papillomavirus (HPV) infection, particularly HPV-16, as a major risk factor, especially among nonsmokers. Understanding the evolving risk factors and the distinct biological behaviors of HPV-positive and HPV-negative HNSCC is critical for developing targeted treatment strategies and improving patient outcomes in this complex and diverse group of cancers. Accurate diagnosis of HPV-positive HNSCC is essential for developing a comprehensive model that integrates the molecular characteristics, immune microenvironment, and clinical outcomes. The aim of this comprehensive review was to summarize the current knowledge and advances in the identification of DNA, RNA, and protein biomarkers in bodily fluids and tissues that have introduced new possibilities for minimally or non-invasive cancer diagnosis, monitoring, and assessment of therapeutic responses.
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Affiliation(s)
- Antea Krsek
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia;
| | - Lara Baticic
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Vlatka Sotosek
- Department of Clinical Medical Sciences I, Faculty of Health Studies, University of Rijeka, 51000 Rijeka, Croatia;
- Department of Anesthesiology, Reanimatology, Emergency and Intensive Care Medicine, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Tamara Braut
- Department of Otorhinolaryngology and Head and Neck Surgery, Clinical Hospital Centre Rijeka, 51000 Rijeka, Croatia;
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2
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Satake E, Krolewski B, Kobayashi H, Md Dom ZI, Ricca J, Wilson JM, Hoon DS, Duffin KL, Pezzolesi MG, Krolewski AS. Preanalytical considerations in quantifying circulating miRNAs that predict end-stage kidney disease in diabetes. JCI Insight 2024; 9:e174153. [PMID: 38912578 DOI: 10.1172/jci.insight.174153] [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: 07/26/2023] [Accepted: 05/08/2024] [Indexed: 06/25/2024] Open
Abstract
Our previous study identified 8 risk and 9 protective plasma miRNAs associated with progression to end-stage kidney disease (ESKD) in diabetes. This study aimed to elucidate preanalytical factors that influence the quantification of circulating miRNAs. Using the EdgeSeq platform, which quantifies 2,002 miRNAs in plasma, including ESKD-associated miRNAs, we compared miRNA profiles in whole plasma versus miRNA profiles in RNA extracted from the same plasma specimens. Less than half of the miRNAs were detected in standard RNA extraction from plasma. Detection of individual and concentrations of miRNAs were much lower when RNA extracted from plasma was quantified by RNA sequencing (RNA-Seq) or quantitative reverse transcription PCR (qRT-PCR) platforms compared with EdgeSeq. Plasma profiles of miRNAs determined by the EdgeSeq platform had excellent reproducibility in assessment and had no variation with age, sex, hemoglobin A1c, BMI, and cryostorage time. The risk ESKD-associated miRNAs were detected and measured accurately only in whole plasma and using the EdgeSeq platform. Protective ESKD-associated miRNAs were detected by all platforms except qRT-PCR; however, correlations among concentrations obtained with different platforms were weak or nonexistent. In conclusion, preanalytical factors have a profound effect on detection and quantification of circulating miRNAs in ESKD in diabetes. Quantification of miRNAs in whole plasma and using the EdgeSeq platform may be the preferable method to study profiles of circulating cell-free miRNAs associated with ESKD and possibly other diseases.
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Affiliation(s)
- Eiichiro Satake
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Bozena Krolewski
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroki Kobayashi
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, Tokyo, Japan
| | - Zaipul I Md Dom
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Ricca
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
| | | | - Dave Sb Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Providence Health and Service, Santa Monica, California, USA
| | | | - Marcus G Pezzolesi
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Andrzej S Krolewski
- Research Division, Joslin Diabetes Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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3
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Guo D, Yang M, Li S, Zhu W, Chen M, Pan J, Long D, Liu Z, Zhang C. Expression and molecular regulation of non-coding RNAs in HPV-positive head and neck squamous cell carcinoma. Front Oncol 2023; 13:1122982. [PMID: 37064141 PMCID: PMC10090466 DOI: 10.3389/fonc.2023.1122982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent malignancy worldwide. Accumulating evidence suggests that persistent HPV infection is closely related to a subset of HNSCC types, and the incidence of human papillomavirus (HPV)-positive HNSCC has been annually increasing in recent decades. Although the carcinogenesis of HPV-positive HNSCC has not been completely elucidated, it has been well confirmed that E6 and E7, the main viral oncoproteins are responsible for the maintenance of malignant transformation, promotion of cell proliferation, and increase in tumor invasion. Moreover, compared with HPV-negative HNSCC, HPV-positive HNSCC shows some special clinical-pathological features, which are possibly related to HPV infection and their specific regulatory mechanisms. Non-coding RNA (ncRNA) is a class of RNA lacking the protein-coding function and playing a critical regulatory role via multiple complex molecular mechanisms. NcRNA is an important regulatory pattern of epigenetic modification, which can exert significant effects on HPV-induced tumorigenesis and progression by deregulating downstream genes. However, the knowledge of ncRNAs is still limited, hence, a better understanding of ncRNAs could provide some insights for exploring the carcinogenesis mechanism and identifying valuable biomarkers in HPV-positive HNSCC. Therefore, in this review, we mainly focused on the expression profile of ncRNAs (including lncRNA, miRNA, and circRNA) and explored their regulatory role in HPV-positive HNSCC, aiming to clarify the regulatory mechanism of ncRNAs and identify valuable biomarkers for HPV-positive HNSCC.
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4
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Kuo CY, Moi SH, Hou MF, Luo CW, Pan MR. Chromatin Remodeling Enzyme Cluster Predicts Prognosis and Clinical Benefit of Therapeutic Strategy in Breast Cancer. Int J Mol Sci 2023; 24:ijms24065583. [PMID: 36982660 PMCID: PMC10055970 DOI: 10.3390/ijms24065583] [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: 01/23/2023] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
The treatment provided for breast cancer depends on the expression of hormone receptors, human epidermal growth factor receptor-2 (HER2), and cancer staging. Surgical intervention, along with chemotherapy or radiation therapy, is the mainstay of treatment. Currently, precision medicine has led to personalized treatment using reliable biomarkers for the heterogeneity of breast cancer. Recent studies have shown that epigenetic modifications contribute to tumorigenesis through alterations in the expression of tumor suppressor genes. Our aim was to investigate the role of epigenetic modifications in genes involved in breast cancer. A total of 486 patients from The Cancer Genome Atlas Pan-cancer BRCA project were enrolled in our study. Hierarchical agglomerative clustering analysis further divided the 31 candidate genes into 2 clusters according to the optimal number. Kaplan–Meier plots showed worse progression-free survival (PFS) in the high-risk group of gene cluster 1 (GC1). In addition, the high-risk group showed worse PFS in GC1 with lymph node invasion, which also presented a trend of better PFS when chemotherapy was combined with radiotherapy than when chemotherapy was administered alone. In conclusion, we developed a novel panel using hierarchical clustering that high-risk groups of GC1 may be promising predictive biomarkers in the clinical treatment of patients with breast cancer.
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Affiliation(s)
- Chia-Yu Kuo
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Sin-Hua Moi
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Feng Hou
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chi-Wen Luo
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Cosmetic Science and Institute of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan
- Correspondence: (C.-W.L.); (M.-R.P.); Tel.: +886-7-3121101 (ext. 2260) (C.-W.L.); +886-7-3121101 (ext. 5092-34) (M.-R.P.); Fax: +886-7-3165011 (C.-W.L.); +886-7-3218309 (M.-R.P.)
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: (C.-W.L.); (M.-R.P.); Tel.: +886-7-3121101 (ext. 2260) (C.-W.L.); +886-7-3121101 (ext. 5092-34) (M.-R.P.); Fax: +886-7-3165011 (C.-W.L.); +886-7-3218309 (M.-R.P.)
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5
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Zheng K, Zhang XL, Wang L, You ZH, Zhan ZH, Li HY. Line graph attention networks for predicting disease-associated Piwi-interacting RNAs. Brief Bioinform 2022; 23:6748487. [PMID: 36198846 DOI: 10.1093/bib/bbac393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and Piwi-Interacting RNAs (piRNAs) are commonly detected in human cancers, especially in germline and somatic tissues, and correlate with poorer clinical outcomes, suggesting that they play a functional role in cancer. As the problem of combinatorial explosions between ncRNA and disease exposes gradually, new bioinformatics methods for large-scale identification and prioritization of potential associations are therefore of interest. However, in the real world, the network of interactions between molecules is enormously intricate and noisy, which poses a problem for efficient graph mining. Line graphs can extend many heterogeneous networks to replace dichotomous networks. In this study, we present a new graph neural network framework, line graph attention networks (LGAT). And we apply it to predict PiRNA disease association (GAPDA). In the experiment, GAPDA performs excellently in 5-fold cross-validation with an AUC of 0.9038. Not only that, it still has superior performance compared with methods based on collaborative filtering and attribute features. The experimental results show that GAPDA ensures the prospect of the graph neural network on such problems and can be an excellent supplement for future biomedical research.
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Affiliation(s)
- Kai Zheng
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | | | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhu-Hong You
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhao-Hui Zhan
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Hao-Yuan Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
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6
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Zheng K, Liang Y, Liu YY, Yasir M, Wang P. A decision support system based on multi-sources information to predict piRNA–disease associations using stacked autoencoder. Soft comput 2022. [DOI: 10.1007/s00500-022-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Chattopadhyay T, Biswal P, Lalruatfela A, Mallick B. Emerging roles of PIWI-interacting RNAs (piRNAs) and PIWI proteins in head and neck cancer and their potential clinical implications. Biochim Biophys Acta Rev Cancer 2022; 1877:188772. [PMID: 35931391 DOI: 10.1016/j.bbcan.2022.188772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/08/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) are among the well-known neoplasms originating in the oral cavity, pharynx, and larynx. Despite advancements in chemotherapy, radiotherapy, and surgery, the survival rates of the patients are low, which has posed a major therapeutic challenge. A growing number of non-coding RNAs (ncRNAs), for instance, microRNAs, have been identified whose abnormal expression patterns have been implicated in HNSCC. However, more recently, several seminal research has shown that piwi-interacting RNAs (piRNAs), a promising and young class of small ncRNA, are linked to the emergence and progression of cancer. They can regulate transposable elements (TE) and gene expression through multiple mechanisms, making them potentially more powerful regulators than miRNAs. Hence, they can be more promising ncRNAs candidates for cancer therapeutic intervention. Here, we surveyed the roles and clinical implications of piRNAs and their PIWI proteins partners in tumorigenesis and associated molecular processes of cancer, with a particular focus on HNSCC, to offer a new avenue for diagnosis, prognosis, and therapeutic interventions for the malignancy, improving patient's outcomes.
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Affiliation(s)
- Trisha Chattopadhyay
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Priyajit Biswal
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Anthony Lalruatfela
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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8
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Feoli A, Viviano M, Cipriano A, Milite C, Castellano S, Sbardella G. Lysine methyltransferase inhibitors: where we are now. RSC Chem Biol 2022; 3:359-406. [PMID: 35441141 PMCID: PMC8985178 DOI: 10.1039/d1cb00196e] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Protein lysine methyltransferases constitute a large family of epigenetic writers that catalyse the transfer of a methyl group from the cofactor S-adenosyl-l-methionine to histone- and non-histone-specific substrates. Alterations in the expression and activity of these proteins have been linked to the genesis and progress of several diseases, including cancer, neurological disorders, and growing defects, hence they represent interesting targets for new therapeutic approaches. Over the past two decades, the identification of modulators of lysine methyltransferases has increased tremendously, clarifying the role of these proteins in different physio-pathological states. The aim of this review is to furnish an updated outlook about the protein lysine methyltransferases disclosed modulators, reporting their potency, their mechanism of action and their eventual use in clinical and preclinical studies.
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Affiliation(s)
- Alessandra Feoli
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Alessandra Cipriano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Ciro Milite
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
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Cutliffe AL, McKenna SL, Chandrashekar DS, Ng A, Devonshire G, Fitzgerald RC, O’Donovan TR, Mackrill JJ. Alterations in the Ca2+ toolkit in oesophageal adenocarcinoma. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2021; 2:543-575. [PMID: 36046118 PMCID: PMC9400700 DOI: 10.37349/etat.2021.00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022] Open
Abstract
Aim: To investigate alterations in transcription of genes, encoding Ca2+ toolkit proteins, in oesophageal adenocarcinoma (OAC) and to assess associations between gene expression, tumor grade, nodal-metastatic stage, and patient survival. Methods: The expression of 275 transcripts, encoding components of the Ca2+ toolkit, was analyzed in two OAC datasets: the Cancer Genome Atlas [via the University of Alabama Cancer (UALCAN) portal] and the oesophageal-cancer, clinical, and molecular stratification [Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS)] dataset. Effects of differential expression of these genes on patient survival were determined using Kaplan-Meier log-rank tests. OAC grade- and metastatic-stage status was investigated for a subset of genes. Adjustment for the multiplicity of testing was made throughout. Results: Of the 275 Ca2+-toolkit genes analyzed, 75 displayed consistent changes in expression between OAC and normal tissue in both datasets. The channel-encoding genes, N-methyl-D-aspartate receptor 2D (GRIN2D), transient receptor potential (TRP) ion channel classical or canonical 4 (TRPC4), and TRP ion channel melastatin 2 (TRPM2) demonstrated the greatest increase in expression in OAC in both datasets. Nine genes were consistently upregulated in both datasets and were also associated with improved survival outcomes. The 6 top-ranking genes for the weighted significance of altered expression and survival outcomes were selected for further analysis: voltage-gated Ca2+ channel subunit α 1D (CACNA1D), voltage-gated Ca2+ channel auxiliary subunit α2 δ4 (CACNA2D4), junctophilin 1 (JPH1), acid-sensing ion channel 4 (ACCN4), TRPM5, and secretory pathway Ca2+ ATPase 2 (ATP2C2). CACNA1D, JPH1, and ATP2C2 were also upregulated in advanced OAC tumor grades and nodal-metastatic stages in both datasets. Conclusions: This study has unveiled alterations of the Ca2+ toolkit in OAC, compared to normal tissue. Such Ca2+ signalling findings are consistent with those from studies on other cancers. Genes that were consistently upregulated in both datasets might represent useful markers for patient diagnosis. Genes that were consistently upregulated, and which were associated with improved survival, might be useful markers for patient outcome. These survival-associated genes may also represent targets for the development of novel chemotherapeutic agents.
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Affiliation(s)
- Alana L. Cutliffe
- Department of Physiology, University College Cork, BioSciences Institute, T12 YT20 Cork, Ireland
| | - Sharon L. McKenna
- Cancer Research, UCC, Western Gateway Building, University College Cork, T12 XF62 Cork, Ireland
| | - Darshan S. Chandrashekar
- Department of Pathology, Molecular & Cellular, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Alvin Ng
- Cancer Research UK Cambridge Institute, University of Cambridge Li Ka Shing Centre, Robinson Way, CB2 0RE Cambridge, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge Li Ka Shing Centre, Robinson Way, CB2 0RE Cambridge, UK
| | - Rebecca C. Fitzgerald
- Cancer Research UK Cambridge Institute, University of Cambridge Li Ka Shing Centre, Robinson Way, CB2 0RE Cambridge, UK
| | - Tracey R. O’Donovan
- Cancer Research, UCC, Western Gateway Building, University College Cork, T12 XF62 Cork, Ireland
| | - John J. Mackrill
- Department of Physiology, University College Cork, BioSciences Institute, T12 YT20 Cork, Ireland
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10
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Hu W, Zhao Y, Su L, Wu Z, Jiang W, Jiang X, Liu M. Silencing the lncRNA NORAD inhibits EMT of head and neck squamous cell carcinoma stem cells via miR‑26a‑5p. Mol Med Rep 2021; 24:743. [PMID: 34435652 PMCID: PMC8430304 DOI: 10.3892/mmr.2021.12383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer stem cells are closely associated with tumor metastasis or recurrence. According to previous literature reports, microRNA (miR)‑26a has an inhibitory effect on head and neck squamous cell carcinoma (HNSCC), and the long non‑coding RNA (lncRNA) non‑coding RNA activated by DNA damage (NORAD) has been found to interact with miR‑26a‑5p. The present study aimed to investigate the regulation and mechanism of NORAD and miR‑26a‑5p in the epithelial‑mesenchymal transition (EMT) of HNSCC stem cells. An ALDEFLUOR stem cell detection kit, a flow cytometer, a self‑renewal ability test and western blotting were used to sort and identify HNSCC stem cells. The ENCORI website and a dual‑luciferase assay were used to assess the relationship between genes. The mRNA and protein expression levels of NORAD, miR‑26a‑5p and EMT‑related genes were detected via reverse transcription‑quantitative PCR and western blotting. Functional experiments (MTT assay, flow cytometry, wound healing assay and Transwell assay) were conducted to analyze the effects of NORAD and miR‑26a‑5p on HNSCC stem cells. The successfully sorted aldehyde dehydrogenase (ALDH)+ cells had a self‑renewal capacity and displayed upregulated expression levels of CD44, Oct‑4 and Nanog. NORAD knockdown, achieved using small interfering (si)RNA, downregulated the expression levels of tumor markers in ALDH+ cells. siNORAD inhibited cell vitality, migration and invasion, as well as promoted apoptosis, increased the expression of epithelial cell markers and decreased the expression of interstitial cell markers in HNSCC stem cells. miR‑26a‑5p was a downstream gene of NORAD, and knockdown of miR‑26a‑5p partially offset the regulatory effect of siNORAD on HNSCC stem cells. Collectively, the present study demonstrated that NORAD knockdown attenuated the migration, invasion and EMT of HNSCC stem cells via miR‑26a‑5p.
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Affiliation(s)
- Weiming Hu
- Department of Otorhinolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Yong Zhao
- Department of Otorhinolaryngology, XIXI Hospital of Hangzhou, Hangzhou, Zhejiang 310012, P.R. China
| | - Lizhong Su
- Department of Otorhinolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Zuliang Wu
- Department of Otorhinolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Wenjing Jiang
- Department of Otorhinolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Xiaoze Jiang
- Department of Otorhinolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Ming Liu
- Department of Otorhinolaryngology, Zhejiang Hospital, Hangzhou, Zhejiang 310012, P.R. China
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11
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Chen S, Ben S, Xin J, Li S, Zheng R, Wang H, Fan L, Du M, Zhang Z, Wang M. The biogenesis and biological function of PIWI-interacting RNA in cancer. J Hematol Oncol 2021; 14:93. [PMID: 34118972 PMCID: PMC8199808 DOI: 10.1186/s13045-021-01104-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Small non-coding RNAs (ncRNAs) are vital regulators of biological activities, and aberrant levels of small ncRNAs are commonly found in precancerous lesions and cancer. PIWI-interacting RNAs (piRNAs) are a novel type of small ncRNA initially discovered in germ cells that have a specific length (24-31 nucleotides), bind to PIWI proteins, and show 2'-O-methyl modification at the 3'-end. Numerous studies have revealed that piRNAs can play important roles in tumorigenesis via multiple biological regulatory mechanisms, including silencing transcriptional and posttranscriptional gene processes and accelerating multiprotein interactions. piRNAs are emerging players in the malignant transformation of normal cells and participate in the regulation of cancer hallmarks. Most of the specific cancer hallmarks regulated by piRNAs are involved in sustaining proliferative signaling, resistance to cell death or apoptosis, and activation of invasion and metastasis. Additionally, piRNAs have been used as biomarkers for cancer diagnosis and prognosis and have great potential for clinical utility. However, research on the underlying mechanisms of piRNAs in cancer is limited. Here, we systematically reviewed recent advances in the biogenesis and biological functions of piRNAs and relevant bioinformatics databases with the aim of providing insights into cancer diagnosis and clinical applications. We also focused on some cancer hallmarks rarely reported to be related to piRNAs, which can promote in-depth research of piRNAs in molecular biology and facilitate their clinical translation into cancer treatment.
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Affiliation(s)
- Silu Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rui Zheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lulu Fan
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China. .,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China.
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12
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Wang Q, Yang W, Peng W, Qian X, Zhang M, Wang T. Integrative Analysis of DNA Methylation Data and Transcriptome Data Identified a DNA Methylation-Dysregulated Four-LncRNA Signature for Predicting Prognosis in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:666349. [PMID: 33869232 PMCID: PMC8047109 DOI: 10.3389/fcell.2021.666349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/15/2021] [Indexed: 11/18/2022] Open
Abstract
Increasing evidence has demonstrated the crosstalk between DNA epigenetic alterations and aberrant expression of long non-coding RNAs (lncRNAs) during carcinogenesis. However, epigenetically dysregulated lncRNAs and their functional and clinical roles in Head and Neck Squamous Cell Carcinoma (HNSCC) are still not explored. In this study, we performed an integrative analysis of DNA methylation data and transcriptome data and identified a DNA methylation-dysregulated four-lncRNA signature (DNAMeFourLncSig) from 596 DNA methylation-dysregulated lncRNAs using a machine-learning-based feature selection method, which classified the patients of the discovery cohort into two risk groups with significantly different survival including overall survival, disease-specific survival, and progression-free survival. Then the DNAMeFourLncSig was implemented to another two HNSCC patient cohorts and showed similar prognostic values in both. Results from multivariable Cox regression analysis revealed that the DNAMeFourLncSig might be an independent prognostic factor. Furthermore, the DNAMeFourLncSig was substantially correlated with the complete response rate of chemotherapy and may predict chemotherapy response. Functional in silico analysis found that DNAMeFourLncSig-related mRNAs were mainly enriched in cell differentiation, tissue development and immune-related pathways. Overall, our study will improve our understanding of underlying transcriptional and epigenetic mechanisms in HNSCC carcinogenesis and provided a new potential biomarker for the prognosis of patients with HNSCC.
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Affiliation(s)
- Qiuxu Wang
- Department of Stomatology, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen Second People's Hospital, Shenzhen, China.,Department of Stomatology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Weiwei Yang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Wei Peng
- Department of Stomatology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Xuemei Qian
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, China
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13
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Genetic Drivers of Head and Neck Squamous Cell Carcinoma: Aberrant Splicing Events, Mutational Burden, HPV Infection and Future Targets. Genes (Basel) 2021; 12:genes12030422. [PMID: 33804181 PMCID: PMC7998272 DOI: 10.3390/genes12030422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/16/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Head and neck cancers include cancers that originate from a variety of locations. These include the mouth, nasal cavity, throat, sinuses, and salivary glands. These cancers are the sixth most diagnosed cancers worldwide. Due to the tissues they arise from, they are collectively named head and neck squamous cell carcinomas (HNSCC). The most important risk factors for head and neck cancers are infection with human papillomavirus (HPV), tobacco use and alcohol consumption. The genetic basis behind the development and progression of HNSCC includes aberrant non-coding RNA levels. However, one of the most important differences between healthy tissue and HNSCC tissue is changes in the alternative splicing of genes that play a vital role in processes that can be described as the hallmarks of cancer. These changes in the expression profile of alternately spliced mRNA give rise to various protein isoforms. These protein isoforms, alternate methylation of proteins, and changes in the transcription of non-coding RNAs (ncRNA) can be used as diagnostic or prognostic markers and as targets for the development of new therapeutic agents. This review aims to describe changes in alternative splicing and ncRNA patterns that contribute to the development and progression of HNSCC. It will also review the use of the changes in gene expression as biomarkers or as the basis for the development of new therapies.
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14
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Zhao Q, Zhang Y, Zhang X, Sun Y, Lin Z. Mining of gene modules and identification of key genes in head and neck squamous cell carcinoma based on gene co-expression network analysis. Medicine (Baltimore) 2020; 99:e22655. [PMID: 33285674 PMCID: PMC7717835 DOI: 10.1097/md.0000000000022655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 11/26/2022] Open
Abstract
To explore the gene modules and key genes of head and neck squamous cell carcinoma (HNSCC), a bioinformatics algorithm based on the gene co-expression network analysis was proposed in this study.Firstly, differentially expressed genes (DEGs) were identified and a gene co-expression network (i-GCN) was constructed with Pearson correlation analysis. Then, the gene modules were identified with 5 different community detection algorithms, and the correlation analysis between gene modules and clinical indicators was performed. Gene Ontology (GO) analysis was used to annotate the biological pathways of the gene modules. Then, the key genes were identified with 2 methods, gene significance (GS) and PageRank algorithm. Moreover, we used the Disgenet database to search the related diseases of the key genes. Lastly, the online software onclnc was used to perform the survival analysis on the key genes and draw survival curves.There were 2600 up-regulated and 1547 down-regulated genes identified in HNSCC. An i-GCN was constructed with Pearson correlation analysis. Then, the i-GCN was divided into 9 gene modules. The result of association analysis showed that, sex was mainly related to mitosis and meiosis processes, event was mainly related to responding to interferons, viruses and T cell differentiation processes, T stage was mainly related to muscle development and contraction, regulation of protein transport activity processes, N stage was mainly related to mitosis and meiosis processes, while M stage was mainly related to responding to interferons and immune response processes. Lastly, 34 key genes were identified, such as CDKN2A, HOXA1, CDC7, PPL, EVPL, PXN, PDGFRB, CALD1, and NUSAP1. Among them, HOXA1, PXN, and NUSAP1 were negatively correlated with the survival prognosis.HOXA1, PXN, and NUSAP1 might play important roles in the progression of HNSCC and severed as potential biomarkers for future diagnosis.
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Affiliation(s)
- Qian Zhao
- College of Information Science and Technology
| | - Yan Zhang
- College of Information Science and Technology
| | - Xue Zhang
- College of Information Science and Technology
| | - Yeqing Sun
- Institute of Environmental System Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
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15
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Shi Y, Zhang Q, Xie M, Feng Y, Ma S, Yi C, Wang Z, Li Y, Liu X, Liu H, Yang H, Yan Y, Zhang Y, Ren X, Luo H. Aberrant methylation‑mediated decrease of lncRNA HNF1A‑AS1 contributes to malignant progression of laryngeal squamous cell carcinoma via EMT. Oncol Rep 2020; 44:2503-2516. [PMID: 33125127 PMCID: PMC7640355 DOI: 10.3892/or.2020.7823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/24/2020] [Indexed: 12/27/2022] Open
Abstract
Aberrant methylation is one of the most frequent epigenetic alterations that regulate the expression levels of genes, including long non-coding RNAs (lncRNAs), in tumors. However, to the best of our knowledge, the expression and function of hepatic nuclear factor 1α antisense RNA 1 (HNF1A-AS1) and its methylation condition have not yet been reported in the development and progression of laryngeal squamous cell carcinoma (LSCC). In the present study, the expression and methylation of HNF1A-AS1 were first examined by reverse transcription-quantitative PCR, bisulfite genomic sequencing and methylation-specific polymerase chain reaction in samples from patients with LSCC, which were based on the in silico analysis using The Cancer Genome Atlas data, and were then further verified in LSCC cell lines with and without 5-Aza-2′-deoxycytidine (5-Aza-dC) treatment. Subsequently, proliferation, cell cycle distribution, migration and invasion of LSCC cells following either knockdown or overexpression of HNF1A-AS1 were determined in vitro. Furthermore, the characteristic of HNF1A-AS1 on epithelial-mesenchymal transition (EMT) changes was investigated in vitro and in vivo. The associations between the expression levels of HNF1A-AS1 and tumorigenicity and cervical lymph node metastasis were assessed in a xenograft model in nude mice. In the present study, downregulation and hypermethylation in CpG sites of HNF1A-AS1 were detected in LSCC tissues as well as metastatic cervical lymph nodes samples when compared with those in the adjacent non-tumor tissues. Additionally, HNF1A-AS1 inhibited proliferation, migration and invasion of LSCC cells in vitro by regulating the process of EMT. Furthermore, HNF1A-AS1 inhibited tumor growth and metastasis by regulating EMT in vivo. Additionally, the migration and invasion abilities, and the expression levels of HNF1A-AS1 and EMT markers in LSCC cells were significantly reversed by treatment with 5-Aza-dC. In summary, HNF1A-AS1 was downregulated by hypermethylation in LSCC and laryngeal cancer cells. These findings suggested that HNF1A-AS1 could serve as a tumor suppressor lncRNA in LSCC by regulating the EMT process, leading to the discovery of novel therapeutic targets and strategies for the treatment of patients with LSCC.
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Affiliation(s)
- Yewen Shi
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Qingqing Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Meng Xie
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Yani Feng
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Sijing Ma
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Chunxi Yi
- Department of Otorhinolaryngology Head and Neck Surgery, Xi'an Central Hospital, Xi'an, Shaanxi 710004, P.R. China
| | - Zihan Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi 710003, P.R. China
| | - Yanju Li
- Department of Pathology, Yanan University Affiliated Hospital, Yan'an, Shaanxi 716000, P.R. China
| | - Xiaohong Liu
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Haiqin Liu
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Hui Yang
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Yan Yan
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Yitong Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Xiaoyong Ren
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Huanan Luo
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
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16
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Wei H, Ding Y, Liu B. iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples. Comput Biol Chem 2020; 88:107361. [PMID: 32916452 DOI: 10.1016/j.compbiolchem.2020.107361] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/31/2020] [Accepted: 08/15/2020] [Indexed: 12/31/2022]
Abstract
As a large group of small non-coding RNAs (ncRNAs), Piwi-interacting RNAs (piRNAs) have been detected to be associated with various diseases. Identifying disease associated piRNAs can provide promising candidate molecular targets to promote the drug design. Although, a few computational ensemble methods have been developed for identifying piRNA-disease associations, the low-quality negative associations even with positive associations used during the training process prevent the predictive performance improvement. In this study, we proposed a new computational predictor named iPiDA-sHN to predict potential piRNA-disease associations. iPiDA-sHN presented the piRNA-disease pairs by incorporating piRNA sequence information, the known piRNA-disease association network, and the disease semantic graph. High-level features of piRNA-disease associations were extracted by the Convolutional Neural Network (CNN). Two-step positive-unlabeled learning strategy based on Support Vector Machine (SVM) was employed to select the high quality negative samples from the unknown piRNA-disease pairs. Finally, the SVM predictor trained with the known piRNA-disease associations and the high quality negative associations was used to predict new piRNA-disease associations. The experimental results showed that iPiDA-sHN achieved superior predictive ability compared with other state-of-the-art predictors.
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Affiliation(s)
- Hang Wei
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China.
| | - Yuxin Ding
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China.
| | - Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China; School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China.
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17
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Lin Y, Zheng J, Lin D. PIWI-interacting RNAs in human cancer. Semin Cancer Biol 2020; 75:15-28. [PMID: 32877760 DOI: 10.1016/j.semcancer.2020.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/16/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022]
Abstract
P-element-induced wimpy testis (PIWI) interacting RNAs (piRNAs) are a class of small regulatory RNAs mechanistically similar to but much less studied than microRNAs and small interfering RNAs. Today the best understood function of piRNAs is transposon control in animal germ cells, which has earned them the name 'guardians of the germline'. Several molecular/cellular characteristics of piRNAs, including high sequence diversity, lack of secondary structures, and target-oriented generation seem to serve this purpose. Recently, aberrant expressions of piRNAs and PIWI proteins have been implicated in a variety of malignant tumors and associated with cancer hallmarks such as cell proliferation, inhibited apoptosis, invasion, metastasis and increased stemness. Researchers have also demonstrated multiple mechanisms of piRNA-mediated target deregulation associated with cancer initiation, progression or dissemination. We review current research findings on the biogenesis, normal functions and cancer associations of piRNAs, highlighting their potentials as cancer diagnostic/prognostic biomarkers and therapeutic tools. Whenever applicable, we draw connections with other research fields to encourage intercommunity conversations. We also offer recommendations and cautions regarding the general process of cancer-related piRNA studies and the methods/tools used at each step. Finally, we call attention to some issues that, if left unsolved, might impede the future development of this field.
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Affiliation(s)
- Yuan Lin
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China; Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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18
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Casamassimi A, Rienzo M, Di Zazzo E, Sorrentino A, Fiore D, Proto MC, Moncharmont B, Gazzerro P, Bifulco M, Abbondanza C. Multifaceted Role of PRDM Proteins in Human Cancer. Int J Mol Sci 2020; 21:ijms21072648. [PMID: 32290321 PMCID: PMC7177584 DOI: 10.3390/ijms21072648] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
The PR/SET domain family (PRDM) comprise a family of genes whose protein products share a conserved N-terminal PR [PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1)] homologous domain structurally and functionally similar to the catalytic SET [Su(var)3-9, enhancer-of-zeste and trithorax] domain of histone methyltransferases (HMTs). These genes are involved in epigenetic regulation of gene expression through their intrinsic HMTase activity or via interactions with other chromatin modifying enzymes. In this way they control a broad spectrum of biological processes, including proliferation and differentiation control, cell cycle progression, and maintenance of immune cell homeostasis. In cancer, tumor-specific dysfunctions of PRDM genes alter their expression by genetic and/or epigenetic modifications. A common characteristic of most PRDM genes is to encode for two main molecular variants with or without the PR domain. They are generated by either alternative splicing or alternative use of different promoters and play opposite roles, particularly in cancer where their imbalance can be often observed. In this scenario, PRDM proteins are involved in cancer onset, invasion, and metastasis and their altered expression is related to poor prognosis and clinical outcome. These functions strongly suggest their potential use in cancer management as diagnostic or prognostic tools and as new targets of therapeutic intervention.
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Affiliation(s)
- Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maria Chiara Proto
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Bruno Moncharmont
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
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19
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Chaudhary R, Wang X, Cao B, De La Iglesia J, Masannat J, Song F, Hernandez-Prera JC, Gimbrone NT, Slebos RJC, Chung CH. Long noncoding RNA, LINC00460, as a prognostic biomarker in head and neck squamous cell carcinoma (HNSCC). Am J Transl Res 2020; 12:684-696. [PMID: 32194915 PMCID: PMC7061833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive epithelial malignancy characterized by frequent mutations and metastasis. Long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis and serve as novel prognostic biomarkers in different cancers. To enhance our understanding of lncRNAs that may have biological significance in HNSCC and may serve as prognostic biomarkers, we globally profiled lncRNAs in HNSCC by analyzing the RNA-seq data from The Atlas of Noncoding RNAs in Cancer (TANRIC) database. Of 3576 lncRNAs, we identified 926 (higher-688, lower-238) lncRNAs with a 2-fold abundance difference among the forty HNSCC and paired adjacent normal tissue. We investigated differential abundance of lncRNAs based on TP53 mutation and p16 status. We found 133 lncRNAs to have differential abundance by 2-fold among the mutant vs wild-type TP53 samples, whereas among p16-negative vs positive samples, we identified 710 lncRNAs with the same criteria. Meanwhile, analysis of the 15 most abundant lncRNAs in the tumor samples identified five lncRNAs whose higher abundance was associated with poor overall patient survival. Among these five, higher abundance of LINC00460 associated with poor patient survival in an independent cohort of 82 HNSCC patients. To further evaluate the potential function of LINC00460, we performed lncRNA-mRNAs co-expression analysis and found that higher abundance of LINC00460 associated with cancer-related biological pathways including EMT and other inflammatory response pathways. In summary, we report LINC00460 is more abundant in tumors compared to adjacent normal tissue and that it may serve as a potential prognostic biomarker in HNSCC.
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Affiliation(s)
- Ritu Chaudhary
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, Moffitt Cancer CenterTampa, FL, USA
| | - Biwei Cao
- Department of Biostatistics and Bioinformatics, Moffitt Cancer CenterTampa, FL, USA
| | - Janis De La Iglesia
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Jude Masannat
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Feifei Song
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | | | - Nicholas T Gimbrone
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Robbert JC Slebos
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
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20
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Ghafouri-Fard S, Mohammad-Rahimi H, Jazaeri M, Taheri M. Expression and function of long non-coding RNAs in head and neck squamous cell carcinoma. Exp Mol Pathol 2020; 112:104353. [DOI: 10.1016/j.yexmp.2019.104353] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022]
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21
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Serafini MS, Lopez-Perez L, Fico G, Licitra L, De Cecco L, Resteghini C. Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures. CANCERS OF THE HEAD & NECK 2020; 5:2. [PMID: 31988797 PMCID: PMC6971871 DOI: 10.1186/s41199-020-0047-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 02/06/2023]
Abstract
For many years, head and neck squamous cell carcinoma (HNSCC) has been considered as a single entity. However, in the last decades HNSCC complexity and heterogeneity have been recognized. In parallel, high-throughput omics techniques had allowed picturing a larger spectrum of the behavior and characteristics of molecules in cancer and a large set of omics web-based tools and informative repository databases have been developed. The objective of the present review is to provide an overview on biological, prognostic and predictive molecular signatures in HNSCC. To contextualize the selected data, our literature survey includes a short summary of the main characteristics of omics data repositories and web-tools for data analyses. The timeframe of our analysis was fixed, encompassing papers published between January 2015 and January 2019. From more than 1000 papers evaluated, 61 omics studies were selected: 33 investigating mRNA signatures, 11 and 13 related to miRNA and other non-coding-RNA signatures and 4 analyzing DNA methylation signatures. More than half of identified signatures (36) had a prognostic value but only in 10 studies selection of a specific anatomical sub-site (8 oral cavity, 1 oropharynx and 1 both oral cavity and oropharynx) was performed. Noteworthy, although the sample size included in many studies was limited, about one-half of the retrieved studies reported an external validation on independent dataset(s), strengthening the relevance of the obtained data. Finally, we highlighted the development and exploitation of three gene-expression signatures, whose clinical impact on prognosis/prediction of treatment response could be high. Based on this overview on omics-related literature in HNSCC, we identified some limits and strengths. The major limits are represented by the low number of signatures associated to DNA methylation and to non-coding RNA (miRNA, lncRNA and piRNAs) and the availability of a single dataset with multiple omics on more than 500 HNSCC (i.e. TCGA). The major strengths rely on the integration of multiple datasets through meta-analysis approaches and on the growing integration among omics data obtained on the same cohort of patients. Moreover, new approaches based on artificial intelligence and informatic analyses are expected to be available in the next future.
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Affiliation(s)
- Mara S Serafini
- 1Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Laura Lopez-Perez
- 2Life Supporting Technologies, Universidad Politécnica de Madrid, Madrid, Spain
| | - Giuseppe Fico
- 2Life Supporting Technologies, Universidad Politécnica de Madrid, Madrid, Spain
| | - Lisa Licitra
- 3Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy.,4University of Milan, Milan, Italy
| | - Loris De Cecco
- 1Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Carlo Resteghini
- 3Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
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22
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Muhammad A, Waheed R, Khan NA, Jiang H, Song X. piRDisease v1.0: a manually curated database for piRNA associated diseases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5527147. [PMID: 31267133 PMCID: PMC6606758 DOI: 10.1093/database/baz052] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/27/2022]
Abstract
In recent years, researches focusing on PIWI-interacting RNAs (piRNAs) have increased rapidly. It has been revealed that piRNAs have strong association with a wide range of diseases; thus, it becomes very important to understand piRNAs’ role(s) in disease diagnosis, prognosis and assessment of treatment response. We searched more than 2500 articles using keywords, such as `PIWI-interacting RNAs’ and `piRNAs’, and further scrutinized the articles to collect piRNAs-disease association data. These data are highly complex and heterogeneous due to various types of piRNA idnetifiers (IDs) and different reference genome versions. We put considerable efforts into removing redundancy and anomalies and thus homogenized the data. Finally, we developed the piRDisease database, which incorporates experimentally supported data for piRNAs’ relationship with wide range of diseases. The piRDisease (piRDisease v1.0) is a novel, comprehensive and exclusive database resource, which provides 7939 manually curated associations of experimentally supported 4796 piRNAs involved in 28 diseases. piRDisease facilitates users by providing detailed information of the piRNA in respective disease, explored by experimental support, brief description, sequence and location information. Considering piRNAs’ role(s) in wide range of diseases, it is anticipated that huge amount of data would be produced in the near future. We thus offer a submitting page, on which users or researches can contribute in to update our piRDisease database.
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Affiliation(s)
- Azhar Muhammad
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China.,Department of Biosciences, COMSATS University Islamabad, Sahiwal 57000, Pakistan
| | - Ramay Waheed
- Pattern Recognition and Information Retrieval lab, University of Science and Technology Beijing, Beijing 100083, China
| | - Nauman Ali Khan
- Key Laboratory of Wireless Optical Communication, Chinese Academy of Sciences, University of Science and Technology China, Hefei 230026, China
| | - Hong Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Xiaoyuan Song
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
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23
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Shao B, Fu X, Li X, Li Y, Gan N. RP11-284F21.9 promotes oral squamous cell carcinoma development via the miR-383-5p/MAL2 axis. J Oral Pathol Med 2019; 49:21-29. [PMID: 31397491 DOI: 10.1111/jop.12946] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Increasing evidence suggests that dysregulated long non-coding RNAs (lncRNAs) are involved in tumorigenesis and progression. RP11-284F21.9, one of the temporally expressed S-phase lncRNAs in cancer cells, was recently identified by nascent RNA capture sequencing. METHODS Cal-27, Tca8113, SCC-9, HB56, and oral squamous cell carcinoma (OSCC) tissues were used in the experiment. RNA extraction, qRT-PCR, plasmid construction, cell proliferation, EdU labeling, Transwell migration, luciferase reporter, and western blotting were used to investigate the exact role and function of RP11-284F21.9 in cancer. RESULTS RP11-284F21.9 was upregulated in human OSCC samples and cell lines. RP11-284F21.9 depletion suppressed the proliferation, migration, and invasion of OSCC cell lines. There was interaction between RP11-284F21.9, miR-383-5p, and MAL2. Increased MAL2 and decreased miR-383-5p expression were also detected in OSCC tissues and cell lines. In addition, RP11-284F21.9 knockdown could reduce MAL2 expression, while miR-383-5p inhibitors abolished this repressive effect. RP11-284F21.9 acted as a competing endogenous RNA (ceRNA) of miR-383-5p, leading to MAL2 upregulation, and subsequently promoted OSCC progression. CONCLUSION RP11-284F21.9/miR-383-5p represents a novel and potential therapeutic target for the treatment of OSCC.
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Affiliation(s)
- Bingyi Shao
- Department of Operative Dentistry and Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaohui Fu
- Department of General Dentistry, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Xian Li
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Li
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Ning Gan
- Department of Operative Dentistry and Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
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24
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Li T, Qin Y, Zhen Z, Shen H, Cong T, Schiferle E, Xiao S. Long non-coding RNA HOTAIR/microRNA-206 sponge regulates STC2 and further influences cell biological functions in head and neck squamous cell carcinoma. Cell Prolif 2019; 52:e12651. [PMID: 31297902 PMCID: PMC6797510 DOI: 10.1111/cpr.12651] [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: 11/06/2018] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 12/23/2022] Open
Abstract
Objective It is essential to characterize underlying molecular mechanism associated with head and neck squamous cell carcinoma (HNSCC) and identify promising therapeutic targets. Herein, we explored role of homeobox transcript antisense RNA (HOTAIR) in HNSCC to regulate stanniocalcin‐2 (STC2) by sponging microRNA‐206 (miR‐206). Methods HNSCC‐related differentially expressed genes and regulation network amongst HOTAIR, miR‐206 and STC2 were identified. Next, effect of HOTAIR on cell biological functions of HNSCC was identified after transfection of cells with HOTAIR overexpressed plasmids or siRNA against HOTAIR. PI3K/AKT signalling pathway‐related gene expression was measured after miR‐206 and STC2 were suppressed. Cell invasion, migration and proliferation were assessed. Finally, tumour growth was assessed to determine the effects of HOTAIR/miR‐206/STC2 axis in vivo. Results HOTAIR specifically bound to miR‐206 and miR‐206 targeted STC2. Downregulated HOTAIR or upregulated miR‐206 suppressed HNSCC cell proliferation, invasion and migration. miR‐206 inhibited PI3K/AKT signalling pathway by down‐regulating STC2. Besides, silenced HOTAIR or overexpressed miR‐206 repressed the tumour growth of nude mice with HNSCC. Conclusion HOTAIR regulated HNSCC cell biological functions by binding to miR‐206 through STC2.
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Affiliation(s)
- Tiancheng Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Yao Qin
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Zhen Zhen
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Hong Shen
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Tiechuan Cong
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Erik Schiferle
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shuifang Xiao
- Department of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
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25
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Sun T, Han X. The disease-related biological functions of PIWI-interacting RNAs (piRNAs) and underlying molecular mechanisms. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-019-0021-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Yu Y, Xiao J, Hann SS. The emerging roles of PIWI-interacting RNA in human cancers. Cancer Manag Res 2019; 11:5895-5909. [PMID: 31303794 PMCID: PMC6612017 DOI: 10.2147/cmar.s209300] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a type of non-coding RNAs that interact with PIWI proteins, which are members of the argonaute family. Originally described in the germline, piRNAs are also expressed in human somatic cells in a tissue-specific manner. piRNAs are involved in spermatogenesis, germ stem-cell maintenance, silencing of transposon, epigenetic and genomic regulation and rearrangement. A large number of studies have demonstrated that expression of piRNAs is involved in many kinds of disease, including cancer. Abnormal expression of piRNAs is emerging as a critical player in cancer cell proliferation, apoptosis, invasion, and migration in vitro and in vivo. Functionally, piRNAs maintain genomic integrity by repressing the mobilization of transposable elements, and regulate the expression of downstream target genes via transcriptional or post-transcriptional mechanisms. Furthermore, altered expression of piRNAs in cancer is linked to clinical outcome, highlighting the important role that they may play as novel diagnostic and prognostic biomarkers, and as therapeutic targets for cancer therapy. In this review, we focus on the biogenesis and the functional roles of piRNAs in cancers, discuss emerging insights into the roles of piRNAs in the occurrence, progression, and treatment of cancers, reveal various mechanisms underlying piRNAs-mediated gene regulation, and highlight their potential clinical utilities as biomarkers as well as potential targets for cancer treatment.
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Affiliation(s)
- Yaya Yu
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine , Guangzhou, Guangdong Province, 510120, People's Republic of China
| | - Jing Xiao
- Department of Gynecology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, People's Republic of China
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine , Guangzhou, Guangdong Province, 510120, People's Republic of China.,Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, People's Republic of China
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27
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Zhang ZL, Zhao LJ, Xu L, Chai L, Wang F, Xu YP, Zhou SH, Fu Y. Transcriptomic model-based lncRNAs and mRNAs serve as independent prognostic indicators in head and neck squamous cell carcinoma. Oncol Lett 2019; 17:5536-5544. [PMID: 31186775 PMCID: PMC6507369 DOI: 10.3892/ol.2019.10213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/06/2017] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSC) is one of most common types of cancer worldwide, and mRNAs and long non-coding RNAs (lncRNAs) have been identified as prognostic biomarkers in HNSC. In the present study, using gene expression datasets from multiple platforms, survival-associated genes in HNSC were identified. Subsequently, a combination of 17 genes (14 mRNAs and 3 lncRNA) was optimized using random forest variable hunting and a risk score model for HNSC prognosis was developed using a cohort from The Cancer Genome Atlas. Patients with high-risk scores tend to have earlier disease recurrence and lower survival rates, compared with those with low-risk scores. This observation was further validated in three independent datasets (GSE41613, GSE10300 and E-MTAB-302). Association analysis revealed that the risk score is independent of other clinicopathological observations. On the basis of the results depicted in the nomogram, the risk score performs better in 3-year survival rate prediction than other clinical observations. In summary, the lncRNA-mRNA signature-based risk score successfully predicts the survival of HNSC and serves as an indicator of prognosis.
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Affiliation(s)
- Zhi-Li Zhang
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Li-Jing Zhao
- Ear, Nose and Throat Department, The Second Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Lin Xu
- Ear, Nose and Throat Department, The Second Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Liang Chai
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Feng Wang
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Ya-Ping Xu
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Shui-Hong Zhou
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Yong Fu
- Ear, Nose and Throat Department, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, P.R. China
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28
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Wu H, Yu DH, Wu MH, Huang T. Long non-coding RNA LOC541471: A novel prognostic biomarker for head and neck squamous cell carcinoma. Oncol Lett 2018; 17:2457-2464. [PMID: 30675311 DOI: 10.3892/ol.2018.9831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 09/14/2018] [Indexed: 12/26/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive cancer. Early detection and management of HNSCC may prevent progression of the disease. Long non-coding RNAs (lncRNAs) may serve as prognostic biomarkers for various cancer types. The current study downloaded an RNA-Seq dataset containing 43 tumor-normal pairs. An independent t-test identified that the expression level of lncRNA LOC541471 was significantly increased in tumor tissues compared with healthy tissues. Additionally, the current study demonstrated that high lncRNA LOC541471 expression was significantly associated with increasing lymph node metastasis classification and perineural invasion. A multivariate Cox regression analysis revealed that high lncRNA LOC541471 expression levels were an independent predictor for reduced overall survival (n=487) and relapse-free survival (n=355). According to the anatomic neoplasm subdivision, HNSCC samples were classified as oropharyngeal carcinoma (n=297), oral carcinoma (n=80), laryngeal carcinoma and hypopharyngeal carcinoma (n=123). A negative association was revealed between lncRNA LOC541471 expression and overall survival in all subtypes of HNSCC. Therefore, lncRNA LOC541471 is significantly negatively associated with overall survival and relapse-free survival of patients with HNSCC and may be considered a potential prognostic factor for HNSCC.
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Affiliation(s)
- Hua Wu
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Da Hai Yu
- Department of Radiation Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China.,Department of Radiation Oncology, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Mian Hua Wu
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Teng Huang
- Department of Radiation Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China.,Department of Radiation Oncology, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
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29
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Cao Y, Shi Q, Wei B, Mu Y, Li J, Chen F, Yu D. Early discovery of disseminated tumor cells during carcinogenesis in a 4NQO-induced mouse model of oral squamous cell carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3328-3337. [PMID: 31949709 PMCID: PMC6962884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/20/2018] [Indexed: 06/10/2023]
Abstract
OBJECTIVES Heterogeneous cells appear in multiple organs during the same time period as the primary lesion of some tumors is clinically detected. These heterogeneous cells are also known as disseminated tumor cells (DTCs). However, the characteristics of DTCs that disseminate during oral carcinogenesis remain unclear. MATERIALS AND METHODS A mouse 4NQO model of lymph node metastasis in oral squamous cell carcinoma was established. Tissue samples of the tongue, bone marrow and submandibular lymph node were collected. Five stages (stage 0~stage IV) of carcinogenesis in each experimental animal were classified by two pathologists. After immunohistochemical staining of cytokeratin, the DTCs were isolated from bone marrow samples (stage II) by the laser capture microdissection (LCM) technique during oral carcinogenesis. Genomic amplification of bone marrow DTCs was performed, and homozygous deletion of the RB1CC1 gene was analyzed. After confirming the presence of disseminated tumor cells in stage II bone marrow samples, a comprehensive study among various stages of lymph node tissue was conducted using the same method. RESULTS DTCs that spread from the primary tumor were discovered in stage II bone marrow samples and in stage I, stage II and stage III submandibular lymph node samples through immunohistochemical staining. These spreading cells had different levels of homozygous exon deletion in the RB1CC1 and TP53 genes. CONCLUSION Early spreading of epithelial cells may occur during the carcinogenesis of oral cancer. DTCs of oral carcinoma may show different chromosome aberrations from matched primary tumor cells.
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Affiliation(s)
- Yong Cao
- College of Stomatology, Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Qiang Shi
- College of Stomatology, Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Baosheng Wei
- College of Stomatology, Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Yun Mu
- College of Stomatology, Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Jing Li
- Department of Stomatology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Fengqiang Chen
- College of Stomatology, Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Dahai Yu
- Department of Stomatology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi, P. R. China
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30
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Zheng M, Liu X, Zhou Q, Liu G. HOTAIRM1 competed endogenously with miR-148a to regulate DLGAP1 in head and neck tumor cells. Cancer Med 2018; 7:3143-3156. [PMID: 29905017 PMCID: PMC6051240 DOI: 10.1002/cam4.1523] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 01/07/2023] Open
Abstract
This study is aimed to explore the regulatory effect of lncRNA HOTAIR/miR-148a/DLGAP1 axis on head and neck tumor (HNT) cell growth, cell mobility, and invasiveness. HOTAIRM1, miR-148a, and DLGAP1 level in HNT tissues and adjacent normal tissues were measured by qRT-PCR. Cell Counting Kit-8 (CCK-8) and Transwell (migration and invasion) assay were used to survey the influence of HOTAIRM1, miR-148a, and DLGAP1 on Fadu cells. Nude mouse xenograft was utilized to validate the influence of HOTAIRM1 in vivo. Dual-luciferase reporter assay confirms the relationship between HOTAIRM1 and miR-148a, miR-148a, and DLGAP1. The expression level of HOTAIRM1 was downregulated in human HNT tissues and cells. Overexpression of HOTAIRM1 significantly moderated Fadu cells proliferation, apoptosis, migration, and invasion in vitro and impaired the tumorigenesis in vivo. The expression level of miR-148a was upregulated in human HNT tissue compared to the adjacent tissues. We identified that miR-148a was a target of HOTAIRM1 and its expression levels were reduced by HOTAIRM1. Transfection of miR-148a mimics increased proliferation, migration, and invasion of Fadu cells. DLGAP1 was identified as a novel target of miR-148a and its expression level was promoted by either HOTAIRM1 overexpression or miR-148a knockdown. Overexpression of DLGAP1 also facilitated the cell viability and metastasis of Fadu cells. HOTAIRM1 was confirmed as a tumor suppressor via sponging miR-148a and promote the expression of DLGAP1, which could be regarded as an important target for the prevention and treatment of HNT.
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Affiliation(s)
- Mei Zheng
- Department of Traditional Chinese MedicineQianfoshan Hospital Affiliated to Shandong UniversityJi'nan250014ShandongChina
| | - Xingguang Liu
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyShandong UniversityJi'nan250012ShandongChina
| | - Qin Zhou
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyShandong UniversityJi'nan250012ShandongChina
| | - Gangli Liu
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyShandong UniversityJi'nan250012ShandongChina
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31
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Koshizuka K, Hanazawa T, Arai T, Okato A, Kikkawa N, Seki N. Involvement of aberrantly expressed microRNAs in the pathogenesis of head and neck squamous cell carcinoma. Cancer Metastasis Rev 2018; 36:525-545. [PMID: 28836104 DOI: 10.1007/s10555-017-9692-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that act as fine-tuners of the post-transcriptional control of protein-coding or noncoding RNAs by repressing translation or cleaving RNA transcripts in a sequence-dependent manner in cells. Accumulating evidence have been indicated that aberrantly expressed miRNAs are deeply involved in human pathogenesis, including cancers. Surprisingly, these small, single-stranded RNAs (18-23 nucleotides) have been shown to function as antitumor or oncogenic RNAs in several types of cancer cells. A single miRNA has regulating hundreds or thousands of different mRNAs, and individual mRNA has been regulated by multiple different miRNAs in normal cells. Therefore, tightly controlled RNA networks can be disrupted by dysregulated of miRNAs in cancer cells. Investigation of novel miRNA-mediated RNA networks in cancer cells could provide new insights in the field of cancer research. In this review, we focus on head and neck squamous cell carcinoma (HNSCC) and discuss current findings of the involvement of aberrantly expressed miRNAs in the pathogenesis of HNSCC.
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Affiliation(s)
- Keiichi Koshizuka
- Department of Functional Genomics, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.,Department of Otorhinolaryngology/Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Atsushi Okato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Naoko Kikkawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
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32
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Feng L, Houck JR, Lohavanichbutr P, Chen C. Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa. Oncotarget 2018; 8:31521-31531. [PMID: 28415559 PMCID: PMC5458226 DOI: 10.18632/oncotarget.16358] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/09/2017] [Indexed: 01/09/2023] Open
Abstract
Oral cavity and oropharyngeal squamous cell carcinoma (OSCC) is a major cancer type in the head and neck region. To better understand the roles long non-coding RNA (lncRNA) play in OSCC carcinogenesis, we compared the expression levels of 3,054 probe sets for lncRNAs between 167 OSCCs and 45 healthy oral mucosa using an Affymetrix HG U133 plus 2.0 array dataset. We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change. We further validated the top differentially expressed lncRNAs in three independent datasets from Gene Expression Omnibus (GEO) repository: GSE42743, GSE9844, and GSE6791. Fourteen lncRNAs (15 probe sets) were validated in all three datasets using the criteria FDR < 0.01: LOC441178, C5orf66-AS1, HCG22, FLG-AS1, CCL14/CCL15-CCL14, LOC100506990, TRIP10, PCBP1-AS1, LINC01315, LINC00478, COX10-AS1/LOC100506974, MLLT4-AS1, MIR31HG, and DUXAP10/LINC01296. Three lncRNAs in the validated list which showed the highest fold change (LOC441178, HCG22 and C5orf66-AS1) were verified by quantitative RT-PCR in a subset of 20 OSCCs and 10 control samples. In silico prediction of their functional role has given us directions for further investigation.
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Affiliation(s)
- Lu Feng
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Head and Neck Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
| | - John R Houck
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pawadee Lohavanichbutr
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Department of Otolaryngology, Head and Neck Surgery, University of Washington, Seattle, Washington, USA
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33
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Haque SU, Niu L, Kuhnell D, Hendershot J, Biesiada J, Niu W, Hagan MC, Kelsey KT, Casper KA, Wise-Draper TM, Medvedovic M, Langevin SM. Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma. Head Neck 2018; 40:1555-1564. [PMID: 29575229 DOI: 10.1002/hed.25136] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/30/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) has emerged as a new avenue of interest due to its various biological functions in cancer. Abnormal expression of lncRNA has been reported in other malignancies but has been understudied in head and neck squamous cell carcinoma (HNSCC). METHODS The lncRNA expression was interrogated via quantitative real-time polymerase chain reaction (qRT-PCR) array for 19 human papillomavirus (HPV)-negative HNSCC tumor-normal pairs. The Cancer Genome Atlas (TCGA) was used to validate these results. The association between differentially expressed lncRNA and survival outcomes was analyzed. RESULTS Differential expression was validated for 5 lncRNA (SPRY4-IT1, HEIH, LUCAT1, LINC00152, and HAND2-AS1). There was also an inverse association between MEG3 expression (not significantly differentially expressed in TCGA tumors but highly variable expression) and 3-year recurrence-free survival (RFS). CONCLUSION We identified and validated differential expression of 5 lncRNA in HPV-negative HNSCC. Low MEG3 expression was associated with favorable 3-year RFS, although the significance of this finding remains unclear.
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Affiliation(s)
- Sulsal-Ul Haque
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Liang Niu
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Damaris Kuhnell
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacob Hendershot
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacek Biesiada
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Wen Niu
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Matthew C Hagan
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Keith A Casper
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan
| | - Trisha M Wise-Draper
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, Cincinnati, Ohio.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
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Lu M, Xu X, Xi B, Dai Q, Li C, Su L, Zhou X, Tang M, Yao Y, Yang J. Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma. Genes (Basel) 2018; 9:E44. [PMID: 29351231 PMCID: PMC5793195 DOI: 10.3390/genes9010044] [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: 12/12/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 12/14/2022] Open
Abstract
RNAs may act as competing endogenous RNAs (ceRNAs), a critical mechanism in determining gene expression regulations in many cancers. However, the roles of ceRNAs in thyroid carcinoma remains elusive. In this study, we have developed a novel pipeline called Molecular Network-based Identification of ceRNA (MNIceRNA) to identify ceRNAs in thyroid carcinoma. MNIceRNA first constructs micro RNA (miRNA)-messenger RNA (mRNA)long non-coding RNA (lncRNA) networks from miRcode database and weighted correlation network analysis (WGCNA), based on which to identify key drivers of differentially expressed RNAs between normal and tumor samples. It then infers ceRNAs of the identified key drivers using the long non-coding competing endogenous database (lnCeDB). We applied the pipeline into The Cancer Genome Atlas (TCGA) thyroid carcinoma data. As a result, 598 lncRNAs, 1025 mRNAs, and 90 microRNA (miRNAs) were inferred to be differentially expressed between normal and thyroid cancer samples. We then obtained eight key driver miRNAs, among which hsa-mir-221 and hsa-mir-222 were key driver RNAs identified by both miRNA-mRNA-lncRNA and WGCNA network. In addition, hsa-mir-375 was inferred to be significant for patients' survival with 34 associated ceRNAs, among which RUNX2, DUSP6 and SEMA3D are known oncogenes regulating cellular proliferation and differentiation in thyroid cancer. These ceRNAs are critical in revealing the secrets behind thyroid cancer progression and may serve as future therapeutic biomarkers.
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Affiliation(s)
- Minjia Lu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Xingyu Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Baohang Xi
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Qi Dai
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Chenli Li
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
| | - Li Su
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
| | - Xiaonan Zhou
- Institute of Basic Medical Sciences, Wannan Medical College, Hefei 241000, China.
| | - Min Tang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA.
| | - Yuhua Yao
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
| | - Jialiang Yang
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA.
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35
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Song W, Sun Y, Lin J, Bi X. Current research on head and neck cancer-associated long noncoding RNAs. Oncotarget 2018; 9:1403-1425. [PMID: 29416703 PMCID: PMC5787447 DOI: 10.18632/oncotarget.22608] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023] Open
Abstract
Head and neck cancers (HNC) are one of the ten leading cancers worldwide, including a range of malignant tumors arising from the upper neck. Due to the complex mechanisms of HNC and lack of effective biomarkers, the 5-year survival rate of HNC has been low and the mortality rate has been high in recent decades. Long noncoding RNAs (lncRNAs), noncoding RNAs longer than 200 bps, are a focus of current cancer research, closely related to tumor biology. LncRNAs have been revealed to be aberrantly expressed in various types of HNC, and the dysregulated lncRNAs participate in HNC progression and induce malignant behavior by modulating gene expression at diverse levels. This review will focus on the functions and molecular mechanisms of dysregulated lncRNAs in HNC tumorigenesis and progression, as well as their diagnostic, therapeutic or prognostic implications in HNC.
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Affiliation(s)
- Wei Song
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yimin Sun
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jie Lin
- Department of Dental Anesthesiology, West China Hospital of Stomatology, State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaoqin Bi
- Department of Head and Neck Oncology, West China Hospital of Stomatology, State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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36
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Nunez Lopez YO, Victoria B, Golusinski P, Golusinski W, Masternak MM. Characteristic miRNA expression signature and random forest survival analysis identify potential cancer-driving miRNAs in a broad range of head and neck squamous cell carcinoma subtypes. Rep Pract Oncol Radiother 2018; 23:6-20. [PMID: 29187807 PMCID: PMC5698002 DOI: 10.1016/j.rpor.2017.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/27/2017] [Accepted: 10/22/2017] [Indexed: 12/13/2022] Open
Abstract
AIM To characterize the miRNA expression profile in head and neck squamous cell carcinoma (HNSSC) accounting for a broad range of cancer subtypes and consequently identify an optimal miRNA signature with prognostic value. BACKGROUND HNSCC is consistently among the most common cancers worldwide. Its mortality rate is about 50% because of the characteristic aggressive behavior of these cancers and the prevalent late diagnosis. The heterogeneity of the disease has hampered the development of robust prognostic tools with broad clinical utility. MATERIALS AND METHODS The Cancer Genome Atlas HNSC dataset was used to analyze level 3 miRNA-Seq data from 497 HNSCC patients. Differential expression (DE) analysis was implemented using the limma package and multivariate linear model that adjusted for the confounding effects of age at diagnosis, gender, race, alcohol history, anatomic neoplasm subdivision, pathologic stage, T and N stages, and vital status. Random forest (RF) for survival analysis was implemented using the randomForestSRC package. RESULTS A characteristic DE miRNA signature of HNSCC, comprised of 11 upregulated (i.e., miR-196b-5p, miR-1269a, miR-196a-5p, miR-4652-3p, miR-210-3p, miR-1293, miR-615-3p, miR-503-5p, miR-455-3p, miR-205-5p, and miR-21-5p) and 9 downregulated (miR-376c-3p, miR-378c, miR-29c-3p, miR-101-3p, miR-195-5p, miR-299-5p, miR-139-5p, miR-6510-3p, miR-375) miRNAs was identified. An optimal RF survival model was built from seven variables including age at diagnosis, miR-378c, miR-6510-3p, stage N, pathologic stage, gender, and race (listed in order of variable importance). CONCLUSIONS The joint differential miRNA expression and survival analysis controlling for multiple confounding covariates implemented in this study allowed for the identification of a previously undetected prognostic miRNA signature characteristic of a broad range of HNSCC.
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Affiliation(s)
- Yury O. Nunez Lopez
- Translational Research Institute for Metabolism & Diabetes, Florida Hospital, 301 East Princeton St., Orlando, FL 32804, USA
| | - Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL 32827, USA
| | - Pawel Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL 32827, USA
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
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37
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Guglas K, Bogaczyńska M, Kolenda T, Ryś M, Teresiak A, Bliźniak R, Łasińska I, Mackiewicz J, Lamperska K. lncRNA in HNSCC: challenges and potential. Contemp Oncol (Pozn) 2017; 21:259-266. [PMID: 29416430 PMCID: PMC5798417 DOI: 10.5114/wo.2017.72382] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 01/17/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cause of cancer mortality in the world. Some progress has been made in the therapy of HNSCC, however treatment remains unsatisfactory. Recent studies have shown that different types of long non-coding RNAs (lncRNAs) are dysregulated in HNSCC and correlate with tumor progression, lymph node metastasis, clinical stage and poor prognosis. lncRNAs are a class of functional RNA molecules that can not be translated into proteins but can modulate the activity of transcription factors or regulate changes in chromatin structure. The lncRNAs might have potential of biomarker in HNSCC diagnosis, prognosis, prediction and targeted treatment. In this review we describe the potential role of lncRNAs as new biomarkers and discuss their features including source of origin, extraction methods, stability, detection methods and data normalization and potential function as biomarkers in HNSCC.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Bogaczyńska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- HAN University of Applied Sciences, Nijmegen, Netherlands
| | - Tomasz Kolenda
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Marcel Ryś
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
- Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
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38
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Krishnan AR, Qu Y, Li PX, Zou AE, Califano JA, Wang-Rodriguez J, Ongkeko WM. Computational methods reveal novel functionalities of PIWI-interacting RNAs in human papillomavirus-induced head and neck squamous cell carcinoma. Oncotarget 2017; 9:4614-4624. [PMID: 29435129 PMCID: PMC5797000 DOI: 10.18632/oncotarget.23464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022] Open
Abstract
Human papillomavirus (HPV) infection is the fastest growing cause of head and neck squamous cell carcinoma (HNSCC) today, but its role in malignant transformation remains unclear. This study aimed to conduct a comprehensive investigation of PIWI-interacting RNA (piRNA) alterations and functionalities in HPV-induced HNSCC. Using 77 RNA-sequencing datasets from TCGA, we examined differential expression of piRNAs between HPV16(+) HNSCC and HPV(–) Normal samples, identifying a panel of 30 HPV-dysregulated piRNAs. We then computationally investigated the potential mechanistic significances of these transcripts in HPV-induced HNSCC, identifying our panel of piRNAs to associate with the protein PIWIL4 as well as the RTL family of retrotransposon-like genes, possibly through direct binding interactions. We also recognized several HPV-dysregulated transcripts for their correlations with well-documented mutations and copy number variations in HNSCC as well as HNSCC clinical variables, demonstrating the potential ability of our piRNAs to play important roles in large-scale modulation of HNSCC in addition to their direct, smaller-scale interactions in this malignancy. The differential expression of key piRNAs, including NONHSAT077364, NONHSAT102574, and NONHSAT128479, was verified in vitro by evaluating endogenous expression in HPV(+) cancer vs. HPV(–) normal cell lines. Overall, our novel study provides a rigorous investigation of piRNA dysregulation in HPV-related HNSCC, and lends critical insight into the idea that these small regulatory transcripts may play crucial and previously unidentified roles in tumor pathogenesis and progression.
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Affiliation(s)
- Aswini R Krishnan
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Yuanhao Qu
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Pin Xue Li
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Angela E Zou
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Jessica Wang-Rodriguez
- Veterans Administration San Diego Healthcare System and Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Weg M Ongkeko
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
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39
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Sannigrahi MK, Sharma R, Panda NK, Khullar M. Role of non-coding RNAs in head and neck squamous cell carcinoma: A narrative review. Oral Dis 2017; 24:1417-1427. [PMID: 28941018 DOI: 10.1111/odi.12782] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/23/2017] [Accepted: 09/08/2017] [Indexed: 12/13/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide with high recurrence, metastasis, and poor treatment outcome. Recent studies have reported that non-coding RNA (ncRNA) might play critical role in regulating different types of cancer. MicroRNAs (miRs) are short ncRNAs (20-25 nucleotides) responsible for post-transcriptional regulation of gene expression and may have a role in oncogenesis by acting as oncomiRs or tumor suppressor miRs. Long non-coding RNAs (lncRNAs) are heterogenous group of ncRNAs more than 200 nucleotides long, can act in cis and/or in trans, and have been also implicated in carcinogenesis. These molecules have been suggested to be promising candidates as diagnostic and prognostic biomarkers and for development of novel therapeutic approaches. In this review, we have summarized recent findings on role of these ncRNAs in HPV-negative (HPV-ve) and HPV-positive (HPV+ve) HNSCC. The available literature supports differential expression of both microRNAs and long non-coding RNAs, which include oncogenic ncRNAs (miR-21, miR-31, miR-155, miR-211, HOTAIR, and MALAT1) and tumor suppressor ncRNAs (let7d, miR-17, miR-375, miR-139, and MEG3) in HPV+ve HNSCC tumors as compared to HPV-ve tumors and they have distinct role in the pathophysiology of these two types of HNSCCs.
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Affiliation(s)
- M K Sannigrahi
- Department of Otolaryngology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - R Sharma
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
| | - N K Panda
- Department of Otolaryngology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - M Khullar
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
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40
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Kolenda T, Guglas K, Ryś M, Bogaczyńska M, Teresiak A, Bliźniak R, Łasińska I, Mackiewicz J, Lamperska KM. Biological role of long non-coding RNA in head and neck cancers. Rep Pract Oncol Radiother 2017; 22:378-388. [PMID: 28794691 DOI: 10.1016/j.rpor.2017.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/26/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) are one of the worst prognosis cancers with high mortality of patients. The treatment strategy is primarily based on surgery and radiotherapy but chemotherapy is also used. Every year the knowledge concerning HNSCC biology is updated with new elements such as the recent discovered molecules - long non-coding RNAs. Long non-coding RNAs are involved in regulatory processes in the cells. It has been revealed that the expression levels of lncRNAs are disturbed in tumor cells what results in the acquisition of their specific phenotype. lncRNAs influence cell growth, cell cycle, cell phenotype, migration and invasion ability as well as apoptosis. Development of the lncRNA panel characteristic for HNSCC and validation of specific lncRNA functions are yet to be elucidated. In this work, we collected available data concerning lncRNAs in HNSCC and characterized their biological role. We believe that the tumor examination, in the context of lncRNA expression, may lead to understanding complex biology of the cancer and improve therapeutic methods in the future.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61th Zwirki i Wigury Street, 02-091 Warszawa, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Marcel Ryś
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Marta Bogaczyńska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands
| | - Anna Teresiak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18th Grunwaldzka Street, 60-786 Poznan, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18th Grunwaldzka Street, 60-786 Poznan, Poland.,Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland.,Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15th Garbary Street, 61-866 Poznan, Poland
| | - Katarzyna M Lamperska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
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41
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Krishnan AR, Zheng H, Kwok JG, Qu Y, Zou AE, Korrapati A, Li PX, Califano JA, Hovell MF, Wang-Rodriguez J, Ongkeko WM. A comprehensive study of smoking-specific microRNA alterations in head and neck squamous cell carcinoma. Oral Oncol 2017; 72:56-64. [PMID: 28797462 DOI: 10.1016/j.oraloncology.2017.07.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/16/2017] [Accepted: 07/07/2017] [Indexed: 02/07/2023]
Abstract
OBJECTIVE While tobacco smoking is a well-known risk factor for head and neck squamous cell carcinoma (HNSCC), the molecular mechanisms underlying tobacco-induced HNSCC remain unclear. This study sought to comprehensively identify microRNA (miRNA) alterations and evaluate their clinical relevance in smoking-induced HNSCC pathogenesis and progression. MATERIALS AND METHODS Using small RNA-sequencing data and clinical data from 145 HNSCC patients, we performed a series of differential expression and correlation analyses to identify a panel of tobacco-dysregulated miRNAs associated with key clinical characteristics in HNSCC. We then examined the expression patterns of these miRNAs in normal epithelial cell lines following exposure to cigarette smoke extract. RESULTS Our analyses revealed distinct panels of miRNAs to be dysregulated with smoking status and associated with additional clinical features, including tumor stage, metastasis, anatomic site, and patient survival. The differential expression of key miRNAs, including miR-101, miR-181b, miR-486, and miR-1301, was verified in cigarette-treated epithelial cell lines, suggesting their potential roles in the early development of smoking-related HNSCCs. CONCLUSION Specific alterations in miRNA expression may be traced to tobacco use and are associated with important HNSCC clinical characteristics. Future studies of these miRNAs may be valuable for furthering the understanding and targeted treatment of smoking-associated HNSCC.
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Affiliation(s)
- Aswini R Krishnan
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Hao Zheng
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - James G Kwok
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Yuanhao Qu
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Angela E Zou
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Avinaash Korrapati
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Pin Xue Li
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Joseph A Califano
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Melbourne F Hovell
- Graduate School of Public Health, San Diego State University, San Diego, CA, United States.
| | - Jessica Wang-Rodriguez
- Veterans Administration Medical Center and Department of Pathology, University of California San Diego, La Jolla, CA, United States.
| | - Weg M Ongkeko
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
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42
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de Lena PG, Paz-Gallardo A, Paramio JM, García-Escudero R. Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates. Clin Epigenetics 2017; 9:36. [PMID: 28405244 PMCID: PMC5385094 DOI: 10.1186/s13148-017-0334-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have emerged as key players in a remarkably variety of biological processes and pathologic conditions, including cancer. Next-generation sequencing technologies and bioinformatics procedures predict the existence of tens of thousands of lncRNAs, from which we know the functions of only a handful of them, and very little is known in cancer types such as head and neck squamous cell carcinomas (HNSCCs). RESULTS Here, we use RNAseq expression data from The Cancer Genome Atlas (TCGA) and various statistic and software tools in order to get insight about the lncRNome in HNSCC. Based on lncRNA expression across 426 samples, we discover five distinct tumor clusters that we compare with reported clusters based on various genomic/genetic features. Results demonstrate significant associations between lncRNA-based clustering and DNA methylation, TP53 mutation, and human papillomavirus infection. Using "guilt-by-association" procedures, we infer the possible biological functions of representative lncRNAs of each cluster. Furthermore, we found that lncRNA clustering is correlated with some important clinical and pathologic features, including patient survival after treatment, tumor grade, or sub-anatomical location. CONCLUSIONS We present a landscape of lncRNAs in HNSCC and provide associations with important genotypic and phenotypic features that may help to understand the disease.
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Affiliation(s)
- Pelayo G de Lena
- Molecular Oncology Unit, CIEMAT, Ave Complutense 40 (ed70A), 28040 Madrid, Spain
| | | | - Jesús M Paramio
- Molecular Oncology Unit, CIEMAT, Ave Complutense 40 (ed70A), 28040 Madrid, Spain.,Biomedical Research Institute I+12, University Hospital 12 de Octubre, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT, Ave Complutense 40 (ed70A), 28040 Madrid, Spain.,Biomedical Research Institute I+12, University Hospital 12 de Octubre, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
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43
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Litwin M, Szczepańska-Buda A, Piotrowska A, Dzięgiel P, Witkiewicz W. The meaning of PIWI proteins in cancer development. Oncol Lett 2017; 13:3354-3362. [PMID: 28529570 PMCID: PMC5431467 DOI: 10.3892/ol.2017.5932] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/01/2017] [Indexed: 12/13/2022] Open
Abstract
Cancer is a histologically and genetically heterogeneous population of tumor cells that exhibits distinct molecular profiles determined by epigenetic alterations. P-element-induced wimpy testis (PIWI) proteins in complex with PIWI-interacting RNA (piRNA) have been previously demonstrated to be involved in epigenetic regulation in germline cells. Recently, reactivation of PIWI expression, primarily PIWI-like protein 1 and 2, through aberrant DNA methylation resulting in genomic silencing has been identified in various types of tumors. It has been suggested that the PIWI-piRNA complex contributes to cancer development and progression by promoting a stem-like state of cancer cells, or cancer stem cells (CSCs). It has been identified that CSCs represent the cells that have undergone epithelial-mesenchymal transition (EMT) and acquired metastatic capacities. However, the molecular association between the EMT process and the stem-cell state remains unclear. Further extensive characterization of CSCs in individual types of tumors is required to identify specific markers for the heterogeneous population of CSCs and therefore selectively target CSCs. Previous studies indicate a reciprocal regulation between PIWI proteins and a complex signaling network linking markers characterized for CSCs and transcription factors involved in EMT. In the present review, studies of PIWI function are summarized, and the potential involvement of PIWI proteins in cancer development and progression is discussed.
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Affiliation(s)
- Monika Litwin
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Poland.,Research and Development Centre Novasome Sp. z o.o., 51-423 Wrocław, Poland
| | - Anna Szczepańska-Buda
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Poland.,Research and Development Centre Novasome Sp. z o.o., 51-423 Wrocław, Poland
| | - Aleksandra Piotrowska
- Department of Histology and Embryology, Wrocław Medical University, 50-368 Wrocław, Poland
| | - Piotr Dzięgiel
- Department of Histology and Embryology, Wrocław Medical University, 50-368 Wrocław, Poland.,Department of Physiotherapy and Occupational Therapy in Conservative and Interventional Medicine, 51-612 Wrocław, Poland
| | - Wojciech Witkiewicz
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Poland
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44
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Krishnan AR, Korrapati A, Zou AE, Qu Y, Wang XQ, Califano JA, Wang-Rodriguez J, Lippman SM, Hovell MF, Ongkeko WM. Smoking status regulates a novel panel of PIWI-interacting RNAs in head and neck squamous cell carcinoma. Oral Oncol 2016; 65:68-75. [PMID: 28109471 DOI: 10.1016/j.oraloncology.2016.12.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/30/2016] [Accepted: 12/17/2016] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Smoking remains a primary etiological factor in head and neck squamous cell carcinoma (HNSCC). Given that non-coding RNAs (ncRNAs), including PIWI-interacting RNAs (piRNAs), have emerged as mediators of initiation and progression in head and neck malignancies, we undertook a global study of piRNA expression patterns in smoking-associated HNSCC. MATERIALS AND METHODS Using RNA-sequencing data from 256 current smoker and lifelong nonsmoker samples in The Cancer Genome Atlas (TCGA), we analyzed the differential expression patterns of 27,127 piRNAs across patient cohorts stratified by tobacco use, with HPV16 status and tumor status taken into account. We correlated their expression to clinical characteristics and to smoking-induced alterations of PIWI proteins, the functional counterparts of piRNAs. Finally, we correlated our identified piRNAs and PIWI proteins to known chromosomal aberrations in HNSCC to understand their wider-ranging genomic effects. RESULTS AND CONCLUSION Our analyses implicated a 13-member piRNA panel in smoking-related HNSCC, among which NONHSAT123636 and NONHSAT113708 associated with tumor stage, NONHSAT067200 with patient survival, and NONHSAT081250 with smoking-altered PIWIL1 protein expression. 6 piRNAs as well as PIWIL1 correlated with genomic alterations common to HNSCC, including TP53 mutation, TP53-3p co-occurrence, and 3q26, 8q24, and 11q13 amplification. Collectively, our findings provide novel insights into the etiology-specific piRNA landscape of smoking-induced HNSCC.
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Affiliation(s)
- Aswini R Krishnan
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Avinaash Korrapati
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Angela E Zou
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Yuanhao Qu
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Xiao Qi Wang
- Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Jessica Wang-Rodriguez
- Veterans Administration Medical Center and Department of Pathology, University of California, San Diego, La Jolla, CA, United States.
| | - Scott M Lippman
- Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States.
| | - Melbourne F Hovell
- Graduate School of Public Health, San Diego State University, San Diego, CA, United States.
| | - Weg M Ongkeko
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
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45
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Khandelwal A, Malhotra A, Jain M, Vasquez KM, Jain A. The emerging role of long non-coding RNA in gallbladder cancer pathogenesis. Biochimie 2016; 132:152-160. [PMID: 27894946 DOI: 10.1016/j.biochi.2016.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/24/2016] [Indexed: 02/08/2023]
Abstract
Gallbladder cancer (GBC) is the most common and aggressive form of biliary tract carcinoma with an alarmingly low 5-year survival rate. Despite its high mortality rate, the underlying mechanisms of GBC pathogenesis are not completely understood. Recently, from a growing volume of literature, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression and appear to play vital roles in many human cancers. To date, a number of lncRNAs have been implicated in GBC, but their potential roles in GBC have not been systematically examined. Thus, in this review, we critically discuss the emerging roles of lncRNAs in GBC, and the pathways involved. Specifically, we note that some lncRNAs show greater expression in T1 and T2 tumor stages compared to T3 and T4 tumor stages and that their dysregulation leads to alterations in cell cycle progression and can cause an increase in GBC cell proliferation or apoptosis. In addition, some lncRNAs control the epithelial-mesenchymal transition process, while others take part in the regulation of ERK/MAPK and Ras cancer-associated signaling pathways. We also present their potential utility in diagnosis, prognosis, and/or treatment of GBC. The overall goal of this review is to stimulate interest in the role of lncRNAs in GBC, which may open new avenues in the determination of GBC pathogenesis and may lead to the development of new preventive and therapeutic strategies for GBC.
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Affiliation(s)
- Akanksha Khandelwal
- Centre for Animal Sciences, Central University of Punjab, Bathinda, Punjab, India; Centre for Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Akshay Malhotra
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, HP, India
| | - Manju Jain
- Centre for Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, Austin, TX, 78723, USA
| | - Aklank Jain
- Centre for Animal Sciences, Central University of Punjab, Bathinda, Punjab, India.
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The emerging role of long noncoding RNAs in oral cancer. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 123:235-241. [PMID: 27989708 DOI: 10.1016/j.oooo.2016.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/12/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023]
Abstract
Although less than 3% of the genome encodes proteins, at least 75% of the genome is transcribed into RNAs with no protein-coding potential (noncoding RNAs [ncRNAs]). On the basis of their size and the arbitrary 200 nucleotides cutoff, ncRNAs are classified into long ncRNAs (lncRNAs) or small ncRNAs (including microRNAs). Over the last few years, the role of microRNAs in oral squamous cells carcinoma (OSCC) has been extensively addressed, but the possible role of lncRNAs in OSCC remains unclear. We aimed to explore and discuss the potential role of lncRNAs in OSCC. The detection of lncRNAs in saliva holds promise not only as a noninvasive diagnostic tool in OSCC but also in the early detection of oral cancer recurrence. lncRNAs are promising future therapeutic targets in the OSCC scenario, and research in this field may expand greatly in the next decade.
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