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Ding M, Ran X, Qian S, Zhang Y, Wang Z, Dong M, Yang Z, Wu S, Feng X, Zhang J, Zhu L, Niu S, Zhang X. Clinical and therapeutical significances of the cluster and signature based on oxidative stress for osteosarcoma. Aging (Albany NY) 2023; 15:15360-15381. [PMID: 38180104 PMCID: PMC10781490 DOI: 10.18632/aging.205354] [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: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND It is of great clinical significance to find out the ideal tumor biomarkers and therapeutic targets to improve the prognosis of patients with osteosarcoma (OS). Oxidative stress (OXS) can directly target intracellular macromolecules and exhibit dual effects of tumor promotion and suppression. METHODS OXS-related genes (OXRGs) were extracted from public databases, including TARGET and GEO. Univariate Cox regression analysis, Random Survival Forest algorithm, and LASSO regression were performed to identify prognostic genes and establish the OXS-signature. The efficacy of the OXS-signature was further evaluated by Kaplan-Meier curves and timeROC package. Evaluation of immunological characteristics was achieved based on ESTIMATE algorithm and ssGSEA. Submap algorithm was used to explore the response to anti-PD1 and anti-CTLA4 therapy for OS. Drug response prediction was conducted by using pRRophetic package. The expression values of related genes in the OXS-signature were detected with PCR assays. RESULTS Two OXS-clusters were identified for OS, with remarkable differences of clusters presented in prognosis. Kyoto Encyclopedia of Genes Genomes (KEGG) analysis showed that differentially expressed genes (DEGs) between the OXS-clusters were significantly enriched in several immune-related pathways. Patients with lower OS-scores attained better clinical outcomes, and presented more sensitivity to ICB therapy. By contrast, OS patients with higher OS-scores revealed more sensitivity to certain drugs. Furthermore, critical genes, RHBDL2 and CGREF1 from the model, were significantly higher expressed in OS cell lines. CONCLUSIONS Our study identified the clusters and signature based on OXS, which would lay the foundation for molecular experimental research, disease prevention and treatment of OS.
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Affiliation(s)
- Mengjie Ding
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xianting Ran
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Siyu Qian
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yue Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zeyuan Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Meng Dong
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenzhen Yang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shaoxuan Wu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaoyan Feng
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jieming Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Linan Zhu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Songtao Niu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xudong Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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2
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Arfin S, Kumar D, Lomagno A, Mauri PL, Di Silvestre D. Differentially Expressed Genes, miRNAs and Network Models: A Strategy to Shed Light on Molecular Interactions Driving HNSCC Tumorigenesis. Cancers (Basel) 2023; 15:4420. [PMID: 37686696 PMCID: PMC10563081 DOI: 10.3390/cancers15174420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is among the most common cancer worldwide, accounting for hundreds thousands deaths annually. Unfortunately, most patients are diagnosed in an advanced stage and only a percentage respond favorably to therapies. To help fill this gap, we hereby propose a retrospective in silico study to shed light on gene-miRNA interactions driving the development of HNSCC. Moreover, to identify topological biomarkers as a source for designing new drugs. To achieve this, gene and miRNA profiles from patients and controls are holistically reevaluated using protein-protein interaction (PPI) and bipartite miRNA-target networks. Cytoskeletal remodeling, extracellular matrix (ECM), immune system, proteolysis, and energy metabolism have emerged as major functional modules involved in the pathogenesis of HNSCC. Of note, the landscape of our findings depicts a concerted molecular action in activating genes promoting cell cycle and proliferation, and inactivating those suppressive. In this scenario, genes, including VEGFA, EMP1, PPL, KRAS, MET, TP53, MMPs and HOXs, and miRNAs, including mir-6728 and mir-99a, emerge as key players in the molecular interactions driving HNSCC tumorigenesis. Despite the heterogeneity characterizing these HNSCC subtypes, and the limitations of a study pointing to relationships that could be context dependent, the overlap with previously published studies is encouraging. Hence, it supports further investigation for key molecules, both those already and not correlated to HNSCC.
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Affiliation(s)
- Saniya Arfin
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, Uttrakhand, India; (S.A.); (D.K.)
| | - Dhruv Kumar
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, Uttrakhand, India; (S.A.); (D.K.)
| | - Andrea Lomagno
- Institute for Biomedical Technologies, National Research Council, F.lli Cervi 93, Segrate, 20054 Milan, Italy; (A.L.); (P.L.M.)
- IRCCS Foundation, Istituto Nazionale dei Tumori, Via Venezian, 1, 20133 Milan, Italy
| | - Pietro Luigi Mauri
- Institute for Biomedical Technologies, National Research Council, F.lli Cervi 93, Segrate, 20054 Milan, Italy; (A.L.); (P.L.M.)
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council, F.lli Cervi 93, Segrate, 20054 Milan, Italy; (A.L.); (P.L.M.)
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3
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Abu-Shahba N, Hegazy E, Khan FM, Elhefnawi M. In Silico Analysis of MicroRNA Expression Data in Liver Cancer. Cancer Inform 2023; 22:11769351231171743. [PMID: 37200943 PMCID: PMC10185868 DOI: 10.1177/11769351231171743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/04/2023] [Indexed: 05/20/2023] Open
Abstract
Abnormal miRNA expression has been evidenced to be directly linked to HCC initiation and progression. This study was designed to detect possible prognostic, diagnostic, and/or therapeutic miRNAs for HCC using computational analysis of miRNAs expression. Methods: miRNA expression datasets meta-analysis was performed using the YM500v2 server to compare miRNA expression in normal and cancerous liver tissues. The most significant differentially regulated miRNAs in our study undergone target gene analysis using the mirWalk tool to obtain their validated and predicted targets. The combinatorial target prediction tool; miRror Suite was used to obtain the commonly regulated target genes. Functional enrichment analysis was performed on the resulting targets using the DAVID tool. A network was constructed based on interactions among microRNAs, their targets, and transcription factors. Hub nodes and gatekeepers were identified using network topological analysis. Further, we performed patient data survival analysis based on low and high expression of identified hubs and gatekeeper nodes, patients were stratified into low and high survival probability groups. Results: Using the meta-analysis option in the YM500v2 server, 34 miRNAs were found to be significantly differentially regulated (P-value ⩽ .05); 5 miRNAs were down-regulated while 29 were up-regulated. The validated and predicted target genes for each miRNA, as well as the combinatorially predicted targets, were obtained. DAVID enrichment analysis resulted in several important cellular functions that are directly related to the main cancer hallmarks. Among these functions are focal adhesion, cell cycle, PI3K-Akt signaling, insulin signaling, Ras and MAPK signaling pathways. Several hub genes and gatekeepers were found that could serve as potential drug targets for hepatocellular carcinoma. POU2F1 and PPARA showed a significant difference between low and high survival probabilities (P-value ⩽ .05) in HCC patients. Our study sheds light on important biomarker miRNAs for hepatocellular carcinoma along with their target genes and their regulated functions.
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Affiliation(s)
- Nourhan Abu-Shahba
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
- Stem Cell Research Group, Medical Research Center of Excellence, National Research Centre, Cairo, Egypt
| | - Elsayed Hegazy
- School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Faiz M. Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Mahmoud Elhefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Mahmoud Elhefnawi, Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, 33, elbohouth street, Cairo 11211, Egypt.
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4
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Exploring craniofacial and dental development with microRNAs. Biochem Soc Trans 2022; 50:1897-1909. [DOI: 10.1042/bst20221042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
microRNAs (miRs) are small RNA molecules that regulate many cellular and developmental processes. They control gene expression pathways during specific developmental time points and are required for tissue homeostasis and stem cell maintenance. miRs as therapeutic reagents in tissue regeneration and repair hold great promise and new technologies are currently being designed to facilitate their expression or inhibition. Due to the large amount of miR research in cells and cancer many cellular processes and gene networks have been delineated however, their in vivo response can be different in complex tissues and organs. Specifically, this report will discuss animal developmental models to understand the role of miRs as well as xenograft, disease, and injury models. We will discuss the role of miRs in clinical studies including their diagnostic function, as well as their potential ability to correct craniofacial diseases.
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Arshinchi Bonab R, Asfa S, Kontou P, Karakülah G, Pavlopoulou A. Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach. PeerJ 2022; 10:e14149. [PMID: 36213495 PMCID: PMC9536303 DOI: 10.7717/peerj.14149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/07/2022] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
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Affiliation(s)
- Reza Arshinchi Bonab
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Seyedehsadaf Asfa
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Panagiota Kontou
- Department of Mathematics, University of Thessaly, Lamia, Greece
| | - Gökhan Karakülah
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
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6
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Immune Infiltration-Related ceRNA Network Revealing Potential Biomarkers for Prognosis of Head and Neck Squamous Cell Carcinoma. DISEASE MARKERS 2022; 2022:1014347. [PMID: 36097539 PMCID: PMC9463596 DOI: 10.1155/2022/1014347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022]
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is a frequently lethal malignancy, and the mortality is considerably high. The tumor microenvironment (TME) has been identified as a critical participation in cancer development, treatment, and prognosis. However, competing endogenous RNA (ceRNA) networks grouping with immune/stromal scores of HNSCC patients need to be further illustrated. Therefore, our study aimed to provide clues for searching promising prognostic markers of TME in HNSCC. Materials and Methods ESTIMATE algorithm was used to calculate immune scores and stromal scores of the enrolled HNSCC patients. Differentially expressed genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified by comparing the expression difference between high and low immune/stromal scores. Then, a ceRNA network and protein-protein interaction (PPI) network were constructed for selecting hub regulators. In addition, survival analysis was performed to access the association between immune scores, stromal scores, and differentially expressed RNAs in the ceRNA network and the overall survival (OS) of HNSCC patients. Then, the GSE65858 datasets from Gene Expression Omnibus (GEO) database was used for verification. At last, the difference between the clinical characteristics and immune cell infiltration in different expression groups of IL10RA, PRF1, and IL2RA was analyzed. Results Survival analysis showed a better OS in the high immune score group, and then we constructed a ceRNA network composed of 97 DEGs, 79 DELs and 22 DEMs. Within the ceRNA network, FOXP3, IL10RA, STAT5A, PRF1, IL2RA, miR-148a-3p, miR-3065-3p, and lncRNAs, including CXCR2P1, HNRNPA1P21, CTA-384D8.36, and IGHV1OR15-2, were closely correlated with the OS of HNSCC patients. Especially, using the data from GSE65858, we successfully verified that IL10RA, PRF1, and IL2RA were not only significantly upregulated in patients high immune scores, but also their high expressions were associated with longer survival time. In addition, stratified analysis showed that PRF1 and IL2RA might be involved in the mechanism of tumor progress. Conclusion In conclusion, we constructed a ceRNA network related to the TME of HNSCC, which provides candidates for therapeutic intervention and prognosis evaluation.
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7
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Zheng J, Qian Y, He J, Kang Z, Deng L. Graph Neural Network with Self-Supervised Learning for Noncoding RNA-Drug Resistance Association Prediction. J Chem Inf Model 2022; 62:3676-3684. [PMID: 35838124 DOI: 10.1021/acs.jcim.2c00367] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncoding RNA(ncRNA) is closely related to drug resistance. Identifying the association between ncRNA and drug resistance is of great significance for drug development. Methods based on biological experiments are often time-consuming and small-scale. Therefore, developing computational methods to distinguish the association between ncRNA and drug resistance is urgent. We develop a computational framework called GSLRDA to predict the association between ncRNA and drug resistance in this work. First, the known ncRNA-drug resistance associations are modeled as a bipartite graph of ncRNA and drug. Then, GSLRDA uses the light graph convolutional network (lightGCN) to learn the vector representation of ncRNA and drug from the ncRNA-drug bipartite graph. In addition, GSLRDA uses different data augmentation methods to generate different views for ncRNA and drug nodes and performs self-supervised learning, further improving the quality of learned ncRNA and drug vector representations through contrastive learning between nodes. Finally, GSLRDA uses the inner product to predict the association between ncRNA and drug resistance. To the best of our knowledge, GSLRDA is the first to apply self-supervised learning in association prediction tasks in the field of bioinformatics. The experimental results show that GSLRDA takes an AUC value of 0.9101, higher than the other eight state-of-the-art models. In addition, case studies including two drugs further illustrate the effectiveness of GSLRDA in predicting the association between ncRNA and drug resistance. The code and data sets of GSLRDA are available at https://github.com/JJZ-code/GSLRDA.
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Affiliation(s)
- Jingjing Zheng
- School of Software, Xinjiang University, Urumqi 830091, China
| | - Yurong Qian
- School of Software, Xinjiang University, Urumqi 830091, China
| | - Jie He
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Zerui Kang
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Lei Deng
- School of Software, Xinjiang University, Urumqi 830091, China.,School of Computer Science and Engineering, Central South University, Changsha 410083, China
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8
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Xie Z, Zhong C, Duan S. miR-1269a and miR-1269b: Emerging Carcinogenic Genes of the miR-1269 Family. Front Cell Dev Biol 2022; 10:809132. [PMID: 35252180 PMCID: PMC8894702 DOI: 10.3389/fcell.2022.809132] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/20/2022] [Indexed: 01/15/2023] Open
Abstract
miRNAs play an important role in the occurrence and development of human cancer. Among them, hsa-mir-1269a and hsa-mir-1269b are located on human chromosomes 4 and 17, respectively, and their mature miRNAs (miR-1269a and miR-1269b) have the same sequence. miR-1269a is overexpressed in 9 cancers. The high expression of miR-1269a not only has diagnostic significance in hepatocellular carcinoma and non-small cell lung cancer but also is related to the poor prognosis of cancer patients such as esophageal cancer, hepatocellular carcinoma, and glioma. miR-1269a can target 8 downstream genes (CXCL9, SOX6, FOXO1, ATRX, RASSF9, SMAD7, HOXD10, and VASH1). The expression of miR-1269a is regulated by three non-coding RNAs (RP11-1094M14.8, LINC00261, and circASS1). miR-1269a participates in the regulation of the TGF-β signaling pathway, PI3K/AKT signaling pathway, p53 signaling pathway, and caspase-9-mediated apoptotic pathway, thereby affecting the occurrence and development of cancer. There are fewer studies on miR-1269b compared to miR-1269a. miR-1269b is highly expressed in hepatocellular carcinoma, non-small cell lung cancer, oral squamous cell carcinoma, and pharyngeal squamous cell carcinoma, but miR-1269b is low expressed in gastric cancer. miR-1269b can target downstream genes (METTL3, CDC40, SVEP1, and PTEN) and regulate the PI3K/AKT signaling pathway. In addition, sequence mutations on miR-1269a and miR-1269b can affect their regulation of cancer. The current studies have shown that miR-1269a and miR-1269b have the potential to be diagnostic and prognostic markers for cancer. Future research on miR-1269a and miR-1269b can focus on elucidating more of their upstream and downstream genes and exploring the clinical application value of miR-1269a and miR-1269b.At present, there is no systematic summary of the research on miR-1269a and miR-1269b. This paper aims to comprehensively analyze the abnormal expression, diagnostic and prognostic value, and molecular regulatory pathways of miR-1269a and miR-1269b in multiple cancers. The overview in our work can provide useful clues and directions for future related research.
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Affiliation(s)
- Zijun Xie
- School of Medicine, Zhejiang University City College, Hangzhou, China
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, China
| | - Chenming Zhong
- School of Medicine, Zhejiang University City College, Hangzhou, China
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, China
| | - Shiwei Duan
- School of Medicine, Zhejiang University City College, Hangzhou, China
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, China
- *Correspondence: Shiwei Duan,
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9
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Nunes ADC, Weigl M, Schneider A, Noureddine S, Yu L, Lahde C, Saccon TD, Mitra K, Beltran E, Grillari J, Kirkland JL, Tchkonia T, Robbins PD, Masternak MM. miR-146a-5p modulates cellular senescence and apoptosis in visceral adipose tissue of long-lived Ames dwarf mice and in cultured pre-adipocytes. GeroScience 2021; 44:503-518. [PMID: 34825304 PMCID: PMC8811002 DOI: 10.1007/s11357-021-00490-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are potent regulators of multiple biological processes. Previous studies have demonstrated that miR-146a-5p increases in normal mice during aging, while long-living Ames dwarf (df/df) mice maintain youthful levels of this miRNA. The aim of this study was to elucidate the involvement of miR-146a-5p in modulating cellular senescence and apoptosis in visceral adipose tissue of df/df mice and cultured pre-adipocytes. To test the effects of miR-146a-5p overexpression on visceral adipose tissue, wild-type, and df/df mice, were treated with miRNA-negative control-base and df/df were transfected with 4 or 8 µg/g of a miR-146a-5p mimetic, respectively. Effects of miR-146a-5p overexpression were also evaluated in 3T3-L1 cells cultured under high and normal glucose conditions. Treatment with miR-146a-5p mimetic increased cellular senescence and inflammation and decreased pro-apoptotic factors in visceral adipose tissue of df/df mice. The miR-146a-5p mimetic induced similar effects in 3T3-L1 cells cultivated at normal but not high glucose levels. Importantly, 3T3-L1 HG cells in high glucose conditions showed significantly higher expression of miR-146a-5p than 3T3-L1 grown in normal glucose conditions. These results indicate that miR-146a-5p can be a marker for cellular senescence. This miRNA represents one of the significant SASP factors that if not precisely regulated, can accentuate inflammatory responses and stimulate senescence in surrounding non-senescent cells. The role of miR-146a-5p is different in healthy versus stressed cells, suggesting potential effects of this miRNA depend on overall organismal health, aging, and metabolic state.
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Affiliation(s)
- Allancer D C Nunes
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
- Institute On the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Moritz Weigl
- Ludwig Boltzmann Institute of Traumatology in Cooperation With AUVA, Vienna, Austria
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Sarah Noureddine
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Lin Yu
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Collin Lahde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | | | - Kunal Mitra
- Biomedical Engineering, Florida Tech, Melbourne, FL, 32901, USA
| | - Esther Beltran
- Florida Space Institute, University of Central Florida, Orlando, FL, 32826, USA
| | - Johannes Grillari
- Ludwig Boltzmann Institute of Traumatology in Cooperation With AUVA, Vienna, Austria
- Institute of Molecular Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - James L Kirkland
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Tamara Tchkonia
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Paul D Robbins
- Institute On the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA.
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, Poznan, Poland.
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10
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Weiss BG, Anczykowski MZ, Ihler F, Bertlich M, Spiegel JL, Haubner F, Canis M, Küffer S, Hess J, Unger K, Kitz J, Jakob M. MicroRNA-182-5p and microRNA-205-5p as potential biomarkers for prognostic stratification of p16-positive oropharyngeal squamous cell carcinoma. Cancer Biomark 2021; 33:331-347. [PMID: 34542062 DOI: 10.3233/cbm-203149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND MicroRNAs constitute promising biomarkers. OBJECTIVE The aim was to investigate diagnostic and prognostic implications of miR-182-5p and miR-205-5p in p16-positive and p16-negative oropharyngeal squamous cell carcinomas (OPSCCs). METHODS Expression of miR-182-5p, miR-205-5p were determined via quantitative real-time-PCR in fresh frozen tissues of 26 p16-positive, 19 p16-negative OPSCCs and 18 HPV-negative oropharyngeal controls. Associations between miRNA-expression, clinicopathological characteristics and prognosis were analyzed. RESULTS Higher miR-182-5p expression was associated with significant inferior disease-specific survival for p16-positive OPSCCs (HR = 1.98E+09, 95% CI 0-Inf; P= 0.028) and a similar trend was observed for p16-negative OPSCCs (HR = 1.56E+09, 95% CI 0-Inf; P= 0.051). Higher miR-205-5p expression was associated with an inferior progression-free survival (HR = 4.62, 95% CI 0.98-21.83; P= 0.034) and local control rate (HR = 2.18E+09, 95% CI 0-Inf; P= 0.048) for p16-positive OPSCCs. CONCLUSIONS Results indicate that miR-182-5p and miR-205-5p can further stratify patients with p16-positive OPSCC into prognostic groups.
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Affiliation(s)
- Bernhard G Weiss
- Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany.,Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Mahalia Zoe Anczykowski
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Göttingen, Göttingen, Germany.,Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Friedrich Ihler
- Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany.,German Center for Vertigo and Balance Disorders (DSGZ), Ludwig-Maximilians University of Munich, Munich, Germany
| | - Mattis Bertlich
- Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Jennifer L Spiegel
- Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Frank Haubner
- Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Stefan Küffer
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Research Center for Environmental Health (GmbH), Munich, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Research Center for Environmental Health (GmbH), Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Research Center for Environmental Health (GmbH), Munich, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Research Center for Environmental Health (GmbH), Munich, Germany
| | - Julia Kitz
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.,Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Mark Jakob
- Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany.,Department of Otorhinolaryngology, Ludwig-Maximilians University of Munich, Munich, Germany
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11
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Piotrowski I, Zhu X, Saccon TD, Ashiqueali S, Schneider A, de Carvalho Nunes AD, Noureddine S, Sobecka A, Barczak W, Szewczyk M, Golusiński W, Masternak MM, Golusiński P. miRNAs as Biomarkers for Diagnosing and Predicting Survival of Head and Neck Squamous Cell Carcinoma Patients. Cancers (Basel) 2021; 13:cancers13163980. [PMID: 34439138 PMCID: PMC8392400 DOI: 10.3390/cancers13163980] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide. It arises from the epithelium of the upper aerodigestive tract. Increasing evidence suggests that there is a significant role of microRNAs in HNSCC formation and progression. The aim of this study was to explore and compare the expression of HNSCC related miRNAs in tumor vs neighboring healthy tissue of HNSCC patients with tumors located in either the oral cavity, oropharynx, or larynx. Our results demonstrated that expression of these miRNAs was significantly different not only between healthy and tumor tissues, but also among tumor locations. Further analysis indicated that microRNA expression could be used to distinguish between tumor and healthy tissues, and prognose the overall survival of patients. Abstract Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide. These tumors originate from epithelial cells of the upper aerodigestive tract. HNSCC tumors in different regions can have significantly different molecular characteristics. While many microRNAs (miRNAs) have been found to be involved in the regulation of the carcinogenesis and pathogenesis of HNSCC, new HNSCC related miRNAs are still being discovered. The aim of this study was to explore potential miRNA biomarkers that can be used to diagnose HNSCC and prognose survival of HNSCC patients. For this purpose, we chose a panel of 12 miRNAs: miR-146a-5p, miR-449a, miR-126-5p, miR-34a-5p, miR-34b-5p, miR-34c-5p, miR-217-5p, miR-378c, miR-6510-3p, miR-96-5p, miR-149-5p, and miR-133a-5p. Expression of these miRNAs was measured in tumor tissue and neighboring healthy tissue collected from patients diagnosed with HNSCC (n = 79) in either the oral cavity, oropharynx, or larynx. We observed a pattern of differentially expressed miRNAs at each of these cancer locations. Our study showed that some of these miRNAs, separately or in combination, could serve as biomarkers distinguishing between healthy and tumor tissue, and their expression correlated with patients’ overall survival.
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Affiliation(s)
- Igor Piotrowski
- Radiobiology Lab, Department of Medical Physics, Greater Poland Cancer Centre, 61-866 Poznan, Poland; (I.P.); (A.S.); (W.B.)
- Department of Electroradiology, Poznan University of Medical Sciences, ul. Garbary 15, 61-866 Poznan, Poland
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (X.Z.); (S.A.); (A.D.d.C.N.); (S.N.); (M.M.M.)
| | - Xiang Zhu
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (X.Z.); (S.A.); (A.D.d.C.N.); (S.N.); (M.M.M.)
| | - Tatiana Dandolini Saccon
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas 96010-610, Brazil;
| | - Sarah Ashiqueali
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (X.Z.); (S.A.); (A.D.d.C.N.); (S.N.); (M.M.M.)
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas 96010-610, Brazil;
| | - Allancer Divino de Carvalho Nunes
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (X.Z.); (S.A.); (A.D.d.C.N.); (S.N.); (M.M.M.)
| | - Sarah Noureddine
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (X.Z.); (S.A.); (A.D.d.C.N.); (S.N.); (M.M.M.)
| | - Agnieszka Sobecka
- Radiobiology Lab, Department of Medical Physics, Greater Poland Cancer Centre, 61-866 Poznan, Poland; (I.P.); (A.S.); (W.B.)
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (M.S.); (W.G.)
| | - Wojciech Barczak
- Radiobiology Lab, Department of Medical Physics, Greater Poland Cancer Centre, 61-866 Poznan, Poland; (I.P.); (A.S.); (W.B.)
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (M.S.); (W.G.)
| | - Mateusz Szewczyk
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (M.S.); (W.G.)
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Wojciech Golusiński
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (M.S.); (W.G.)
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (X.Z.); (S.A.); (A.D.d.C.N.); (S.N.); (M.M.M.)
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (M.S.); (W.G.)
| | - Paweł Golusiński
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, 65-417 Zielona Gora, Poland
- Department of Maxillofacial Surgery, Poznan University of Medical Sciences, 61-701 Poznan, Poland
- Correspondence:
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12
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Liang F, Wang R, Du Q, Zhu S. An Epithelial-Mesenchymal Transition Hallmark Gene-Based Risk Score System in Head and Neck Squamous-Cell Carcinoma. Int J Gen Med 2021; 14:4219-4227. [PMID: 34393501 PMCID: PMC8354775 DOI: 10.2147/ijgm.s327632] [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: 07/02/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022] Open
Abstract
Background Epithelial-to-mesenchymal transition (EMT) program plays a critical role in cancer. Thus, we attempted to generate a risk score system according to the expression pattern of different EMT hallmark genes in head and neck squamous-cell carcinoma (HNSC). Methods Differentially expressed EMT hallmark genes were screened to generate a risk score (RS) on TCGA HNSC dataset. The relative prognostic value of the RS compared to clinicopathological characteristics was explored using multivariable Cox analysis. Functional enrichment analysis was performed to reveal the biological characteristics. An external dataset was applied to validate the prognostic value of the RS. Results Nine genes constituted the EMT hallmark gene-based RS, which is significantly associated with poor prognosis and could successfully divide patients with HNSC into high- and low-risk groups. The RS was also an independent prognostic indicator compared to routine clinical factors. Conclusion We proposed and validated a nine-EMT hallmark gene-based risk score system in HNSC.
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Affiliation(s)
- Feifei Liang
- Department of Radiation Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Rensheng Wang
- Department of Radiation Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qinghua Du
- Department of Radiation Oncology, Second Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Shangyong Zhu
- Department of Ultrasound, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
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13
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Özdaş S, Canatar İ, Özdaş T. Effects of Knockdown of XPO5 by siRNA on the Biological Behavior of Head and Neck Cancer Cells. Laryngoscope 2021; 132:569-577. [PMID: 34328643 DOI: 10.1002/lary.29787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/26/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES/HYPOTHESIS Dysregulated expression of microRNAs (miRNAs) and dysregulation of the mechanisms that regulate them are associated with carcinogenesis. Exportin-5 (XPO5), a member of the Karyopherin family, is responsible for the transfer of pre-miRNAs from the nucleus to the cytoplasm. Despite the high oncogenic potential of XPO5 as a critical regulator of the biogenesis of miRNAs, its role in head and neck squamous cell carcinoma (HNSCC) biology has not been explained yet. STUDY DESIGN In-vitro translational. METHODS The expression of XPO5 at the mRNA, protein, and intracellular level in SCC-9, FaDu SCC-90, and Detroit-562 cell lines were evaluated with quantitative reverse transcription polymerase chain reaction, Western-blot analysis, and immunofluorescence staining, respectively. The functional role of XPO5 in HNSCC was analyzed by silencing the gene expression with XPO5-small interfering RNA (siRNA) in the in vitro model. Cell proliferation, migration capacity, and apoptosis in XPO5 knockdown HNSCC cell lines were evaluated by MTT, wound-healing, and caspase-3 assay, respectively. RESULTS Expression of XPO5 was determined to be upregulated at mRNA, protein, and intracellular level in metastatic cells compared to primary cells in HNSCC. XPO5 gene expression was knockdown by XPO5-siRNA transfection, verifying that it was suppressed at the mRNA, protein, and intracellular level. Silencing XPO5 caused a decrease in cell proliferation, delay in wound healing, and increase in Caspase-3 enzyme activity in HNSCC cell lines compared to control. CONCLUSIONS This report is the first to describe the oncogenic role of XPO5 in HNSCC biology by in vitro experiments. Consequently, XPO5 can be used as a potential biomarker and therapeutic target molecule against the disease in the diagnosis-treatment-follow-up of HNSCC. LEVEL OF EVIDENCE N/A Laryngoscope, 2021.
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Affiliation(s)
- Sibel Özdaş
- Department of Bioengineering, Faculty of Engineering Sciences, Adana Alpaslan Türkeş Science and Technology University, Adana, Turkey
| | - İpek Canatar
- Department of Bioengineering, Faculty of Engineering Sciences, Adana Alpaslan Türkeş Science and Technology University, Adana, Turkey
| | - Talih Özdaş
- Department of ENT, Adana City Training and Research Hospital, Health Science University, Adana, Turkey
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14
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Turkistani S, Sugita BM, Fadda P, Marchi R, Afsari A, Naab T, Apprey V, Copeland RL, Campbell MC, Cavalli LR, Kanaan Y. A panel of miRNAs as prognostic markers for African-American patients with triple negative breast cancer. BMC Cancer 2021; 21:861. [PMID: 34315420 PMCID: PMC8317413 DOI: 10.1186/s12885-021-08573-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND To investigate the global expression profile of miRNAs, their impact on cellular signaling pathways, and their association with poor prognostic parameters in African-American (AA) patients with triple negative breast cancer (TNBC). METHODS Twenty-five samples of AA TNBC patients were profiled for global miRNA expression and stratified considering three clinical-pathological parameters: tumor size, lymph node (LN), and recurrence (REC) status. Differential miRNA expression analysis was performed for each parameter, and their discriminatory power was determined by Receiver Operating Characteristic (ROC) curve analysis. KMplotter was assessed to determine the association of the miRNAs with survival, and functional enrichment analysis to determine the main affected pathways and miRNA/mRNA target interactions. RESULTS A panel of eight, 23 and 27 miRNAs were associated with tumor size, LN, and REC status, respectively. Combined ROC analysis of two (miR-2117, and miR-378c), seven (let-7f-5p, miR-1255b-5p, miR-1268b, miR-200c-3p, miR-520d, miR-527, and miR-518a-5p), and three (miR-1200, miR-1249-3p, and miR-1271-3p) miRNAs showed a robust discriminatory power based on tumor size (AUC = 0.917), LN (AUC = 0.945) and REC (AUC = 0.981) status, respectively. Enrichment pathway analysis revealed their involvement in proteoglycans and glycan and cancer-associated pathways. Eight miRNAs with deregulated expressions in patients with large tumor size, positive LN metastasis, and recurrence were significantly associated with lower survival rates. Finally, the construction of miRNA/mRNA networks based in experimentally validated mRNA targets, revealed nodes of critical cancer genes, such as AKT1, BCL2, CDKN1A, EZR and PTEN. CONCLUSIONS Altogether, our data indicate that miRNA deregulated expression is a relevant biological factor that can be associated with the poor prognosis in TNBC of AA patients, by conferring to their TNBC cells aggressive phenotypes that are reflected in the clinical characteristics evaluated in this study.
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Affiliation(s)
- Safaa Turkistani
- Department of Microbiology, Howard University Cancer Center, Howard University, Washington DC, USA
| | - Bruna M Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Paolo Fadda
- Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rafael Marchi
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Ali Afsari
- Department of Pathology, Howard University Hospital, Washington DC, USA
| | - Tammey Naab
- Department of Pathology, Howard University Hospital, Washington DC, USA
| | - Victor Apprey
- Department of Community and Family Medicine, Howard University, Washington DC, USA
| | - Robert L Copeland
- Department of Pharmacology, College of Medicine and Cancer Center, Howard University, Washington DC, USA
| | | | - Luciane R Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA.
| | - Yasmine Kanaan
- Department of Microbiology, Howard University Cancer Center, Howard University, Washington DC, USA
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15
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Karmakar M, Lai PC, Sinha S, Glaser S, Chakraborty S. Identification of miR-203a, mir-10a, and miR-194 as predictors for risk of lymphovascular invasion in head and neck cancers. Oncotarget 2021; 12:1499-1519. [PMID: 34316330 PMCID: PMC8310671 DOI: 10.18632/oncotarget.28022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Lymphovascular invasion (LVI) is an important prognostic indicator of lymph node metastasis and disease aggressiveness but clear molecular mechanisms mediating this in head and neck cancers (HNSC) remain undefined. To identify important microRNAs (miRNAs) in HNSC that associate with and are also predictive of increased risk of LVI, we used a combination of clustering algorithms, multiple regression analyses and machine learning approaches and analyzed miRNA expression profiles in the TCGA HNSC database. As the first step, we identified miRNAs with increased association with LVI as a binary variable. In order to determine whether the identified miRNAs would show functional clusters that are also indicative of increased risk for LVI, we carried out unsupervised as well as supervised clustering. Our results identified distinct clusters of miRNAs that are predictive of increased LVI. We further refined these findings using a Random forest approach, and miR-203a-3p, mir-10a-5p, and miR-194-5p to be most strongly associated with LVI. Pathway enrichment analysis showed these miRNAs targeted genes involved in Hippo signaling and fatty acid oxidation pathways that are mediators of lymph node metastasis. Specific association was also identified between the miRNAs associated with LVI and expression of several lymphangiogenic genes that could be critical for determination of therapeutic strategies.
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Affiliation(s)
- Moumita Karmakar
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA
| | - Pei-Chun Lai
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA
| | - Samiran Sinha
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA
| | - Shannon Glaser
- Department of Medical Physiology, Texas A&M Health Science Center, College of Medicine, Medical Research and Education Building, Bryan, TX 77807, USA
| | - Sanjukta Chakraborty
- Department of Medical Physiology, Texas A&M Health Science Center, College of Medicine, Medical Research and Education Building, Bryan, TX 77807, USA
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Statistical and machine learning methods for analysis of multiplex protein data from a novel proximity extension assay in patients with ST-elevation myocardial infarction. Sci Rep 2021; 11:13787. [PMID: 34215806 PMCID: PMC8253786 DOI: 10.1038/s41598-021-93162-3] [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: 01/27/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
Using data from patients with ST-elevation myocardial infarction (STEMI), we explored how machine learning methods can be used for analysing multiplex protein data obtained from proximity extension assays. Blood samples were obtained from 48 STEMI-patients at admission and after three months. A subset of patients also had blood samples obtained at four and 12 h after admission. Multiplex protein data were obtained using a proximity extension assay. A random forest model was used to assess the predictive power and importance of biomarkers to distinguish between the acute and the stable phase. The similarity of response profiles was investigated using K-means clustering. Out of 92 proteins, 26 proteins were found to significantly distinguish the acute and the stable phase following STEMI. The five proteins tissue factor pathway inhibitor, azurocidin, spondin-1, myeloperoxidase and myoglobin were found to be highly important for differentiating between the acute and the stable phase. Four of these proteins shared response profiles over the four time-points. Machine learning methods can be used to identify and assess novel predictive biomarkers as showcased in the present study population of patients with STEMI.
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17
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Saccon TD, Schneider A, Marinho CG, Nunes ADC, Noureddine S, Dhahbi J, Nunez Lopez YO, LeMunyan G, Salvatori R, Oliveira CRP, Oliveira‐Santos AA, Musi N, Bartke A, Aguiar‐Oliveira MH, Masternak MM. Circulating microRNA profile in humans and mice with congenital GH deficiency. Aging Cell 2021; 20:e13420. [PMID: 34118183 PMCID: PMC8282278 DOI: 10.1111/acel.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/10/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Reduced inflammation, increased insulin sensitivity, and protection against cancer are shared between humans and mice with GH/IGF1 deficiency. Beyond hormone levels, miRNAs are important regulators of metabolic changes associated with healthy aging. We hypothesized that GH deficiency in humans alters the abundance of circulating miRNAs and that a subset of those miRNAs may overlap with those found in GH-deficient mice. In this study, subjects with untreated congenital isolated GH deficiency (IGHD; n = 23) and control subjects matched by age and sex (n = 23) were recruited and serum was collected for miRNA sequencing. Serum miRNAs from young (6 month) and old (22 month) Ames dwarf (df/df) mice with GH deficiency and their WT littermates (n = 5/age/genotype group) were used for comparison. We observed 14 miRNAs regulated with a genotype by age effect and 19 miRNAs regulated with a genotype effect independent of age in serum of IGHD subjects. These regulated miRNAs are known for targeting pathways associated with longevity such as mTOR, insulin signaling, and FoxO. The aging function was overrepresented in IGHD individuals, mediated by hsa-miR-31, hsa-miR-146b, hsa-miR-30e, hsa-miR-100, hsa-miR-181b-2, hsa-miR-195, and hsa-miR-181b-1, which target the FoxO and mTOR pathways. Intriguingly, miR-181b-5p, miR-361-3p, miR-144-3p, and miR-155-5p were commonly regulated in the serum of humans and GH-deficient mice. In vitro assays confirmed target genes for the main up-regulated miRNAs, suggesting miRNAs regulated in IGHD individuals can regulate the expression of age-related genes. These findings indicate that systemic miRNAs regulated in IGHD individuals target pathways involved in aging in both humans and mice.
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Affiliation(s)
- Tatiana D. Saccon
- Centro de Desenvolvimento Tecnológico Universidade Federal de Pelotas Pelotas Brazil
- Burnett School of Biomedical Sciences College of Medicine University of Central Florida Orlando FL USA
| | - Augusto Schneider
- Faculdade de Nutrição Universidade Federal de Pelotas Pelotas Brazil
| | - Cindi G. Marinho
- Division of Endocrinology Health Sciences Graduate Program Federal University of Sergipe Aracaju Brazil
| | - Allancer D. C. Nunes
- Burnett School of Biomedical Sciences College of Medicine University of Central Florida Orlando FL USA
| | - Sarah Noureddine
- Burnett School of Biomedical Sciences College of Medicine University of Central Florida Orlando FL USA
| | - Joseph Dhahbi
- Department of Medical Education School of Medicine California University of Science & Medicine San Bernardino CA USA
| | - Yury O. Nunez Lopez
- Advent Health Translational Research Institute for Metabolism and Diabetes Orlando FL USA
| | - Gage LeMunyan
- Department of Medical Education School of Medicine California University of Science & Medicine San Bernardino CA USA
| | - Roberto Salvatori
- Division of Endocrinology, Diabetes and Metabolism Department of Medicine The Johns Hopkins University School of Medicine Baltimore MD USA
| | - Carla R. P. Oliveira
- Division of Endocrinology Health Sciences Graduate Program Federal University of Sergipe Aracaju Brazil
| | - Alécia A. Oliveira‐Santos
- Division of Endocrinology Health Sciences Graduate Program Federal University of Sergipe Aracaju Brazil
| | - Nicolas Musi
- Barshop Institute for Longevity and Aging Studies Center for Healthy Aging University of Texas Health Sciences Center at San Antonio and South Texas Veterans Health Care System San Antonio TX USA
- San Antonio Geriatric Research Education and Clinical Center South Texas Veterans Health Care System San Antonio TX USA
| | - Andrzej Bartke
- Department of Internal Medicine Southern Illinois University School of Medicine Springfield IL USA
| | - Manuel H. Aguiar‐Oliveira
- Division of Endocrinology Health Sciences Graduate Program Federal University of Sergipe Aracaju Brazil
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences College of Medicine University of Central Florida Orlando FL USA
- Department of Head and Neck Surgery Poznan University of Medical Sciences Poznan Poland
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Li G, Wang Q, Li Z, Shen Y. Serum miR-21 and miR-210 as promising non-invasive biomarkers for the diagnosis and prognosis of colorectal cancer. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2021; 112:832-837. [PMID: 33054296 DOI: 10.17235/reed.2020.6801/2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE this study aimed to investigate the expression and clinical significance of miR-21 and miR-210 in serum of patients with colorectal cancer (CRC). METHODS the expression levels of serum miR-21 and miR-210 in 40 CRC patients (CRC group) and 20 healthy patients (control group) were measured by qRT-PCR. Correlation analysis was performed of the relationship between serum miR-21 and miR-210 levels with clinical characteristics, including gender, age, tumor location, tumor size, tumor stage, local invasion and TNM staging. The expression levels of miR-21 and miR-210 in the CRC group were separately measured before and after surgery. ROC analysis was performed to evaluate the diagnostic value of miR-21 and miR-210. RESULTS serum miR-21 and miR-210 in the CRC group were much higher than those in the control group. Meanwhile, the levels of serum miR-21 and miR-210 were closely related to tumor size (p = 0.028, p = 0.047), lymphatic metastasis (p = 0.038, p = 0.028), TNM staging (p = 0.014, p = 0.047) and tumor stage (p = 0.014, p = 0.017), but independent of gender, age and tumor location. In addition, serum miR-21 and miR-210 in the CRC group (n = 18) after surgery were lower than those before surgery (p < 0.001). ROC curves showed that miR-21 (AUC = 0.863) and miR-210 (AUC = 0.818) both had diagnostic efficacy in CRC patients. CONCLUSION miR-21 and miR-210 can be used as novel non-invasive biomarkers for CRC diagnosis and prognosis.
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Affiliation(s)
- Gang Li
- Colorectal Surgery, Shaoxing People's Hospital
| | - Qi Wang
- Colorectal Surgery, Shaoxing People's Hospital
| | - Zhenjun Li
- Colorectal Surgery, Shaoxing People's Hospital
| | - Yi Shen
- Colorectal Surgery, Shaoxing People's Hospital,
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Kabzinski J, Maczynska M, Majsterek I. MicroRNA as a Novel Biomarker in the Diagnosis of Head and Neck Cancer. Biomolecules 2021; 11:844. [PMID: 34198889 PMCID: PMC8228566 DOI: 10.3390/biom11060844] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Head and neck squamous cell carcinoma is the sixth most common cancer worldwide, with 890,000 new cases and 450,000 deaths in 2018, and although the survival statistics for some patient groups are improving, there is still an urgent need to find a fast and reliable biomarker that allows early diagnosis. This niche can be filled by microRNA, small single-stranded non-coding RNA molecules, which are expressed in response to specific events in the body. This article presents the potential use of microRNAs in the diagnosis of HNSCC, compares the advances in this field to other diseases, especially other cancers, and discusses the detailed use of miRNA as a biomarker in profiling and predicting the treatment outcome with radiotherapy and immunotherapy. Potential problems and difficulties related to the development of this promising technology, and areas on which future research should be focused in order to overcome these difficulties, were also indicated.
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Affiliation(s)
| | | | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, al. Kościuszki 4, 90-419 Łódź, Poland; (J.K.); (M.M.)
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20
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miRNA-Based Feature Classifier Is Associated with Tumor Mutational Burden in Head and Neck Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1686480. [PMID: 33490233 PMCID: PMC7787755 DOI: 10.1155/2020/1686480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/07/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023]
Abstract
Tumor mutation burden (TMB) is considered to be an independent genetic biomarker that can predict the tumor patient's response to immune checkpoint inhibitors (ICIs). Meanwhile, microRNA (miRNA) plays a key role in regulating the anticancer immune response. However, the correlation between miRNA expression patterns and TMB is not elucidated in HNSCC. In the HNSCC cohort of the TCGA dataset, miRNAs that were differentially expressed in high TMB and low TMB samples were screened. The least absolute contraction and selection operator (LASSO) method is used to construct a miRNA-based feature classifier to predict the TMB level in the training set. The test set is used to verify the classifier. The correlation between the miRNA-based classifier index and the expression of three immune checkpoints (PD1, PDL1, and CTLA4) was explored. We further perform functional enrichment analysis on the miRNA contained in the miRNA-based feature classifier. Twenty-five differentially expressed miRNAs are used to build miRNA-based feature classifiers to predict TMB levels. The accuracy of the 25-miRNA-based signature classifier is 0.822 in the training set, 0.702 in the test set, and 0.774 in the total set. The miRNA-based feature classifier index showed a low correlation with PD1 and PDL1, but no correlation with CTLA4. The enrichment analysis of these 25 miRNAs shows that they are involved in many immune-related biological processes and cancer-related pathways. The miRNA expression patterns are related to tumor mutation burden, and miRNA-based feature classifiers can be used as biomarkers to predict TMB levels in HNSCC.
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Carron J, Torricelli C, Silva JK, Queiroz GSR, Ortega MM, Lima CSP, Lourenço GJ. microRNAs deregulation in head and neck squamous cell carcinoma. Head Neck 2020; 43:645-667. [PMID: 33159410 DOI: 10.1002/hed.26533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/30/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Head and neck (HN) squamous cell carcinoma (SCC) is the eighth most common human cancer worldwide. Besides tobacco and alcohol consumption, genetic and epigenetic alterations play an important role in HNSCC occurrence and progression. microRNAs (miRNAs) are small noncoding RNAs that regulate cell cycle, proliferation, development, differentiation, and apoptosis by interfering in gene expression. Expression profiling of miRNAs showed that some miRNAs are upregulated or downregulated in tumor cells when compared with the normal cells. The present review focuses on the role of miRNAs deregulations in HNSCC, enrolled in risk, development, outcome, and therapy sensitivity. Moreover, the influence of single nucleotide variants in miRNAs target sites, miRNAs seed sites, and miRNAs-processing genes in HNSCC was also revised. Due to its potential for cancer diagnosis, progression, and as a therapeutic target, miRNAs may bring new perspectives in HNSCC understanding and therapy, especially for those patients with no or insufficient treatment options.
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Affiliation(s)
- Juliana Carron
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Caroline Torricelli
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Janet K Silva
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Gabriela S R Queiroz
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Manoela M Ortega
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista, Brazil
| | - Carmen S P Lima
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Gustavo J Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas, Brazil
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Huang Y, Liu Z, Zhong L, Wen Y, Ye Q, Cao D, Li P, Liu Y. Construction of an 11-microRNA-based signature and a prognostic nomogram to predict the overall survival of head and neck squamous cell carcinoma patients. BMC Genomics 2020; 21:691. [PMID: 33023466 PMCID: PMC7542341 DOI: 10.1186/s12864-020-07104-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/24/2020] [Indexed: 12/16/2022] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is a fatal malignancy owing to the lack of effective tools to predict overall survival (OS). MicroRNAs (miRNAs) play an important role in HNSCC occurrence, development, invasion and metastasis, significantly affecting the OS of patients. Thus, the construction of miRNA-based risk signatures and nomograms is desirable to predict the OS of patients with HNSCC. Accordingly, in the present study, miRNA sequencing data of 71 HNSCC and 13 normal samples downloaded from The Cancer Genome Atlas (TCGA) were screened to identify differentially expressed miRNAs (DEMs) between HNSCC patients and normal controls. Based on the exclusion criteria, the clinical information and miRNA sequencing data of 67 HNSCC samples were selected and used to establish a miRNA-based signature and a prognostic nomogram. Forty-three HNSCC samples were assigned to an internal validation cohort for verifying the credibility and accuracy of the primary cohort. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore the functions of 11 miRNA target genes. Results In total, 11 DEMs were successfully identified. An 11-miRNA risk signature and a prognostic nomogram were constructed based on the expression levels of these 11 DEMs and clinical information. The signature and nomogram were further validated by calculating the C-index, area under the curve (AUC) in receiver-operating characteristic curve analysis, and calibration curves, which revealed their promising performance. The results of the internal validation cohort shown the reliable predictive accuracy both of the miRNA-based signature and the prognostic nomogram. GO and KEGG analyses revealed that a mass of signal pathways participated in HNSCC proliferation and metastasis. Conclusion Overall, we constructed an 11-miRNA-based signature and a prognostic nomogram with excellent accuracy for predicting the OS of patients with HNSCC.
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Affiliation(s)
- Yusheng Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, No. 12 Airport Road, Baiyun District, Guangzhou, 510407, China
| | - Zhiguo Liu
- Department of Oral and Maxillofacial Surgery, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, 56 Lingyuanxi Road, Guangzhou, China
| | - Limei Zhong
- Department of Laboratory Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yi Wen
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, No. 12 Airport Road, Baiyun District, Guangzhou, 510407, China
| | - Qixiang Ye
- Department of Pediatrics, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Donglin Cao
- Department of Laboratory Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Peiwu Li
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, No. 12 Airport Road, Baiyun District, Guangzhou, 510407, China.
| | - Yufeng Liu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, No. 12 Airport Road, Baiyun District, Guangzhou, 510407, China. .,Guangzhou First People's Hospital, Guangzhou, 510000, China.
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Kolenda T, Guglas K, Baranowski D, Sobocińska J, Kopczyńska M, Teresiak A, Bliźniak R, Lamperska K. cfRNAs as biomarkers in oncology - still experimental or applied tool for personalized medicine already? Rep Pract Oncol Radiother 2020; 25:783-792. [PMID: 32904167 PMCID: PMC7451588 DOI: 10.1016/j.rpor.2020.07.007] [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: 11/05/2019] [Revised: 02/13/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, the challenges of contemporary oncology are focused mainly on the development of personalized medicine and precise treatment, which could be achieved through the use of molecular biomarkers. One of the biological molecules with great potential are circulating free RNAs (cfRNAs) which are present in various types of body fluids, such as blood, serum, plasma, and saliva. Also, different types of cfRNA particles can be distinguished depending on their length and function: microRNA (miRNA), PIWI-interacting RNA (piRNA), tRNA-derived RNA fragments (tRFs), circular RNA (circRNA), long non-coding RNA (lncRNA), and messenger RNA (mRNA). Moreover, cfRNAs occur in various forms: as a free molecule alone, in membrane vesicles, such as exosomes, or in complexes with proteins and lipids. One of the modern approaches for monitoring patient's condition is a "liquid biopsy" that provides a non-invasive and easily available source of circulating RNAs. Both the presence of specific cfRNA types as well as their concentration are dependent on many factors including cancer type or even reaction to treatment. Despite the possibility of using circulating free RNAs as biomarkers, there is still a lack of validated diagnostic panels, defined protocols for sampling, storing as well as detection methods. In this work we examine different types of cfRNAs, evaluate them as possible biomarkers, and analyze methods of their detection. We believe that further research on cfRNA and defining diagnostic panels could lead to better and faster cancer identification and improve treatment monitoring.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Dawid Baranowski
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, 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 Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
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Wu C, Tong L, Wu C, Chen D, Chen J, Li Q, Jia F, Huang Z. Two miRNA prognostic signatures of head and neck squamous cell carcinoma: A bioinformatic analysis based on the TCGA dataset. Cancer Med 2020; 9:2631-2642. [PMID: 32064753 PMCID: PMC7163094 DOI: 10.1002/cam4.2915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 12/28/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs(miRNAs) are maladjusted in multifarious malignant tumor and can be considered as both carcinogens and tumor‐inhibiting factor. In the present study, we analyzed the miRNAs expression profiles and clinical information of 481 patients with head and neck squamous cell carcinoma (HNSCC) through the TCGA dataset to identify the prognostic miRNAs signature. A total of 114 significantly differentially expressed miRNAs (SDEMs) were identified, consisting of 60 up‐adjusted and 54 down‐adjusted miRNAs. The Kaplan‐Meier survival method identified the prognostic function of 2 miRNAs (miR‐4652‐5p and miR‐99a‐3P). Univariate and multivariate Cox regression analyses indicated that the 2 miRNAs were significant prognostic elements of HNSCC. Furthermore, bioinformatic analysis was conducted by means of 4 online gene predicted toolkits to recognize the target genes, and enrichment analysis was performed on the target genes by DAVID. The outcomes depicted that target genes were correlated with calcium, as well as cell proliferation, circadian entrainment, EGFR, PI3K‐Akt‐mTOR, and P53 signaling pathways. Finally, the PPI network was conducted in view of STRING database and Cytoscape. Eight hub genes were identified by CytoHubba and MCODE app, respectively, CBL, SKP1, H2AFX, HGF, POLR2F, UBE2I, VAMP2, and GNAI2 genes. As a result, we identified 2 miRNAs signatures, 8 hub genes, and significant signaling pathways for estimating the prognosis of HNSCC. In order to further explore the molecular mechanism of HNSCC occurrence and development, more comprehensive basic and clinical studies are needed.
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Affiliation(s)
- Chaoying Wu
- Department of Otolaryngology Head and Neck SurgeryThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouLiaoningChina
| | - Lingxia Tong
- Department of UltrasoundJilin Cancer HospitalChangchunJilinChina
| | - Chaoqun Wu
- Department of General MedicineNingbo Medical Center Lihuili HospitalNingboZhejiangChina
| | - Dong Chen
- Department of Otolaryngology Head and Neck SurgeryThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouLiaoningChina
| | - Jianguo Chen
- Department of Otolaryngology Head and Neck SurgeryThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouLiaoningChina
| | - Qianyun Li
- Department of Otolaryngology Head and Neck SurgeryThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouLiaoningChina
| | - Fang Jia
- Department of Otolaryngology Head and Neck SurgeryThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouLiaoningChina
| | - Zirui Huang
- Jinzhou Medical UniversityJinzhouLiaoningChina
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Liu XL, Pan WG, Li KL, Mao YJ, Liu SD, Zhang RM. miR-1293 Suppresses Tumor Malignancy by Targeting Hydrocyanic Oxidase 2: Therapeutic Potential of a miR-1293/Hydrocyanic Oxidase 2 Axis in Renal Cell Carcinoma. Cancer Biother Radiopharm 2020; 35:377-386. [PMID: 31971830 DOI: 10.1089/cbr.2019.2957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Renal cell carcinoma (RCC) is a common cancer, and extensive research suggests that microRNA may play an important role in the progression of RCC. The emphasis of this article was to reveal the function and mechanism of microRNA-1293(miR-1293) in the development of RCC tumors. First, the authors carried out bioinformatics analysis. The differential expression of miR-1293 in RCC tumor and normal cells was analyzed using the data from The Cancer Genome Atlas database, and Kaplan-Meier survival analysis was carried out to test the survival rate. Subsequently, the miR-1293 expression in RCC cell lines was examined by quantitative real-time PCR. Then Cell counting kit-8 and Transwell assays were executed to detect the function of miR-1293 in RCC. Bioinformatics prediction, western blotting, and dual-luciferase reporter assay were set to check the target gene of miR-1293. Finally, they conducted rescue experiments to verify whether the regulation of miR-1293 on the biological function of RCC cells was achieved by regulating hydrocyanic oxidase 2 (HAO2). Bioinformatics results showed that miR-1293 was highly expressed in RCC, and the miR-1293 high-expression group showed a lower survival rate than the miR-1293 low-expression group, which suggested that the high expression of miR-1293 was related to unfavorable prognosis in RCC. Subsequent assays evidenced that upregulation of miR-1293 expression significantly increased the cell viability and promoted cell migration and invasion in RCC. Silencing miR-1293 expression showed opposite results. Furthermore, HAO2 was confirmed to be a direct target gene of miR-1293 by dual-luciferase reporter assay, and miR-1293 negatively regulated the expression of HAO2. Moreover, rescue experiments evidenced that miR-1293 reduced the cell viability, invasion, and migration of RCC by regulating HAO2. In sum, miR-1293 can regulate the viability, invasion, and migration of RCC tumor cells by targeting HAO2, suggesting that miR-1293 can be used as a new biomarker for clinical treatment of RCC.
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Affiliation(s)
- Xiao-Li Liu
- Department of Kidney Transplantation and The Second Hospital, Shandong University, Jinan, People's Republic of China
| | - Wen-Gu Pan
- Department of Kidney Transplantation and The Second Hospital, Shandong University, Jinan, People's Republic of China
| | - Kai-Lin Li
- Department of Central Research Lab, The Second Hospital, Shandong University, Jinan, People's Republic of China
| | - Yi-Jie Mao
- Department of Kidney Transplantation and The Second Hospital, Shandong University, Jinan, People's Republic of China
| | - Shuang-De Liu
- Department of Kidney Transplantation and The Second Hospital, Shandong University, Jinan, People's Republic of China
| | - Rong-Mei Zhang
- Department of Kidney Transplantation and The Second Hospital, Shandong University, Jinan, People's Republic of China
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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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Chen C, Lohavanichbutr P, Zhang Y, Houck JR, Upton MP, Abedi-Ardekani B, Agudo A, Ahrens W, Alemany L, Anantharaman D, Conway DI, Futran ND, Holcatova I, Günther K, Hansen BT, Healy CM, Itani D, Kjaerheim K, Monroe MM, Thomson PJ, Witt BL, Nakoneshny S, Peterson LA, Schwartz SM, Zarins KR, Hashibe M, Brennan P, Rozek LS, Wolf G, Dort JC, Wang P. Prediction of survival of HPV16-negative, p16-negative oral cavity cancer patients using a 13-gene signature: A multicenter study using FFPE samples. Oral Oncol 2020; 100:104487. [PMID: 31835136 PMCID: PMC7386199 DOI: 10.1016/j.oraloncology.2019.104487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/26/2019] [Accepted: 11/21/2019] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To test the performance of an oral cancer prognostic 13-gene signature for the prediction of survival of patients diagnosed with HPV-negative and p16-negative oral cavity cancer. MATERIALS AND METHODS Diagnostic formalin-fixed paraffin-embedded oral cavity cancer tumor samples were obtained from the Fred Hutchinson Cancer Research Center/University of Washington, University of Calgary, University of Michigan, University of Utah, and seven ARCAGE study centers coordinated by the International Agency of Research on Cancer. RNA from 638 Human Papillomavirus (HPV)-negative and p16-negative samples was analyzed for the 13 genes using a NanoString assay. Ridge-penalized Cox regressions were applied to samples randomly split into discovery and validation sets to build models and evaluate the performance of the 13-gene signature in predicting 2-year oral cavity cancer-specific survival overall and separately for patients with early and late stage disease. RESULTS Among AJCC stage I/II patients, including the 13-gene signature in the model resulted in substantial improvement in the prediction of 2-year oral cavity cancer-specific survival. For models containing age and sex with and without the 13-gene signature score, the areas under the Receiver Operating Characteristic Curve (AUC) and partial AUC were 0.700 vs. 0.537 (p < 0.001), and 0.046 vs. 0.018 (p < 0.001), respectively. Improvement in predicting prognosis for AJCC stage III/IV disease also was observed, but to a lesser extent. CONCLUSIONS If confirmed using tumor samples from a larger number of early stage oral cavity cancer patients, the 13-gene signature may inform personalized treatment of early stage HPV-negative and p16-negative oral cavity cancer patients.
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Affiliation(s)
- Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific St, Seattle, WA, USA; Department of Otolaryngology -- Head and Neck Surgery, University of Washington, 1959, NE Pacific St, Seattle, WA, USA.
| | - Pawadee Lohavanichbutr
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Yuzheng Zhang
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - John R Houck
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Melissa P Upton
- Department of Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA, USA
| | | | - Antonio Agudo
- Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, Avinguda de la Granvia, 199, 08908, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany; Institute of Statistics, Bremen University, Achterstraße 30, 28359 Bremen, Germany
| | - Laia Alemany
- Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, Avinguda de la Granvia, 199, 08908, L'Hospitalet de Llobregat, Barcelona, Spain; Epidemiology and Public Health, Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Devasena Anantharaman
- Rajiv Gandhi Centre for Biotechnology, Melarannoor Road, Thycaud, Thiruvananthapuram, India
| | - David I Conway
- School of Medicine, Dentistry, and Nursing, University of Glasgow, University Avenue, Glasgow, UK
| | - Neal D Futran
- Department of Otolaryngology -- Head and Neck Surgery, University of Washington, 1959, NE Pacific St, Seattle, WA, USA
| | - Ivana Holcatova
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Opletalova 38, 110 00 Staré Město, Charles University, Prague, Czech Republic
| | - Kathrin Günther
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
| | - Bo T Hansen
- Cancer Registry of Norway, Ullernchausseen 64, 0379 Oslo, Norway
| | - Claire M Healy
- Dublin Dental University Hospital, Trinity College Dublin, Lincoln Pl, Dublin, Ireland
| | - Doha Itani
- Section of Otolaryngology -- Head & Neck Surgery, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary Alberta, Canada
| | | | - Marcus M Monroe
- University of Utah, 201 Presidents Cir, Salt Lake City, UT, USA
| | - Peter J Thomson
- Oral & Maxillofacial Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Benjamin L Witt
- University of Utah, 201 Presidents Cir, Salt Lake City, UT, USA
| | - Steven Nakoneshny
- Section of Otolaryngology -- Head & Neck Surgery, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary Alberta, Canada
| | | | - Stephen M Schwartz
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific St, Seattle, WA, USA
| | - Katie R Zarins
- University of Michigan, 500 S State St, Ann Arbor, MI, USA
| | - Mia Hashibe
- University of Utah, 201 Presidents Cir, Salt Lake City, UT, USA
| | - Paul Brennan
- International Agency of Research on Cancer, 150 Cours Albert Thomas, Lyon, France
| | - Laura S Rozek
- University of Michigan, 500 S State St, Ann Arbor, MI, USA
| | - Gregory Wolf
- University of Michigan, 500 S State St, Ann Arbor, MI, USA
| | - Joseph C Dort
- Section of Otolaryngology -- Head & Neck Surgery, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary Alberta, Canada
| | - Pei Wang
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, USA
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Cao W, Zhao Y, Wang L, Huang X. Circ0001429 regulates progression of bladder cancer through binding miR-205-5p and promoting VEGFA expression. Cancer Biomark 2019; 25:101-113. [PMID: 30909190 DOI: 10.3233/cbm-182380] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE This study investigates expressions of circ0001429, miR-205-5p and vascular endothelial growth factor (VEGFA) in bladder cancer tissues and their effects on the proliferation, migration and apoptosis. METHODS Arraystar Human CircRNA chip was applied to analyzing the differential expression of circRNA in four bladder cancer tissues and paired adjacent normal bladder tissues. Real time quantitative PCR was utilized to detect the expression of circ0001429 in tissue specimens. Bioinformatics, RNA immunoprecipitation and luciferase reporter assays were used to verify the relationship among circ0001429, miR-205-5p and VEGFA in bladder cancer. Cell propagation was determined by CCK8 assay and roles of circ0001429 and miR-205-5p in cell migration were verified with transwell migration assay. Flow cytometry and TUNEL staining were conducted to observe the impact on cell apoptosis ability. Xenograft experiment was also performed to validate the influence of circ0001429 on tumor growth in vivo. RESULTS Expressions of circ0001429 and VEGFA were up-regulated, whereas miR-205-5p expression was down-regulated in bladder cancer tissues in comparison with paired adjacent normal bladder tissues. Circ0001429 enhanced the propagation and metastasis abilities of T24 cells and 5637 cells in vitro, but reduced cell apoptosis. In vivo experiments revealed the inhibitor role of sh-circ0001429 in tumor growth and lung metastasis. Circ0001429 sponged miR-205-5p that targeted VEGFA, thereby modulating the protein level of VEGFA. Meanwhile, miR-205-5p restrained the cell viability and mobility and promoted the apoptosis in bladder cancer. Circ0001429 could accelerate cell propagation, migration and invasiveness through increasing VEGFA expression via miR-205-5p. CONCLUSION Circ0001429 and VEGFA were highly expressed in bladder cancer, while miR-205-5p were lowly expressed in bladder cancer. The circ0001429 could target at miR-205-5p to regulate VEGFA and promote the development of bladder cancer.
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Dhahbi J, Nunez Lopez YO, Schneider A, Victoria B, Saccon T, Bharat K, McClatchey T, Atamna H, Scierski W, Golusinski P, Golusinski W, Masternak MM. Profiling of tRNA Halves and YRNA Fragments in Serum and Tissue From Oral Squamous Cell Carcinoma Patients Identify Key Role of 5' tRNA-Val-CAC-2-1 Half. Front Oncol 2019; 9:959. [PMID: 31616639 PMCID: PMC6775249 DOI: 10.3389/fonc.2019.00959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer and, as indicated by The Oral Cancer Foundation, kills at an alarming rate of roughly one person per hour. With this study, we aimed at better understanding disease mechanisms and identifying minimally invasive disease biomarkers by profiling novel small non-coding RNAs (specifically, tRNA halves and YRNA fragments) in both serum and tumor tissue from humans. Small RNA-Sequencing identified multiple 5' tRNA halves and 5' YRNA fragments that displayed significant differential expression levels in circulation and/or tumor tissue, as compared to control counterparts. In addition, by implementing a modification of weighted gene coexpression network analysis, we identified an upregulated genetic module comprised of 5' tRNA halves and miRNAs (miRNAs were described in previous study using the same samples) with significant association with the cancer trait. By consequently implementing miRNA-overtargeting network analysis, the biological function of the module (and by "guilt by association," the function of the 5' tRNA-Val-CAC-2-1 half) was found to involve the transcriptional targeting of specific genes involved in the negative regulation of the G1/S transition of the mitotic cell cycle. These findings suggest that 5' tRNA-Val-CAC-2-1 half (reduced in serum of OSCC patients and elevated in the tumor tissue) could potentially serve as an OSCC circulating biomarker and/or target for novel anticancer therapies. To our knowledge, this is the first time that the specific molecular function of a 5'-tRNA half is specifically pinpointed in OSCC.
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Affiliation(s)
- Joseph Dhahbi
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Yury O. Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, United States
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Tatiana Saccon
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Krish Bharat
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Thaddeus McClatchey
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Hani Atamna
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Wojciech Scierski
- Department of Otorhinolaryngology and Laryngological Oncology in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Golusinski
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Zielona Gora, Poland
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
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Lin S, Tan L, Luo D, Peng X, Zhu Y, Li H. Linc01278 inhibits the development of papillary thyroid carcinoma by regulating miR-376c-3p/DNM3 axis. Cancer Manag Res 2019; 11:8557-8569. [PMID: 31572010 PMCID: PMC6756842 DOI: 10.2147/cmar.s217886] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Purpose Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy, and its incidence has continuously increased in recent years. Therefore, it is essential to develop more useful therapeutic strategies. Methods We collected 56 pairs of PTC tissues and adjacent normal tissues and determined the expression patterns of linc01278, miR-376c-3p and DNM3. In addition, we analyzed the relationship between linc01278 expression and pathological information of PTC patients. Furthermore, the effects of linc01278, miR-376c-3p and DNM3 overexpression on proliferation, clonality, apoptosis, migration and invasion of PTC cell lines TPC1 and BCPAP were evaluated. The dual luciferase reporter assay was used to confirm the direct interaction between miR-376c-3p and linc01278. Results Linc01278 and DNM3 were remarkably down-regulated in PTC tissues and cell lines, whereas miR-376c-3p was significantly up-regulated. In addition, lower linc01278 expression was associated with increased tumor size, lymph node metastasis and higher clinical stage. Linc01278 inhibited cell proliferation of PTC cells by inducing apoptosis, and demonstrated attenuating effects on migration and invasion abilities of PTC cells by regulating the EMT process. More importantly, dual luciferase reporter experiments demonstrated the direct interaction between miR-376c-3p and linc01278, which revealed that DNM3 was a novel target of miR-376c-3p. The miR-376c-3p mimic significantly promoted the proliferation, migration and invasion of PTC cells, and inhibited cell apoptosis. Overexpression of DNM3 abolished the effects of the miR-376c-3p mimic on PTC cells. DNM3 expression was negatively correlated with miR-376c-3p expression, but was positively correlated with linc01278 expression. Conclusion Overall, we found that linc01278 can act as a competing endogenous RNA (ceRNA) to sponge miR-376c-3p, thereby positively regulating DNM3 expression and ultimately acting as a tumor suppressor gene in PTC progression.
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Affiliation(s)
- Shaojian Lin
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Langping Tan
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Dingyuan Luo
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Xinzhi Peng
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Yue Zhu
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Honghao Li
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
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Valenti F, Sacconi A, Ganci F, Grasso G, Strano S, Blandino G, Di Agostino S. The miR-205-5p/BRCA1/RAD17 Axis Promotes Genomic Instability in Head and Neck Squamous Cell Carcinomas. Cancers (Basel) 2019; 11:E1347. [PMID: 31514456 PMCID: PMC6771082 DOI: 10.3390/cancers11091347] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
Defective DNA damage response (DDR) is frequently associated with tumorigenesis. Abrogation of DDR leads to genomic instability, which is one of the most common characteristics of human cancers. TP53 mutations with gain-of-function activity are associated with tumors under high replicative stress, high genomic instability, and reduced patient survival. The BRCA1 and RAD17 genes encode two pivotal DNA repair proteins required for proper cell-cycle regulation and maintenance of genomic stability. We initially evaluated whether miR-205-5p, a microRNA (miRNA) highly expressed in head and neck squamous cell carcinoma (HNSCC), targeted BRCA1 and RAD17 expression. We found that, in vitro and in vivo, BRCA1 and RAD17 are targets of miR-205-5p in HNSCC, leading to inefficient DNA repair and increased chromosomal instability. Conversely, miR-205-5p downregulation increased BRCA1 and RAD17 messenger RNA (mRNA) levels, leading to a reduction in in vivo tumor growth. Interestingly, miR-205-5p expression was significantly anti-correlated with BRCA1 and RAD17 targets. Furthermore, we documented that miR-205-5p expression was higher in tumoral and peritumoral HNSCC tissues than non-tumoral tissues in patients exhibiting reduced local recurrence-free survival. Collectively, these findings unveil miR-205-5p's notable role in determining genomic instability in HNSCC through its selective targeting of BRCA1 and RAD17 gene expression. High miR-205-5p levels in the peritumoral tissues might be relevant for the early detection of minimal residual disease and pre-cancer molecular alterations involved in tumor development.
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Affiliation(s)
- Fabio Valenti
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Andrea Sacconi
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Federica Ganci
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Giuseppe Grasso
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Sabrina Strano
- Molecular Chemoprevention Group, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.
| | - Silvia Di Agostino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.
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Gmerek L, Martyniak K, Horbacka K, Krokowicz P, Scierski W, Golusinski P, Golusinski W, Schneider A, Masternak MM. MicroRNA regulation in colorectal cancer tissue and serum. PLoS One 2019; 14:e0222013. [PMID: 31469874 PMCID: PMC6716664 DOI: 10.1371/journal.pone.0222013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/20/2019] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer is recognized as the fourth leading cause of cancer-related deaths worldwide. Thus, there is ongoing search for potential new biomarkers allowing quicker and less invasive detection of the disease and prediction of the treatment outcome. Therefore, the aim of our study was to identify colorectal cancer specific miRNAs expressed in cancerous and healthy tissue from the same patient and to further correlate the presence of the same miRNAs in the circulation as potential biomarkers for diagnosis. In the current study we detected a set of 40 miRNAs differentially regulated in tumor tissue when comparing with healthy tissue. Additionally, we found 8 miRNAs differentially regulated in serum of colorectal cancer patients. Interestingly, there was no overlap in miRNAs regulated in tissue and serum, suggesting that serum regulated miRNAs may be not actively secreted from colorectal tumor cells. However, four of differentially expressed miRNAs, including miR-21, miR-17, miR-20a and miR-32 represent the miRNAs characteristic for different tumor types, including breast, colon, lung, pancreas, prostate and stomach cancer. This finding suggests important groups of miRNAs which can be further validated as markers for diagnosis of tumor tissue and regulation of carcinogenesis.
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Affiliation(s)
- Lukasz Gmerek
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States of America.,Department of General and Colorectal Surgery, Poznan University of Medical Sciences, Poznan, Poland
| | - Kari Martyniak
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States of America
| | - Karolina Horbacka
- Department of General and Colorectal Surgery, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Krokowicz
- Department of General and Colorectal Surgery, Poznan University of Medical Sciences, Poznan, Poland
| | - Wojciech Scierski
- Department of Otorhinolaryngology and Laryngological Oncology in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Golusinski
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Zielona Gora, Poland.,Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Michal M Masternak
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States of America.,Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
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Lu Y, Li Y, Wang Z, Xie S, Wang Q, Lei X, Ruan Y, Li J. Downregulation of RGMA by HIF-1A/miR-210-3p axis promotes cell proliferation in oral squamous cell carcinoma. Biomed Pharmacother 2019; 112:108608. [PMID: 30798120 DOI: 10.1016/j.biopha.2019.108608] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/16/2019] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Repulsive guidance molecules comprise a group of proteins that play an important role in carcinogenesis through interactions with their receptors, but their function in oral squamous cell carcinoma (OSCC) is unclear. Here, we investigated the potential role of the RGM family members in oral cancer pathogenesis. Our study showed that only RGMA was significantly downregulated in the OSCC tissues analyzed by TCGA and validated this finding in OSCC cells. The decreased expression of RGMA was strongly associated with the T stage and with poor prognosis. The ectopic expression of RGMA significantly inhibited the proliferation of OSCC cells both in vitro and in vivo. Moreover, we confirmed that RGMA was a target of miR-210-3p in OSCC and miR-210-3p overexpression contributed to the acceleration of OSCC growth. Further experiments revealed that HIF1A specifically interacted with the promoter of miR-210-3p and enhanced its expression. In summary, our research indicates that RGMA is regulated by the HIF1A/miR-210-3p axis and inhibits OSCC cell proliferation; thus, in the future, the development of therapies that target the HIF1A/miR-210-3p/RGMA axis may aid in the treatment of aggressive cancers.
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Affiliation(s)
- Yingjuan Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China; Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Yingru Li
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510120, China; Department of Gastroenterology, Hernia and Abdominal Wall Surgery, The sixth affiliated Hospital, Sun Yat_Sen University, Guangzhou, 510120, China
| | - Zhangsong Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China; Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Shule Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China; Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Qing Wang
- Department of Dentistry, Weifang Peoples' Hospital, Weifang, 261000, Shandong Province, China
| | - Xinyuan Lei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China; Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Yi Ruan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China; Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Jinsong Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China; Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
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Nunez Lopez YO, Retnakaran R, Zinman B, Pratley RE, Seyhan AA. Predicting and understanding the response to short-term intensive insulin therapy in people with early type 2 diabetes. Mol Metab 2019; 20:63-78. [PMID: 30503831 PMCID: PMC6358589 DOI: 10.1016/j.molmet.2018.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/05/2018] [Accepted: 11/12/2018] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE Short-term intensive insulin therapy (IIT) early in the course of type 2 diabetes acutely improves beta-cell function with long-lasting effects on glycemic control. However, conventional measures cannot determine which patients are better suited for IIT, and little is known about the molecular mechanisms determining response. Therefore, this study aimed to develop a model that could accurately predict the response to IIT and provide insight into molecular mechanisms driving such response in humans. METHODS Twenty-four patients with early type 2 diabetes were assessed at baseline and four weeks after IIT, consisting of basal detemir and premeal insulin aspart. Twelve individuals had a beneficial beta-cell response to IIT (responders) and 12 did not (nonresponders). Beta-cell function was assessed by multiple methods, including Insulin Secretion-Sensitivity Index-2. MicroRNAs (miRNAs) were profiled in plasma samples before and after IIT. The response to IIT was modeled using a machine learning algorithm and potential miRNA-mediated regulatory mechanisms assessed by differential expression, correlation, and functional network analyses (FNA). RESULTS Baseline levels of circulating miR-145-5p, miR-29c-3p, and HbA1c accurately (91.7%) predicted the response to IIT (OR = 121 [95% CI: 6.7, 2188.3]). Mechanistically, a previously described regulatory loop between miR-145-5p and miR-483-3p/5p, which controls TP53-mediated apoptosis, appears to also occur in our study population of humans with early type 2 diabetes. In addition, significant (fold change > 2, P < 0.05) longitudinal changes due to IIT in the circulating levels of miR-138-5p, miR-192-5p, miR-195-5p, miR-320b, and let-7a-5p further characterized the responder group and significantly correlated (|r| > 0.4, P < 0.05) with the changes in measures of beta-cell function and insulin sensitivity. FNA identified a network of coordinately/cooperatively regulated miRNA-targeted genes that potentially drives the IIT response through negative regulation of apoptotic processes that underlie beta cell dysfunction and concomitant positive regulation of proliferation. CONCLUSIONS Responses to IIT in people with early type 2 diabetes are associated with characteristic miRNA signatures. This study represents a first step to identify potential responders to IIT (a current limitation in the field) and provides important insight into the pathophysiologic determinants of the reversibility of beta-cell dysfunction. ClinicalTrial.gov identifier: NCT01270789.
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Affiliation(s)
- Yury O Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL 32804, USA
| | - Ravi Retnakaran
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bernard Zinman
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Richard E Pratley
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL 32804, USA.
| | - Attila A Seyhan
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL 32804, USA; The Chemical Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Fiscon G, Conte F, Farina L, Pellegrini M, Russo F, Paci P. Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM. Methods Mol Biol 2019; 1970:169-181. [PMID: 30963493 DOI: 10.1007/978-1-4939-9207-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) involved in several biological processes and diseases. MiRNAs regulate gene expression at the posttranscriptional level, mostly downregulating their targets by binding specific regions of transcripts through imperfect sequence complementarity. Prediction of miRNA-binding sites is challenging, and target prediction algorithms are usually based on sequence complementarity. In the last years, it has been shown that by adding miRNA and protein coding gene expression, we are able to build tissue-, cell line-, or disease-specific networks improving our understanding of complex biological scenarios. In this chapter, we present an application of a recently published software named SWIM, that allows to identify key genes in a network of interactions by defining appropriate "roles" of genes according to their local/global positioning in the overall network. Furthermore, we show how the SWIM software can be used to build miRNA-disease networks, by applying the approach to tumor data obtained from The Cancer Genome Atlas (TCGA).
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy
- SysBio Centre for Systems Biology, Milan, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy
- SysBio Centre for Systems Biology, Milan, Italy
| | - Lorenzo Farina
- Department of Computer, Control, and Management Engineering Antonio Ruberti, Sapienza University of Rome, Rome, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics, National Research Council, Pisa, Italy
| | - Francesco Russo
- Faculty of Health and Medical Sciences¸ Novo Nordisk Foundation Center for Protein Research, Translational Disease Systems Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Paola Paci
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy.
- SysBio Centre for Systems Biology, Milan, Italy.
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Cen WN, Pang JS, Huang JC, Hou JY, Bao WG, He RQ, Ma J, Peng ZG, Hu XH, Ma FC. The expression and biological information analysis of miR-375-3p in head and neck squamous cell carcinoma based on 1825 samples from GEO, TCGA, and peer-reviewed publications. Pathol Res Pract 2018; 214:1835-1847. [PMID: 30243807 DOI: 10.1016/j.prp.2018.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/26/2018] [Accepted: 09/11/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND The specific expression level and clinical significance of miR-375-3p in HNSCC had not been fully stated, as well as the overall biological function and molecular mechanisms. Therefore, we purpose to carry out a comprehensive meta-analysis to further explore the clinical significance and potential function mechanism of miR-375-3p in HNSCC. METHODS HNSCC-related data was gained from Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and peer-reviewed journals. A meta-analysis was carried out to comprehensively explore the relationship between miR-375-3p expression level and clinicopathological features of HNSCC. And summary receiver operating characteristic (SROC) curve analysis was applied for evaluating disease diagnosis value of miR-375-3p. In addition, a biological pathway analysis was also performed to assess the possible molecular mechanism of miR-375-3p in HNSCC. RESULTS A total of 24 available records and references were added into analysis. The overall pooled meta-analysis outcome revealed a relatively lower expression level of miR-375-3p in HNSCC specimens than that in non-cancerous controls (P < 0.001). And SROC curve analysis showed that the pooled area under the SROC curve (AUC) was 0.90 (95%CI: 0.88-0.93). In addition, biological pathway analysis indicated that LAMC1, EDIL3, FN1, VEGFA, IGF2BP2, and IGF2BP3 maybe the latent target genes of miR-375-3p, which were greatly enriched in the pathways of beta3 integrin cell surface interactions and the binding of RNA via the insulin-like growth factor-2 mRNA-binding protein (IGF2BPs/IMPs/VICKZs). CONCLUSION MiR-375-3p expression clearly decreased in HNSCC samples compared with non-cancerous controls. Meanwhile, miR-375-3p may serve as a tumor suppressor via regulating tumor-related genes LAMC1, EDIL3, FN1, VEGFA, IGF2BP2, and IGF2BP3 in HNSCC.
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Affiliation(s)
- Wei-Ning Cen
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jin-Shu Pang
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jia-Cheng Huang
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jia-Yin Hou
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Wen-Guang Bao
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jie Ma
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Zhi-Gang Peng
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Xiao-Hua Hu
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Fu-Chao Ma
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China.
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Sobecka A, Blaszczak W, Barczak W, Golusinski P, Rubis B, Masternak MM, Suchorska WM, Golusinski W. hTERT promoter methylation status in peripheral blood leukocytes as a molecular marker of head and neck cancer progression. J Appl Genet 2018; 59:453-461. [PMID: 30088231 DOI: 10.1007/s13353-018-0458-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/13/2018] [Accepted: 07/18/2018] [Indexed: 01/02/2023]
Abstract
Cancer cells, including head and neck cancer cell carcinoma (HNSCC), are characterized by an increased telomerase activity. This enzymatic complex is active in approximately 80-90% of all malignancies, and is regulated by various factors, including methylation status of hTERT gene promoter. hTERT methylation pattern has been thoroughly studied so far. It was proved that hTERT is aberrantly methylated in tumor tissue versus healthy counterparts. However, such effect has not yet been investigated in PBLs (peripheral blood leukocytes) of cancer patients. The aim of this study was to analyze the hTERT gene promoter methylation status in blood leukocytes. DNA was extracted from PBL of 92 patients with histologically diagnosed HNSCC and 53 healthy controls. Methylation status of whole hTERT promoter fragment with independent analysis of each 19 CpG sites was performed using bisulfide conversion technique followed by sequencing of PCR products. Not significant (p = 0.0532) differences in the general frequency of hTERT CpG sites methylation were detected between patients and healthy controls. However, it was discovered that some of analyzed positions (CpG islands: 1 [p = 0.0235], 5 [p = 0.0462], 8 [p = 0.0343]) are significantly more often methylated in HNSCC patients than in controls. The opposite finding was observed in case of CpG position 2 (p = 0.0210). Furthermore, closer analysis of single CpG positions revealed differences in methylation status dependent on anatomical site and TNM classification. To conclude, hTERT promoter methylation status (general or single CpG sites) would be considered as a molecular markers of HNSCC diagnostics.
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Affiliation(s)
- Agnieszka Sobecka
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15 Str, 61-866, Poznan, Poland
- Radiobiology Laboratory, The Greater Poland Cancer Centre, Garbary 15 Str, 61-866, Poznan, Poland
| | - Wiktoria Blaszczak
- Radiobiology Laboratory, The Greater Poland Cancer Centre, Garbary 15 Str, 61-866, Poznan, Poland
| | - Wojciech Barczak
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15 Str, 61-866, Poznan, Poland.
- Radiobiology Laboratory, The Greater Poland Cancer Centre, Garbary 15 Str, 61-866, Poznan, Poland.
| | - Pawel Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15 Str, 61-866, Poznan, Poland
- Head and Neck Cancer Biology Laboratory, Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznan, Poland
| | - Blazej Rubis
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Przybyszewskiego 49 Str, 60-355, Poznan, Poland
| | - Michal M Masternak
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15 Str, 61-866, Poznan, Poland
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Wiktoria M Suchorska
- Radiobiology Laboratory, The Greater Poland Cancer Centre, Garbary 15 Str, 61-866, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Garbary 15 Str, 61-866, Poznan, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15 Str, 61-866, Poznan, Poland
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38
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Liu X, Yao B, Wu Z. miRNA-199a-5p suppresses proliferation and invasion by directly targeting NF-κB1 in human ovarian cancer cells. Oncol Lett 2018; 16:4543-4550. [PMID: 30214589 DOI: 10.3892/ol.2018.9170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/28/2018] [Indexed: 12/12/2022] Open
Abstract
The aberrant expression of microRNA (miRNA)-199a-5p has been frequently reported in a number of cancer types, but to the best of our knowledge, this has not been reported in ovarian cancer (OC). The role and the molecular mechanism of miR-199a-5p in OC have not been reported. Therefore, the present study investigated the effects of miR-199a-5p overexpression on the proliferation and invasion of OC cells. The level of miR-199a-5p in OC cell lines was determined by reverse transcription-quantitative polymerase chain reaction. The miR-199a-5p mimic was transiently transfected into OC cells using Lipofectamine™ 2000 reagent. Subsequently, the BrdU-ELISA results indicated that the exogenous expression of miR-199a-5p inhibited cell proliferation. In addition, miR-199a-5p overexpression was able to inhibit the invasion of HO-8910 and ES-2 cells. RT-qPCR was performed to determine the expression of matrix metalloproteinase (MMP)-2 and -9 in OC cells. NF-κB1 expression was reduced by upregulation of miR-199a-5p. Bioinformatics analysis predicted that NF-κB1 was a potential target of miR-199a-5p. Luciferase reporter assay further confirmed that miR-199a-5p was able to directly target the 3'UTR of NF-κB1. In conclusion, miRNA-199a-5p may suppress the proliferation and invasion of human ovarian cancer cells by directly targeting NF-κB1.
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Affiliation(s)
- Xiaoxiao Liu
- Department of Internal Medicine-Oncology, Xinchang People's Hospital of Zhejiang, Shaoxing, Zhejiang 312500, P.R. China
| | - Baofeng Yao
- Department of Intensive Care Unit, Putuo Hospital of Zhejiang, Zhoushan, Zhejiang 316100, P.R. China
| | - Zhiming Wu
- Department of General Surgery, Shaoxing Hospital of China Medical University, Shaoxing, Zhejiang 312030, P.R. China
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39
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Chen YT, Yao JN, Qin YT, Hu K, Wu F, Fang YY. Biological role and clinical value of miR-99a-5p in head and neck squamous cell carcinoma (HNSCC): A bioinformatics-based study. FEBS Open Bio 2018; 8:1280-1298. [PMID: 30087832 PMCID: PMC6070648 DOI: 10.1002/2211-5463.12478] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/19/2018] [Accepted: 06/11/2018] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are confirmed to be tumor promoters or suppressors in multiple squamous cell carcinomas (SCCs). miR‐99a‐5p has been demonstrated to be downregulated in cancerous tissues, but its functional role in head and neck SCC (HNSCC) and its mechanism of action have not been fully elucidated. Here, we studied the expression of miR‐99a‐5p in HNSCC and performed a clinical value assessment and then extracted mature expression data from The Cancer Genome Atlas (TCGA) and microarrays from Gene Expression Omnibus (GEO). Furthermore, biological analysis was constructed via online prediction tools. The results revealed that miR‐99a‐5p expression was markedly lower in HNSCC tissues than in normal tissues, which also showed significance in the prognosis of HNSCC. However, its diagnostic value could not be verified due to the lack of body fluid samples. Additionally, miR‐99a‐5p was expressed at higher levels in patients with low histological grade neoplasms than those with high histological grade neoplasms. The age of the patient might also be a possible clinical parameter affecting miR‐99a‐5p expression. Furthermore, miR‐99a‐5p significantly influenced HNSCC progression by regulating the PI3K‐Akt signaling pathway, in which the key target genes were upregulated in 519 HNSCC tissues compared to 44 normal tissues, as determined by the Gene Expression Profiling Interactive Analysis (GEPIA). In conclusion, our study may provide insights into the expression and mechanism of miR‐99a‐5p in HNSCC. Further studies are required to elucidate the role of miR‐99a‐5p and its potential clinical applications for HNSCC.
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Affiliation(s)
- Yu-Ting Chen
- Department of Pathology First Affiliated Hospital of Guangxi Medical University Nanning Guangxi China
| | - Jian-Ni Yao
- Department of Pathology First Affiliated Hospital of Guangxi Medical University Nanning Guangxi China
| | - Yu-Tao Qin
- Department of Radiation Oncology Radiation Oncology Clinical Medical Research Center of Guangxi First Affiliated Hospital of Guangxi Medical University Nanning Guangxi China
| | - Kai Hu
- Department of Radiation Oncology Radiation Oncology Clinical Medical Research Center of Guangxi First Affiliated Hospital of Guangxi Medical University Nanning Guangxi China
| | - Fang Wu
- Department of Radiation Oncology Radiation Oncology Clinical Medical Research Center of Guangxi First Affiliated Hospital of Guangxi Medical University Nanning Guangxi China
| | - Ye-Ying Fang
- Department of Radiation Oncology Radiation Oncology Clinical Medical Research Center of Guangxi First Affiliated Hospital of Guangxi Medical University Nanning Guangxi China
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40
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Allen B, Schneider A, Victoria B, Nunez Lopez YO, Muller M, Szewczyk M, Pazdrowski J, Majchrzak E, Barczak W, Golusinski W, Golusinski P, Masternak MM. Blood Serum From Head and Neck Squamous Cell Carcinoma Patients Induces Altered MicroRNA and Target Gene Expression Profile in Treated Cells. Front Oncol 2018; 8:217. [PMID: 29942793 PMCID: PMC6004400 DOI: 10.3389/fonc.2018.00217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/25/2018] [Indexed: 12/16/2022] Open
Abstract
The head and neck squamous cell carcinoma (HNSCC) represents one of the most common cancers in humans. Close to 600,000 new diagnoses are made every year worldwide and over half of diagnosed patients will not survive. In view of this low survival rate, the development of novel cell-based assays for HNSCC will allow more mechanistic approaches for specific diagnostics for each individual patient. The cell-based assays will provide more informative data predicting cellular processes in treated patient, which in effect would improve patient follow up. More importantly, it will increase the specificity and effectiveness of therapeutic approaches. In this study, we investigated the role of serum from HNSCC patients on the regulation of microRNA (miRNA) expression in exposed cells in vitro. Next-generation sequencing of miRNA revealed that serum from HNSCC patients induced a different miRNA expression profile than the serum from healthy individuals. Out of 377 miRNA detected, we found that 16 miRNAs were differentially expressed when comparing cells exposed to serum from HNSCC or healthy individuals. The analysis of gene ontologies and pathway analysis revealed that these miRNA target genes were involved in biological cancer-related processes, including cell cycle and apoptosis. The real-time PCR analysis revealed that serum from HNSCC patients downregulate the expression level of five genes involved in carcinogenesis and two of these genes-P53 and SLC2A1-are direct targets of detected miRNAs. These novel findings provide new insight into how cancer-associated factors in circulation regulate the expression of genes and regulatory elements in distal cells in favor of tumorigenesis. This has the potential for new therapeutic approaches and more specific diagnostics with tumor-specific cell lines or single-cell in vitro assays for personalized treatment and early detection of primary tumors or metastasis.
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Affiliation(s)
- Brittany Allen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Yury O Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL, United States
| | - Mark Muller
- Epigenetics Division, TopoGEN Inc, Buena Vista, CO, United States
| | - Mateusz Szewczyk
- Department of Head and Neck Surgery, Poznań University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
| | - Jakub Pazdrowski
- Department of Head and Neck Surgery, Poznań University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
| | - Ewa Majchrzak
- Department of Head and Neck Surgery, Poznań University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
| | - Wojciech Barczak
- Department of Head and Neck Surgery, Poznań University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznań University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
| | - Pawel Golusinski
- Department of Head and Neck Surgery, Poznań University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland.,Biology and Environmental Studies, Head and Neck Cancer Biology Laboratory, Poznań University of Medical Sciences, Poznan, Poland
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States.,Department of Head and Neck Surgery, Poznań University of Medical Sciences, The Greater Poland Cancer Centre, Poznan, Poland
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