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Han H, Fu X, Zhang Y, Luo D, Zhang X, Wu X. Expression and Prognostic Value of m6A RNA Methylation-Related Genes in Thyroid Cancer. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:1902-1916. [PMID: 38033847 PMCID: PMC10682584 DOI: 10.18502/ijph.v52i9.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/19/2023] [Indexed: 12/02/2023]
Abstract
Background N6-methyladenosine (m6A) methylation modification is involved in tumorigenesis and progression and can affect various stages of RNA processing. We aimed to determine m6A methylation modifications on a transcriptome-wide scale in thyroid cancer. Methods RNA samples from cancerous tissues and adjacent tissues extracted from patients with papillary thyroid carcinoma (PTC) from Hangzhou First People's Hospital, Zhejiang, China from January 2019 to January 2020 were used for m6A-sequencing. The biological function of differentially expressed genes (DEGs) was analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Correlation analysis between the results of transcriptome sequencing and m6A-sequencing was also performed. The key m6A immune-related genes were downloaded from Immport. LASSO regression was performed on the resulting genes to establish a prognostic risk model, which was verified by multivariate Cox proportional hazards regression analyses, receiver operating characteristic (ROC) curves and Kaplan-Meier survival analysis. Results An increase in m6A content in the total RNA of PTC was observed. A total of 123 genes with significant differential expression and differential methylation sites in thyroid cancer were selected, related to protein digestion and absorption, linoleic acid metabolism, legionellosis and alpha-linolenic acid metabolism. Seven genes (GDNF, EBI3, CCL2, BMP5, TGFB2, CGB3 and RLN2) were found to be predictive of PTC. Conclusion We analyzed the expression, enrichment pathways and functions of m6A methylation-related genes in the whole transcriptome of thyroid cancer and provided a prognostic risk model for thyroid cancer patients.
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Affiliation(s)
- Hui Han
- Department of Endocrinology, the Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, Zhejiang, China
| | - Xiaodan Fu
- Department of Endocrinology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Zhang
- Department of Surgical Oncology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hang-zhou, Zhejiang, China
| | - Dingcun Luo
- Department of Surgical Oncology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hang-zhou, Zhejiang, China
| | - Xianfeng Zhang
- Department of Endocrinology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaohong Wu
- Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
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Liu H, Ma H, Li Y, Zhao H. Advances in epigenetic modifications and cervical cancer research. Biochim Biophys Acta Rev Cancer 2023; 1878:188894. [PMID: 37011697 DOI: 10.1016/j.bbcan.2023.188894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Cervical cancer (CC) is an important public health problem for women, and perspectives and information regarding its prevention and treatment are quickly evolving. Human papilloma virus (HPV) has been recognized as a major contributor to CC development; however, HPV infection is not the only cause of CC. Epigenetics refers to changes in gene expression levels caused by non-gene sequence changes. Growing evidence suggests that the disruption of gene expression patterns which were governed by epigenetic modifications can result in cancer, autoimmune diseases, and various other maladies. This article mainly reviews the current research status of epigenetic modifications in CC based on four aspects, respectively DNA methylation, histone modification, noncoding RNA regulation and chromatin regulation, and we also discuss their functions and molecular mechanisms in the occurrence and progression of CC. This review provides new ideas for early screening, risk assessment, molecular targeted therapy and prognostic prediction of CC.
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Zhao S, Zhang D, Liu S, Huang J. The roles of NOP56 in cancer and SCA36. Pathol Oncol Res 2023; 29:1610884. [PMID: 36741964 PMCID: PMC9892063 DOI: 10.3389/pore.2023.1610884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023]
Abstract
NOP56 is a highly conserved nucleolar protein. Amplification of the intron GGCCTG hexanucleotide repeat sequence of the NOP56 gene results in spinal cerebellar ataxia type 36 (SCA36). NOP56 contains an N-terminal domain, a coiled-coil domain, and a C-terminal domain. Nucleolar protein NOP56 is significantly abnormally expressed in a number of malignant tumors, and its mechanism is different in different tumors, but its regulatory mechanism in most tumors has not been fully explored. NOP56 promotes tumorigenesis in some cancers and inhibits tumorigenesis in others. In addition, NOP56 is associated with methylation in some tumors, suggesting that NOP56 has the potential to become a tumor-specific marker. This review focuses on the structure, function, related signaling pathways, and role of NOP56 in the progression of various malignancies, and discusses the progression of NOP56 in neurodegenerative and other diseases.
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Affiliation(s)
- Shimin Zhao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dongdong Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Sicheng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Jun Huang,
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Ji T, Gao X, Li D, Huai S, Chi Y, An X, Ji W, Yang S, Li J. Identification and validation of signature for prognosis and immune microenvironment in gastric cancer based on m6A demethylase ALKBH5. Front Oncol 2023; 12:1079402. [PMID: 36686788 PMCID: PMC9853004 DOI: 10.3389/fonc.2022.1079402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023] Open
Abstract
Background N6-methyladenosine (m6A) RNA regulators play important roles in cancers, but their functions and mechanism have not been demonstrated clearly in gastric cancer (GC). Methods In this study, the GC samples with clinical information and RNA transcriptome were downloaded from The Cancer Genome Atlas database. The different expression genes were compared by the absolute value and median ± standard deviation. Samples with complete information were randomly divided into a training dataset and a test dataset. The differential expression genes (DEGs) between ALKBH5-low and ALKBH5-high subgroups were identified in the training dataset and constructed a risk model by Cox and least absolute shrinkage and selection operator regression. The model was testified in test datasets, overall survival (OS) was compared with the Kaplan-Meier method, and immune cell infiltration was calculated by the CIBERSORT algorithm in the low-risk and high-risk subgroups based on the model. The protein levels of ALKBH5 were detected with immunohistochemistry. The relative expression of messenger-ribonucleic acid (mRNA) was detected with quantitative polymerase chain reaction. Results ALKBH5 was the only regulator whose expression was lower in tumor samples than that in normal samples. The low expression of ALKBH5 led to the poor OS of GC patients and seemed to be an independent protective factor. The model based on ALKBH5-regulated genes was validated in both datasets (training/test) and displayed a potential capacity to predict a clinical prognosis. Gene Ontology analysis implied that the DEGs were involved in the immune response; CIBERSORT results indicated that ALKBH5 and its related genes could alter the immune microenvironment of GC. The protein levels of ALKBH5 were verified as lowly expressed in GC tissues. SLC7A2 and CGB3 were downregulated with ALKBH5 knockdown. Conclusions In this study, we found that ALKBH5 might be a suppressor of GC; ALKBH5 and its related genes were latent biomarkers and immunotherapy targets.
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Affiliation(s)
- Tiannan Ji
- Medical School of Chinese PLA, Beijing, China,Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xiaohui Gao
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,Department of Clinical Medicine, Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Dan Li
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Siyuan Huai
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yajing Chi
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,School of Medicine, Nankai University, Tianjin, China
| | - Xian An
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Wenyu Ji
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,Department of Clinical Medicine, Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Siming Yang
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jianxiong Li
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,*Correspondence: Jianxiong Li,
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Cárdenas AM, Campos-Bijit V, Di Francesco F, Schwarz F, Cafferata EA, Vernal R. Electrolyzed water for the microbiologic control in the pandemic dental setting: a systematic review. BMC Oral Health 2022; 22:579. [PMID: 36494635 PMCID: PMC9733258 DOI: 10.1186/s12903-022-02528-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/21/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Electrolyzed water has brought recent attention due to its antimicrobial properties. Indeed, electrolyzed water has been proposed to sterilize dental materials and instruments without compromising their structural integrity. In addition, electrolyzed water has been proposed as a mouthwash to control bacterial and viral oral infections without detrimental effects on the oral mucosa. However, no current consensus or evidence synthesis could indicate its potentially favorable use in the dental setting, particularly during the COVID-19 context. Therefore, this systematic review aimed to elucidate whether electrolyzed water could improve microbiologic control in the COVID-19 pandemic dental setting. METHODS MEDLINE via Pubmed, EMBASE, Cochrane's CENTRAL, Scopus, LILACS, and Web of Science databases were searched up to September 2021 to identify experimental studies utilizing electrolyzed water for eliminating microorganisms in a dental setting. Besides, a manual and a grey literature search were performed. The data selection and extraction were performed individually and in duplicate. The Risk of Bias (RoB) was assessed with the Nature Publication Quality Improvement Project (NPQIP) score sheet. The study protocol was registered at PROSPERO CRD42020206986. RESULTS From a total of 299 articles, 63 studies met the inclusion criteria. The included studies assessed several types of electrolyzed waters, which showed a high disinfection potential when used to deal with different oral conditions. Electrolyzed water demonstrated a broad antimicrobial spectrum and was highly efficient in the dental office disinfection against viruses, fungi, and bacteria, being compatible with most dental materials. In addition, electrolyzed water could protect against SARS-CoV-2 infection and contamination in the dental office. Regarding the RoB, only 35.18% of entries were answered as 'Yes', thus achieving less than half of the reporting sheet. CONCLUSION Electrolyzed water effectively disinfects contaminated surfaces, dental materials, and equipment. Therefore, their use is recommendable in the SARS-CoV-2 pandemic dental setting.
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Affiliation(s)
- Angélica M. Cárdenas
- grid.443909.30000 0004 0385 4466Periodontal Biology Laboratory, Faculty of Dentistry, Universidad de Chile, Sergio Livingstone Pohlhammer 943, 8380492 Santiago, Independencia Chile ,grid.442190.a0000 0001 1503 9395Faculty of Dentistry, Universidad Santo Tomás, Bucaramanga, Colombia ,Department of Science and Innovation, BIOMEP Research Group, Bucaramanga, Colombia
| | - Vanessa Campos-Bijit
- grid.443909.30000 0004 0385 4466Periodontal Biology Laboratory, Faculty of Dentistry, Universidad de Chile, Sergio Livingstone Pohlhammer 943, 8380492 Santiago, Independencia Chile
| | - Fabrizio Di Francesco
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Campania University Luigi Vanvitelli, Naples, Italy
| | - Frank Schwarz
- grid.7839.50000 0004 1936 9721Department of Oral Surgery and Implantology, Carolinum, Johann Wolfgang Goethe-University Frankfurt, Frankfurt, Germany
| | - Emilio A. Cafferata
- grid.7839.50000 0004 1936 9721Department of Oral Surgery and Implantology, Carolinum, Johann Wolfgang Goethe-University Frankfurt, Frankfurt, Germany ,grid.430666.10000 0000 9972 9272Department of Periodontology, School of Dentistry, Universidad Científica del Sur, Av. Paseo de la República 5544, 15074 Lima, Miraflores Peru
| | - Rolando Vernal
- grid.443909.30000 0004 0385 4466Periodontal Biology Laboratory, Faculty of Dentistry, Universidad de Chile, Sergio Livingstone Pohlhammer 943, 8380492 Santiago, Independencia Chile
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Singh P, Kitkumthorn N, Yanatatsaneejit P. Identification of Malignancy in PAP Smear Samples Using the CGB3 and NOP56 Genes as Methylation Markers. Asian Pac J Cancer Prev 2022; 23:3541-3551. [PMID: 36308381 PMCID: PMC9924328 DOI: 10.31557/apjcp.2022.23.10.3541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Although various improvements have been made in the reporting of the Papanicolaou (PAP) test in recent years, there remain several challenges that have yet to be addressed in terms of determining a standardized methodology for categorizing atypical squamous cells of undetermined significance (ASC US). METHODS The present study focuses on evaluating the performance of the methylation status of two genes (CGB3 and NOP56) using a total of 200 PAP samples, which were divided into the "determined" group, with 78 samples based on cytology, and the "undetermined" group (ASC US), with 122 samples. The promoter methylation status of the CGB3 and NOP56 genes was detected for the 200 PAP samples using methylation specific PCR (MSP). The diagnostic abilities of the CGB3 and NOP56 genes in PAP samples were measured, and receiver operating characteristic (ROC) curves were generated using Python programming language. RESULTS Based on the validation of CGB3 and NOP56 methylation in the 200 PAP samples, both genes exhibited higher methylation percentages in abnormal samples compared with normal samples. In addition, on the basis of diagnostic performance analysis, the CGB3 gene exhibited the highest sensitivity and specificity in both histology based ASC US and cytology based 'determined' PAP samples, with significant diagnostic abilities [area under the curve (AUC) values of 0.83 and 0.74, respectively, where AUC ≥0.5 was determined to be significant] to distinguish between the "normal" and "abnormal" samples. CONCLUSION The findings of the present study will contribute toward identifying a DNA methylation marker for the early detection of abnormal samples before they reach the initial stages of cervical cancer, and should prove to be helpful for clinicians in terms of diagnosing patients whose cells are ASC US.<br />.
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Affiliation(s)
- Palak Singh
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330 Thailand.
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400 Thailand.
| | - Pattamawadee Yanatatsaneejit
- Human Genetics Research Group, Department of Botany, Faculty of Science, Chulalongkorn University, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok 10330, Thailand. ,For Correspondence:
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Vega-Benedetti AF, Loi E, Zavattari P. DNA methylation alterations caused by Leishmania infection may generate a microenvironment prone to tumour development. Front Cell Infect Microbiol 2022; 12:984134. [PMID: 36105147 PMCID: PMC9465093 DOI: 10.3389/fcimb.2022.984134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/10/2022] [Indexed: 01/10/2023] Open
Abstract
DNA methylation is an epigenetic signature consisting of a methyl group at the 5’ cytosine of CpG dinucleotides. Modifications in DNA methylation pattern have been detected in cancer and infectious diseases and may be associated with gene expression changes. In cancer development DNA methylation aberrations are early events whereas in infectious diseases these epigenetic changes may be due to host/pathogen interaction. In particular, in leishmaniasis, a parasitic disease caused by the protozoan Leishmania, DNA methylation alterations have been detected in macrophages upon infection with Leishmania donovani and in skin lesions from patients with cutaneous leishmaniasis. Interestingly, different types of cancers, such as cutaneous malignant lesions, lymphoma and hepatocellular carcinoma, have been diagnosed in patients with a history of leishmaniasis. In fact, it is known that there exists an association between cancer and infectious diseases. Leishmania infection may increase susceptibility to develop cancer, but the mechanisms involved are not entirely clear. Considering these aspects, in this review we discuss the hypothesis that DNA methylation alterations induced by Leishmania may trigger tumorigenesis in long term infection since these epigenetic modifications may enhance and accumulate during chronic leishmaniasis.
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Sjöblom A, Carpén T, Stenman UH, Jouhi L, Haglund C, Syrjänen S, Mattila P, Mäkitie A, Hagström J. The Role of Human Chorionic Gonadotropin Beta (hCGβ) in HPV-Positive and HPV-Negative Oropharyngeal Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14122830. [PMID: 35740496 PMCID: PMC9221036 DOI: 10.3390/cancers14122830] [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: 05/07/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022] Open
Abstract
Background: This study was carried out to observe the upregulation of the free β-subunit of human chorionic gonadotropin (hCGβ) and its prognostic significance in human papillomavirus (HPV)-positive and HPV-negative oropharyngeal squamous cell carcinoma (OPSCC). Materials and methods: A total of 90 patients with OPSCC treated with curative intent at the Helsinki University Hospital (HUS), Helsinki, Finland, during 2012−2016 were included. Serum samples were collected prospectively, and their hCGβ concentrations (S-hCGβ) were determined by an immunofluorometric assay. The expression of hCGβ in tumor tissues was defined by immunohistochemistry (IHC). HPV determination was performed by combining p16-INK4 IHC and HPV DNA PCR genotyping. Overall survival (OS) and disease-specific survival (DSS) were used as survival endpoints. Results: S-hCGβ positivity correlated with poor OS in the whole patient cohort (p < 0.001) and in patients with HPV-negative OPSCC (p < 0.001). A significant correlation was seen between S-hCGβ and poor DSS in the whole cohort (p < 0.001) and in patients with HPV-negative OPSCC (p = 0.007). In a multivariable analysis, S-hCGβ was associated with poor DSS. Of the clinical characteristics, higher cancer stage and grade were associated with S-hCGβ positivity. No statistically significant correlation with tissue positivity of hCGβ was seen in these analyses. Conclusion: S-hCGβ may be a potential independent factor indicating poor prognosis, notably in HPV-negative OPSCC.
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Affiliation(s)
- Anni Sjöblom
- Department of Pathology, University of Helsinki and Helsinki University Hospital, P.O. Box 21, FI-00014 Helsinki, Finland
| | - Timo Carpén
- Department of Pathology, University of Helsinki and Helsinki University Hospital, P.O. Box 21, FI-00014 Helsinki, Finland
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 263, FI-00029 HUS Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, P.O. Box 63, FI-00014 Helsinki, Finland
| | - Lauri Jouhi
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 263, FI-00029 HUS Helsinki, Finland
| | - Caj Haglund
- Research Programs Unit, Translational Cancer Medicine, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
- Department of Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 440, FI-00029 Helsinki, Finland
| | - Stina Syrjänen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, P.O. Box 63, FI-00014 Helsinki, Finland
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Petri Mattila
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 263, FI-00029 HUS Helsinki, Finland
| | - Antti Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, P.O. Box 263, FI-00029 HUS Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska Hospital, SE-171 76 Stockholm, Sweden
| | - Jaana Hagström
- Department of Pathology, University of Helsinki and Helsinki University Hospital, P.O. Box 21, FI-00014 Helsinki, Finland
- Research Programs Unit, Translational Cancer Medicine, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
- Department of Oral Pathology and Oral Radiology, University of Turku, Lemminkäisenkatu 2, 20520 Turku, Finland
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