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Lim I, Tan J, Alam A, Idrees M, Brenan PA, Coletta RD, Kujan O. Epigenetics in the diagnosis and prognosis of head and neck cancer: A systematic review. J Oral Pathol Med 2024; 53:90-106. [PMID: 38316046 DOI: 10.1111/jop.13513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/01/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Aberrant epigenetic modifications significantly develop and progress human malignancies including head and neck squamous cell carcinoma (HNSCC). Taking into account issues of late diagnosis and poor prognosis associated with HNSCC, this systematic review is designed to provide an up-to-date insight of epigenetic changes in the management of HNSCC. METHODS All studies that assessed the diagnostic and prognostic utilities of epigenetic changes (DNA methylation and histone modifications) among patients diagnosed with HNSCC or oral potentially malignant disorders (OPMDs) were considered for inclusion till June 2023. Pre-defined Medical Subject Headings terms were used to search Web of Science, Pubmed, Scopus and Embase Ovid databases. RESULTS Twenty-five studies were deemed eligible for inclusion with a total number of 3790 samples (2123 HNSCCs, 334 OPMDs and 1333 as controls). DNA methylation was investigated in 18 studies while the role of histone modifications was assessed in seven studies. The most investigated biomarkers among the studies were H3, DAPK and TIMP3. The diagnostic accuracy of the epigenetic biomarkers in detecting HNSCC was assessed in eight studies where the following biomarkers showed the highest area under the curve values: TIPM3, DCC, DAPK, SEPT9, SHOX9, HOXA9 and TRH. None of the studies assessed the predictability of the epigenetic biomarkers in HNSCC and OPMDs. CONCLUSION Although initial promising results were seen using the epigenetic biomarkers in the early detection of HNSCC, the limited number of patients and the absence of well-designed longitudinal studies limit the clinical applicability of the outcomes.
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Affiliation(s)
- Isaac Lim
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Jade Tan
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Anneka Alam
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Majdy Idrees
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Peter A Brenan
- Department of Oral and Maxillofacial Surgery, Queen Alexandra Hospital, Portsmouth, UK
| | - Ricardo Della Coletta
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Omar Kujan
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
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Common Expression Quantitative Trait Loci Shared by Histone Genes. Int J Genomics 2017; 2017:6202567. [PMID: 28929106 PMCID: PMC5591967 DOI: 10.1155/2017/6202567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 11/17/2022] Open
Abstract
A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined. We identified 31 eQTLs for 29 histone genes through genome-wide analysis using 29 histone genes (P < 2.97 × 10−10). Among them, 12 eQTLs were associated with the expression of multiple histone genes. Transcriptome-wide association analysis using the identified eQTLs showed their associations with additional 80 genes (P < 4.75 × 10−6). In particular, expression of RPPH1, SCARNA2, and SCARNA7 genes was associated with 26, 25, and 23 eQTLs, respectively. This study suggests that histone genes shared 12 common eQTLs that might regulate cell cycle-dependent transcription of histone and other genes. Further investigations are needed to elucidate the transcriptional mechanisms of these genes.
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Webber LP, Wagner VP, Curra M, Vargas PA, Meurer L, Carrard VC, Squarize CH, Castilho RM, Martins MD. Hypoacetylation of acetyl-histone H3 (H3K9ac) as marker of poor prognosis in oral cancer. Histopathology 2017; 71:278-286. [DOI: 10.1111/his.13218] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/18/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Liana P Webber
- Experimental Pathology Unit; Hospital de Clínicas de Porto Alegre; Porto Alegre RS Brazil
- Department of Oral Pathology; School of Dentistry; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
- Laboratory of Epithelial Biology; Department of Periodontics and Oral Medicine; University of Michigan School of Dentistry; Ann Arbor MI USA
| | - Vivian P Wagner
- Experimental Pathology Unit; Hospital de Clínicas de Porto Alegre; Porto Alegre RS Brazil
- Department of Oral Pathology; School of Dentistry; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - Marina Curra
- Experimental Pathology Unit; Hospital de Clínicas de Porto Alegre; Porto Alegre RS Brazil
- Department of Oral Pathology; School of Dentistry; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - Pablo A Vargas
- Department of Oral Diagnosis; Piracicaba Dental School; State University of Campinas; Piracicaba SP Brazil
| | - Luise Meurer
- Experimental Pathology Unit; Hospital de Clínicas de Porto Alegre; Porto Alegre RS Brazil
- Department of Pathology; School of Medicine; Universidade Federal do Rio Grande do Sul; Porto Alegre Rio Grande do Sul Brazil
| | - Vinícius C Carrard
- Department of Oral Pathology; School of Dentistry; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - Cristiane H Squarize
- Laboratory of Epithelial Biology; Department of Periodontics and Oral Medicine; University of Michigan School of Dentistry; Ann Arbor MI USA
| | - Rogério M Castilho
- Laboratory of Epithelial Biology; Department of Periodontics and Oral Medicine; University of Michigan School of Dentistry; Ann Arbor MI USA
| | - Manoela D Martins
- Experimental Pathology Unit; Hospital de Clínicas de Porto Alegre; Porto Alegre RS Brazil
- Department of Oral Pathology; School of Dentistry; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
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Identification of Significant Pathways Induced by PAX5 Haploinsufficiency Based on Protein-Protein Interaction Networks and Cluster Analysis in Raji Cell Line. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5326370. [PMID: 28316978 PMCID: PMC5339483 DOI: 10.1155/2017/5326370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/23/2017] [Accepted: 01/30/2017] [Indexed: 12/02/2022]
Abstract
PAX5 encodes a transcription factor essential for B-cell differentiation, and PAX5 haploinsufficiency is involved in tumorigenesis. There were few studies on how PAX5 haploinsufficiency regulated genes expression to promote tumorigenesis. In this study, we constructed the cell model of PAX5 haploinsufficiency using gene editing technology in Raji cells, detected differentially expressed genes in PAX5 haploinsufficiency Raji cells, and used protein-protein interaction networks and cluster analysis to comprehensively investigate the cellular pathways involved in PAX5 haploinsufficiency. The clusters of gene transcription, inflammatory and immune response, and cancer pathways were identified as three important pathways associated with PAX5 haploinsufficiency in Raji cells. These changes hinted that the mechanism of PAX5 haploinsufficiency promoting tumorigenesis may be related to genomic instability, immune tolerance, and tumor pathways.
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5
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Rui Y, Peng WJ, Wang M, Wang Q, Liu ZL, Chen YQ, Huang LN. HIST1H3D: A promising therapeutic target for lung cancer. Int J Oncol 2017; 50:815-822. [PMID: 28112369 DOI: 10.3892/ijo.2017.3856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/01/2016] [Indexed: 11/05/2022] Open
Abstract
HIST1H3D gene encodes histone H3.1 and is involved in gene-silencing and heterochromatin formation. HIST1H3D expression is upregulated in primary gastric cancer tissue. In this study, we explored the effects of HIST1H3D expression on lung cancer, and its mechanisms. HIST1H3D expression was measured by immunohistochemistry and RT-PCR in lung cancer tissues and human lung cancer cell lines. Cell proliferation was assessed by MTT assay. Flow cytometric analysis was used to determine cell cycle distribution and apoptosis. Levels of related proteins were detected by western blotting. Bioinformatics analysis was performed to investigate related signaling pathways. cDNA microarray analysis was performed to identify differentially expressed genes following HIST1H3D knockdown. HIST1H3D expression was upregulated in lung cancer tissue samples and the H1299 human lung cancer cell line (P<0.01). Regulation of HIST1H3D expression in nucleus of cells in lung cancer tissues was significant associated with tumor stage (P=0.02) and lymph node metastases (P=0.04). Downregulation of HIST1H3D expression led to suppression of proliferation and colony forming ability, cell cycle arrest at the G0/G1 phase, and promotion of cell apoptosis. The microarray data revealed 522 genes that were differentially expressed after HIST1H3D knockdown in H1299 cells. These genes were shown to be linked to numerous pathways, including the cell cycle, p53 signaling, and MCM. Western blot analysis confirmed upregulated expression of the THBS1 and TP53I3 genes, and downregulated expression of the CDK6, CDKN1 and CCNE2 genes. In conclusion, our results suggest that HIST1H3D is highly expressed in lung cancer cell lines and tissues. Furthermore, HIST1H3D may be important in cell proliferation, apoptosis and cell cycle progression, and is implicated as a potential therapeutic target for lung cancer.
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Affiliation(s)
- Yan Rui
- Department of Respiration and Critical Care Medicine, The First Affiliated Hospital of Bengbu Medical College, Lung Cancer Diagnosis and Treatment Center of Anhui Province, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, Bengbu, Anhui 233004, P.R. China
| | - Wen-Jia Peng
- Department of Epidemiology and Health Statistics, Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Ming Wang
- Department of Respiration and Critical Care Medicine, The First Affiliated Hospital of Bengbu Medical College, Lung Cancer Diagnosis and Treatment Center of Anhui Province, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, Bengbu, Anhui 233004, P.R. China
| | - Qian Wang
- Department of Respiration and Critical Care Medicine, The First Affiliated Hospital of Bengbu Medical College, Lung Cancer Diagnosis and Treatment Center of Anhui Province, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, Bengbu, Anhui 233004, P.R. China
| | - Zi-Li Liu
- Department of Respiration and Critical Care Medicine, The First Affiliated Hospital of Bengbu Medical College, Lung Cancer Diagnosis and Treatment Center of Anhui Province, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, Bengbu, Anhui 233004, P.R. China
| | - Yu-Qing Chen
- Department of Respiration and Critical Care Medicine, The First Affiliated Hospital of Bengbu Medical College, Lung Cancer Diagnosis and Treatment Center of Anhui Province, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, Bengbu, Anhui 233004, P.R. China
| | - Li-Nian Huang
- Department of Respiration and Critical Care Medicine, The First Affiliated Hospital of Bengbu Medical College, Lung Cancer Diagnosis and Treatment Center of Anhui Province, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, Bengbu, Anhui 233004, P.R. China
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Juodzbalys G, Kasradze D, Cicciù M, Sudeikis A, Banys L, Galindo-Moreno P, Guobis Z. Modern molecular biomarkers of head and neck cancer. Part I. Epigenetic diagnostics and prognostics: Systematic review. Cancer Biomark 2017; 17:487-502. [DOI: 10.3233/cbm-160666] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Gintaras Juodzbalys
- Department of Maxillofacial Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - David Kasradze
- Department of Maxillofacial Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Marco Cicciù
- Department of Biomedical and Dental Sciences, Morphological and Functional Images, School of Dentistry University of Messina, Messina, Italy
| | - Aurimas Sudeikis
- Department of Maxillofacial Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Laurynas Banys
- Department of Maxillofacial Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Pablo Galindo-Moreno
- Oral Surgery and Implant Dentistry Department, University of Granada, Granada, Spain
- Periodontics and Oral Medicine at University of Michigan, MI, USA
| | - Zygimantas Guobis
- Department of Dental and Oral Diseases, Lithuanian University of Health Sciences, Kaunas, Lithuania
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Fan H, Guo Z, Wang C. Combinations of gene ontology and pathway characterize and predict prognosis genes for recurrence of gastric cancer after surgery. DNA Cell Biol 2015; 34:579-87. [PMID: 26154702 DOI: 10.1089/dna.2015.2923] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Gastric cancer (GC) is the second leading cause of death from cancer globally. The most common cause of GC is the infection of Helicobacter pylori, but ∼11% of cases are caused by genetic factors. However, recurrences occur in approximately one-third of stage II GC patients, even if they are treated with adjuvant chemotherapy or chemoradiotherapy. This is potentially due to expression variation of genes; some candidate prognostic genes were identified in patients with high-risk recurrences. The objective of this study was to develop an effective computational method for meaningfully interpreting these GC-related genes and accurately predicting novel prognostic genes for high-risk recurrence patients. We employed properties of genes (gene ontology [GO] and KEGG pathway information) as features to characterize GC-related genes. We obtained an optimal set of features for interpreting these genes. By applying the minimum redundancy maximum relevance algorithm, we predicted the GC-related genes. With the same approach, we further predicted the genes for the prognostic of high-risk recurrence. We obtained 1104 GO terms and KEGG pathways and 530 GO terms and KEGG pathways, respectively, that characterized GC-related genes and recurrence-related genes well. Finally, three novel prognostic genes were predicted to help supplement genetic markers of high-risk GC patients for recurrence after surgery. An in-depth text mining indicated that the results are quite consistent with previous knowledge. Survival analysis of patients confirmed the novel prognostic genes as markers. By analyzing the related genes, we developed a systematic method to interpret the possible underlying mechanism of GC. The novel prognostic genes facilitate the understanding and therapy of GC recurrences after surgery.
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Affiliation(s)
- Haiyan Fan
- 1 Department of Gastroenterology and Hepatology, The Fourth Hospital of Hebei Medical University , Shijiazhuang, People's Republic of China
| | - Zhanjun Guo
- 1 Department of Gastroenterology and Hepatology, The Fourth Hospital of Hebei Medical University , Shijiazhuang, People's Republic of China
| | - Cuijv Wang
- 2 Department of Gynecology Ultrasound, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
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González-Ramírez I, Soto-Reyes E, Sánchez-Pérez Y, Herrera LA, García-Cuellar C. Histones and long non-coding RNAs: the new insights of epigenetic deregulation involved in oral cancer. Oral Oncol 2014; 50:691-5. [PMID: 24844984 DOI: 10.1016/j.oraloncology.2014.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/04/2014] [Accepted: 04/20/2014] [Indexed: 01/24/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is a category of aggressive malignancies that represent clinically, molecularly, and etiologically heterogeneous tumors. The majority of OSCCs are associated with tobacco and alcohol use, acting both independently and synergistically, which suggests that the environment plays an important role in carcinogenesis; however, the mechanisms associated with the development of OSCC are not well understood. It has been proposed that the epigenetic components could be implicated in the initiation and progression of OSCC. Primarily, aberrant DNA methylation patterns have been widely addressed in the study of OSCC. Diverse studies have proposed that other epigenetic processes such as post-translational histone modification, the deposition of histone variants, histone chaperones, and recently non-coding RNA, can be also involved in the development of oral cancer. In this review we focus on describing the new insights of the epigenetics processes that are related with OSCC as histones variants and long non-coding RNAs.
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Affiliation(s)
- I González-Ramírez
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico
| | - E Soto-Reyes
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico
| | - Y Sánchez-Pérez
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico
| | - L A Herrera
- Unidad de Investigación Biomédica en Cáncer, INCan; Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM)
| | - C García-Cuellar
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico.
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Iwaya T, Fukagawa T, Suzuki Y, Takahashi Y, Sawada G, Ishibashi M, Kurashige J, Sudo T, Tanaka F, Shibata K, Endo F, Katagiri H, Ishida K, Kume K, Nishizuka S, Iinuma H, Wakabayashi G, Mori M, Sasako M, Mimori K. Contrasting expression patterns of histone mRNA and microRNA 760 in patients with gastric cancer. Clin Cancer Res 2013; 19:6438-49. [PMID: 24097871 DOI: 10.1158/1078-0432.ccr-12-3186] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE Recent studies revealed that both disseminated tumor cells and noncancerous cells contributed to cancer progression cooperatively in the bone marrow. Here, RNA-seq analysis of bone marrow from gastric cancer patients was performed to identify prognostic markers for gastric cancer. EXPERIMENTAL DESIGN Bone marrow samples from eight gastric cancer patients (stages I and IV: n = 4 each) were used for RNA-seq analysis. Results were validated through quantitative real-time PCR (qRT-PCR) analysis of HIST1H3D expression in 175 bone marrow, 92 peripheral blood, and 115 primary tumor samples from gastric cancer patients. miR-760 expression was assayed using qRT-PCR in 105 bone marrow and 96 primary tumor samples. Luciferase reporter assays were performed to confirm whether histone mRNAs were direct targets of miR-760. miR-760 expression was also evaluated in noncancerous cells from gastric cancer patients. RESULTS RNA-seq analysis of bone marrow samples from gastric cancer patients revealed higher expression of multiple histone mRNAs in stage IV patients. HIST1H3D expression in the bone marrow, peripheral blood, and primary tumor of stage IV patients was higher than that in stage I patients (P = 0.0284, 0.0243, and 0.0006, respectively). In contrast, miR-760 was downregulated in the bone marrow and primary tumor of stage IV patients compared with stage I patients (P = 0.0094 and 0.0018, respectively). Histone mRNA and miR-760 interacted directly. Furthermore, miR-760 was downregulated in noncancerous mucosa in stage IV gastric cancer patients. CONCLUSION Histone mRNA was upregulated, whereas miR-760 was downregulated in the bone marrow and primary tumor of advanced gastric cancer patients, suggesting that the histone mRNA/miR-760 axis had a crucial role in the development of gastric cancer.
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Affiliation(s)
- Takeshi Iwaya
- Authors' Affiliations: Department of Surgery, Kyushu University Beppu Hospital, Beppu; Department of Surgery, Iwate Medical University, Morioka; Department of Gastric Surgery Division, National Cancer Center Hospital; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa-shi, Chiba; Department of Surgery, Teikyo University School of Medicine, Tokyo; Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka, University, Suita; and Department of Digestive Surgery, Hyogo Medical College, Japan
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