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Sarkar N, Mishra R, Gopal C, Kumar A. miR-617 interacts with the promoter of DDX27 and positively regulates its expression: implications for cancer therapeutics. Front Oncol 2024; 14:1411539. [PMID: 38939334 PMCID: PMC11208480 DOI: 10.3389/fonc.2024.1411539] [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: 04/03/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Background Pervasive transcription of the eukaryotic genome generates noncoding RNAs (ncRNAs), which regulate messenger RNA (mRNA) stability and translation. MicroRNAs (miRNAs/miRs) represent a group of well-studied ncRNAs that maintain cellular homeostasis. Thus, any aberration in miRNA expression can cause diseases, including carcinogenesis. According to microRNA microarray analyses, intronic miR-617 is significantly downregulated in oral squamous cell carcinoma (OSCC) tissues compared to normal oral tissues. Methods The miR-617-mediated regulation of DDX27 is established by performing experiments on OSCC cell lines, patient samples, and xenograft nude mice model. Overexpression plasmid constructs, bisulphite sequencing PCR, bioinformatics analyses, RT-qPCR, Western blotting, dual-luciferase reporter assay, and cell-based assays are utilized to delineate the role of miR-617 in OSCC. Results The present study shows that miR-617 has an anti-proliferative role in OSCC cells and is partly downregulated in OSCC cells due to the hypermethylation of its independent promoter. Further, we demonstrate that miR-617 upregulates DDX27 gene by interacting with its promoter in a dose-dependent and sequence-specific manner, and this interaction is found to be biologically relevant in OSCC patient samples. Subsequently, we show that miR-617 regulates cell proliferation, apoptosis, and anchorage-independent growth of OSCC cells by modulating DDX27 levels. Besides, our study shows that miR-617 exerts its effects through the PI3K/AKT/MTOR pathway via regulating DDX27 levels. Furthermore, the OSCC xenograft study in nude mice shows the anti-tumorigenic potential of miR-617. Conclusion miR-617-mediated upregulation of DDX27 is a novel mechanism in OSCC and underscores the therapeutic potential of synthetic miR-617 mimics in cancer therapeutics. To the best of our knowledge, miR-617 is the 15th example of a miRNA that upregulates the expression of a protein-coding gene by interacting with its promoter.
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Affiliation(s)
- Neelanjana Sarkar
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Radha Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Champaka Gopal
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Arun Kumar
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
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Zhang XY, Liu Y, Rong Q, Qi MY, Guo H. RUVBL1 accelerates tongue squamous cell carcinoma by mediating CRaf/MEK/ERK pathway. iScience 2024; 27:109434. [PMID: 38523780 PMCID: PMC10960137 DOI: 10.1016/j.isci.2024.109434] [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: 10/07/2023] [Revised: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
RAF/MEK/ERK pathway is frequently activated in tumor. Therefore, this study will investigate the function of RUVBL1 (RAF-binding protein) in tongue squamous cell carcinoma (TSCC). Bioinformatics was performed to identify differentially expressed mRNAs (DE-mRNAs) in TCGA-oral squamous cell carcinoma, GSE13601, and GSE34105 datasets. A total of 672 shared DE-mRNAs were identified in three datasets, and they are regulating metastasis and angiogenesis. Patients with RUVBL1 low expression had high overall survival. Overexpressing RUVBL1 enhanced the viability, wound healing percentage, invasion, sphere formation, angiogenesis, and resistance to cisplatin and 5-fluorouracil in CAL-27 and SCC-4 cells, and the opposite results were obtained by knocking down RUVBL1. Moreover, overexpression of RUVBL1 bolstered tumor growth in vivo. Strikingly, RUVBL1 diminished the phosphorylation of CRAF Ser259, which led to activation of the MEK/ERK pathway. In conclusion, RUVBL1 contributes to the malignant biological behavior of TSCC via activating the CRAF/MEK/ERK pathway. This provides molecular mechanisms and perspectives for targeted therapy of the CRAF/MEK/ERK pathway.
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Affiliation(s)
- Xin-yu Zhang
- The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province 650032, China
| | - Yang Liu
- Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Qiong Rong
- The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province 650032, China
| | - Ming-yue Qi
- Kunming University of Science and Technology, Kunming, Yunnan Province 650500, China
| | - Hui Guo
- The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province 650032, China
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Dou H, Song C, Wang X, Feng Z, Su Y, Wang H. Integrated bioinformatics analysis of SEMA3C in tongue squamous cell carcinoma using machine-learning strategies. Cancer Cell Int 2024; 24:58. [PMID: 38321460 PMCID: PMC10845809 DOI: 10.1186/s12935-024-03247-y] [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: 11/26/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
Tongue squamous cell carcinoma (TSCC) is an aggressive oral cancer with a high incidence of metastasis and poor prognosis. We aim to identify and verify potential biomarkers for TSCC using bioinformatics analysis. To begin with, we examined clinical and RNA expression information of individuals with TSCC from the Gene Expression Omnibus (GEO) database. Differential expression analysis and functional analysis were conducted. Multiple machine-learning strategies were next employed to screen and determine the hub gene, and receiver operating characteristic (ROC) analysis was used to assess diagnostic value. Semaphorin3C (SEMA3C) was identified as a critical biomarker, presenting high diagnostic accuracy for TSCC. In the validation cohorts, SEMA3C exhibited high expression levels in TSCC. The high expression of SEMA3C was a poor prognostic factor in TSCC by the Kaplan-Meier curve. Based on the Gene Ontology (GO) analysis, SEMA3C was mapped in terms related to cell adhesion, positive regulation of JAK-STAT, positive regulation of stem cell maintenance, and positive regulation of NF-κB activity. Single-cell RNA sequencing (ScRNA-seq) analysis showed cells expressing SEMA3C were predominantly tumor cells. Then, we further verified that SEMA3C had high expression in TSCC clinical samples. In addition, the knockdown of SEMA3C suppressed the proliferation, migration, and invasion of TSCC cells in vitro. This study is the first to report the involvement of SEMA3C in TSCC, suggesting that upregulated SEMA3C could be a novel and critical potential biomarker for future predictive diagnostics, prevention, prognostic assessment, and personalized medical services in TSCC.
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Affiliation(s)
- Huixin Dou
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Can Song
- Research and Development Department, Allife Medicine Inc., Beijing, China
| | - Xiaoyan Wang
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Capital Medical University, Beijing, China
| | - Zhien Feng
- Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Yingying Su
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
| | - Hao Wang
- Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
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Kumar K, Hallikeri K, Oli A, Goni M, Jain A, Poyya J, Shilpasree AS, Javaregowda PK. Quantitative analysis of lncRNA in formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. Biotechniques 2023; 75:133-142. [PMID: 37589188 DOI: 10.2144/btn-2023-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
The study evaluated expression profiles of few regulatory lncRNAs in oral squamous cell carcinoma and normal mucosa adjacent to oral cancer using paired fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues stored at a different duration of time (1-5 years) using real-time quantitative PCR. The quantity and quality of total RNA isolated from FFPE tissues was less compared with that of fresh frozen tissues, which resulted in a noncorrelation of quantification cycle values. Following normalization, the expression of lncRNAs in the paired tissues did not differ significantly. The differential expression of the lncRNAs in the study was consistent with The Cancer Genome Atlas head and neck squamous cell carcinoma database. The study findings demonstrate the possibility of performing accurate quantitative analysis of lncRNAs using short amplicons and standardized real-time quantitative PCR assays in oral squamous cell carcinoma FFPE samples.
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Affiliation(s)
- Kiran Kumar
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, SDM College of Dental Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Kaveri Hallikeri
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, SDM College of Dental Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Ajaykumar Oli
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Mallikarjun Goni
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Apoorva Jain
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Jagadeesha Poyya
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Alagilavada S Shilpasree
- Department of Biochemistry, SDM College of Medical Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Palaksha Kanive Javaregowda
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
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5
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Sapkota D, Sharma S, Søland TM, Braz-Silva PH, Teh MT. Expression profile of SARS-CoV-2 cellular entry proteins in normal oral mucosa and oral squamous cell carcinoma. Clin Exp Dent Res 2021; 8:117-122. [PMID: 34726347 PMCID: PMC8653086 DOI: 10.1002/cre2.510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/29/2021] [Accepted: 10/02/2021] [Indexed: 12/30/2022] Open
Abstract
Objective Besides angiotensin converting enzyme 2 (ACE2), an active involvement of proteases (FURIN and/or TMPRSS2) is important for cellular entry of SARS‐CoV‐2. Therefore, a simultaneous expression profiling of entry proteins in a tissue might provide a better risk assessment of SARS‐CoV‐2 infection as compared to individual proteins. In an attempt to understand the relative susceptibility of oral squamous cell carcinoma (OSCC) lesions as compared to the normal oral mucosa (NOM) for SARS‐CoV‐2 attachment/entry, this study examined the mRNA and protein expression profiles of ACE2, FURIN, and TMPRSS2 in the corresponding tissues using public transcriptomic and proteomics datasets. Methods and methods Public transcriptomic and proteomics datasets (the Cancer Genome Atlas (TCGA)/the Genotype‐Tissue Expression (GTEx), the Human Protein Atlas (HPA), and two independent microarray datasets) were used to examine the expression profiles of ACE2, TMPRSS2 and FURIN in NOM and OSCC. Results ACE2, TMPRSS2, and FURIN mRNAs were detected in NOM, however, at lower levels as compared to other body tissues. Except for moderate up‐regulation of FURIN, expression levels of ACE2 and TMPRSS2 mRNA were unchanged/down‐regulated in OSCC as compared to the NOM. Conclusions These results indicate that NOM may serve as a possible site for SARS‐CoV‐2 attachment, however, to a lesser extent as compared to organs with higher expression levels of the SARS‐CoV‐2 entry proteins. However, the evidence is lacking to suggest that expression status of entry proteins predisposes OSCC lesions to additional risk for SARS‐CoV‐2 attachment/entry as compared to NOM.
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Affiliation(s)
- Dipak Sapkota
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Sunita Sharma
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Tine M Søland
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.,Department of Pathology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Paulo H Braz-Silva
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Virology, Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Muy-Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Stomatological Hospital of Guizhou Medical University, Guiyang, China
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6
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Li P, Zhang S, Mo Y, Zhang L, Wang Y, Xiong F, Zhang S, Liu J, Xu Y, Zeng Z, Xiong W, Li Y, Gong Z. Long non-coding RNA expression profiles and related regulatory networks in areca nut chewing-induced tongue squamous cell carcinoma. Oncol Lett 2020; 20:302. [PMID: 33093911 DOI: 10.3892/ol.2020.12165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
Areca nut chewing is an important risk factor for developing tongue squamous cell carcinoma (TSCC), although the underlying molecular mechanism is unknown. To determine the potential molecular mechanisms of areca nut chewing-induced TSCC, the present study performed whole-genome detection with five pairs of TSCC and adjacent normal tissues, via mRNA- and long non-coding (lnc)RNA-gene chip analysis. A total of 3,860 differentially expressed genes were identified, including 2,193 lncRNAs and 1,667 mRNAs. Gene set-enrichment analysis revealed that the differentially expressed mRNAs were enriched in chromosome 22q13, 8p21 and 3p21 regions, and were regulated by nuclear factor kappa B (NF-κB) and interferon regulatory factors (IRFs). The results of ingenuity pathway analysis revealed that these mRNAs were significantly enriched for inflammatory immune-related signaling pathways. A co-expression network of mRNAs and lncRNAs was constructed by performing weighted gene co-expression network analysis. The present study focused on NF-κB-, IRF- and Th cell-signaling pathway-related lncRNAs and the corresponding mRNA-lncRNA regulatory networks. To the best of our knowledge, the present study was the first to investigate differential mRNA- and lncRNA-expression profiles in TSCCs induced by areca nut chewing. Inflammation-related mRNA-lncRNA regulatory networks driven by IRFs and NF-κB were identified, as well as the Th cell-related signaling pathways that play important carcinogenic roles in areca nut chewing-induced TSCC. These differentially expressed mRNAs and lncRNAs, and their regulatory networks provide insight for further analysis on the molecular mechanism of areca nut chewing-induced TSCC, candidate molecular markers and targets for further clinical intervention.
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Affiliation(s)
- Panchun Li
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Shanshan Zhang
- Department of Stomatology, The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yongzhen Mo
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Lishen Zhang
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yumin Wang
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Fang Xiong
- Department of Stomatology, The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Shuai Zhang
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jiang Liu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yuming Xu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yong Li
- Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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7
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Yao Z, Du L, Xu M, Li K, Guo H, Ye G, Zhang D, Coppes RP, Zhang H. MTA3-SOX2 Module Regulates Cancer Stemness and Contributes to Clinical Outcomes of Tongue Carcinoma. Front Oncol 2019; 9:816. [PMID: 31552166 PMCID: PMC6736560 DOI: 10.3389/fonc.2019.00816] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/09/2019] [Indexed: 02/05/2023] Open
Abstract
Cancer cell plasticity plays critical roles in both tumorigenesis and tumor progression. Metastasis-associated protein 3 (MTA3), a component of the nucleosome remodeling and histone deacetylase (NuRD) complex and multi-effect coregulator, can serve as a tumor suppressor in many cancer types. However, the role of MTA3 in tongue squamous cell cancer (TSCC) remains unclear although it is the most prevalent head and neck cancer and often with poor prognosis. By analyzing both published datasets and clinical specimens, we found that the level of MTA3 was lower in TSCC compared to normal tongue tissues. Data from gene set enrichment analysis (GSEA) also indicated that MTA3 was inversely correlated with cancer stemness. In addition, the levels of MTA3 in both samples from TSCC patients and TSCC cell lines were negatively correlated with SOX2, a key regulator of the plasticity of cancer stem cells (CSCs). We also found that SOX2 played an indispensable role in MTA3-mediated CSC repression. Using the mouse model mimicking human TSCC we demonstrated that the levels of MTA3 and SOX2 decreased and increased, respectively, during the process of tumorigenesis and progression. Finally, we showed that the patients in the MTA3low/SOX2high group had the worst prognosis suggesting that MTA3low/SOX2high can serve as an independent prognostic factor for TSCC patients. Altogether, our data suggest that MTA3 is capable of repressing TSCC CSC properties and tumor growth through downregulating SOX2 and MTA3low/SOX2high might be a potential prognostic factor for TSCC patients.
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Affiliation(s)
- Zhimeng Yao
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Liang Du
- Cancer Research Center, Shantou University Medical College, Shantou, China
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Cell Biology and Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Min Xu
- Department of Head and Neck Surgery, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Kai Li
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Haipeng Guo
- Department of Head and Neck Surgery, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Guodong Ye
- Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, China
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Robert P. Coppes
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Cell Biology and Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Hao Zhang
- Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, China
- Research Centre of Translational Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
- *Correspondence: Hao Zhang
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8
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Chen W, Wu K, Zhang H, Fu X, Yao F, Yang A. Odd-skipped related transcription factor 1 (OSR1) suppresses tongue squamous cell carcinoma migration and invasion through inhibiting NF-κB pathway. Eur J Pharmacol 2018; 839:33-39. [PMID: 30244004 DOI: 10.1016/j.ejphar.2018.09.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 09/09/2018] [Accepted: 09/18/2018] [Indexed: 01/13/2023]
Abstract
Tongue squamous cell carcinoma (TSCC) is the most common cancers of oral, owing to the high invasive and metastatic ability, patients with TSCC have poor prognosis, it's important to explore the regulatory mechanism of TSCC invasion and metastasis. Previous studies suggest OSR1 suppresses the progression of gastric cancer and renal cell carcinoma, but its role in TSCC hasn't been studied. Here, we found OSR1 was downregulated in TSCC cells and specimens, Transwell and 3D spheroid invasion assay suggested OSR1 overexpression inhibited TSCC cell migration and invasion, while its knockdown promoted TSCC cell migration and invasion. Mechanism analysis found OSR1 expression was negatively correlated with NF-κB pathway and its targets. Western blot and NF-κB activity analysis suggested OSR1 inhibited NF-κB activity. Double inhibition of OSR1 and NF-κB significantly inhibited TSCC cell migration and invasion. These findings suggested OSR1 inhibited TSCC cell migration and invasion through inhibiting NF-κB pathway.
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Affiliation(s)
- Weichao Chen
- Department of Head and Neck, Hospital of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, China
| | | | - Huayong Zhang
- Department of Head and Neck, Hospital of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, China
| | - Xiaoyan Fu
- Department of Head and Neck, Hospital of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, China
| | - Fan Yao
- Department of Head and Neck, Hospital of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, China
| | - Ankui Yang
- Department of Head and Neck, Hospital of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, China.
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9
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Osathanon T, Nowwarote N, Pavasant P. Expression and influence of Notch signaling in oral squamous cell carcinoma. J Oral Sci 2017; 58:283-94. [PMID: 27349552 DOI: 10.2334/josnusd.15-0535] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Notch signaling dysregulation plays an important role in altering cancer cell behaviors; however, its role in oral squamous cell carcinoma (OSCC) remains controversial. This study aimed to investigate the role of Notch signaling related genes in human OSCC using a meta-analysis of Gene Expression Omnibus database (GEO-publicly available gene expression microarray data) and to examine the role of Notch signaling in OSCC behaviors. The meta-analysis included 13 GEO datasets and was performed by combining effect sizes in a random effect model. The results demonstrated that in OSCC dysregulated genes participated in the metabolic process and protein binding as determined by gene ontology analysis. Enriched pathway analysis demonstrated the majority of the dysregulated genes were involved in pathway categories as follow; pathway in cancers, small cell lung cancer, extracellular matrix-receptor interaction, focal adhesion, and cell cycle progression. Interestingly, the enriched pathway analysis also demonstrated that OSCC samples exhibited an upregulation of genes in Notch signaling pathway, namely JAG1, JAG2, ADAM17, NCSTN, PSEN1, NCOR2, NUMB, DVL3, HDAC1, and HDAC2. Furthermore, Notch signaling inhibition by a γ-secretase inhibitor significantly decreased OSCC cell proliferation in vitro, corresponding with a decrease in C-FOS mRNA expression. The study demonstrated that Notch signaling is dysregulated in human OSCC and plays a role in cell proliferation. (J Oral Sci 58, 283-294, 2016).
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Affiliation(s)
- Thanaphum Osathanon
- Mineralized Tissue Research Unit, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University
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10
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Duchnowska R, Jarząb M, Żebracka-Gala J, Matkowski R, Kowalczyk A, Radecka B, Kowalska M, Pfeifer A, Foszczyńska-Kłoda M, Musolino A, Czartoryska-Arłukowicz B, Litwiniuk M, Surus-Hyla A, Szabłowska-Siwik S, Karczmarek-Borowska B, Dębska-Szmich S, Głodek-Sutek B, Sosińska-Mielcarek K, Chmielowska E, Kalinka-Warzocha E, Olszewski WP, Patera J, Żawrocki A, Pliszka A, Tyszkiewicz T, Rusinek D, Oczko-Wojciechowska M, Jassem J, Biernat W. Brain Metastasis Prediction by Transcriptomic Profiling in Triple-Negative Breast Cancer. Clin Breast Cancer 2016; 17:e65-e75. [PMID: 27692773 DOI: 10.1016/j.clbc.2016.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/14/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) lacks expression of steroid hormone receptors (estrogen receptor α and progesterone) and epidermal growth factor receptor type 2. This phenotype shows high metastatic potential, with particular predilection to lungs and brain. Determination of TNBC transcriptomic profiles associated with high risk of brain metastasis (BM) might identify patients requiring alternative, more aggressive, or specific preventive and therapeutic approaches. PATIENTS AND METHODS Using a cDNA-mediated annealing, selection, extension, and ligation assay, we investigated expression of 29,369 gene transcripts in primary TNBC tumor samples from 119 patients-71 in discovery cohort A and 48 in independent cohort B-that included best discriminating genes. Expression of mRNA was correlated with the occurrence of symptomatic BM. RESULTS In cohort A, the difference at the noncorrected P < .005 was found for 64 transcripts (P = .23 for global test), but none showed significant difference at a preset level of false-discovery rate of < 10%. Of the 30 transcripts with the largest differences between patients with and without BM in cohort A, none was significantly associated with BM in cohort B. CONCLUSION Analysis based on the primary tumor gene transcripts alone is unlikely to predict BM development in advanced TNBC. Despite its negative findings, the study adds to the knowledge on the biology of TNBC and paves the way for future projects using more advanced molecular assays.
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Affiliation(s)
- Renata Duchnowska
- Department of Oncology, Military Institute of Medicine, Warsaw, Poland.
| | - Michał Jarząb
- 3rd Department of Radiotherapy and Chemotherapy, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland
| | - Jadwiga Żebracka-Gala
- Laboratory of Molecular Diagnostics and Functional Genomics, Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, Wrocław, Poland
| | - Anna Kowalczyk
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Małgorzata Kowalska
- Laboratory of Molecular Diagnostics and Functional Genomics, Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland
| | - Aleksandra Pfeifer
- Laboratory of Molecular Diagnostics and Functional Genomics, Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland
| | | | | | | | - Maria Litwiniuk
- Department of Oncology, Greater Poland Cancer Center, Poznań, Poland
| | - Anna Surus-Hyla
- Department of Oncology, Warmia and Masuria Oncology Center, Olsztyn, Poland
| | | | | | | | | | | | | | | | - Wojciech P Olszewski
- Department of Pathology and Laboratory Diagnostic, Oncology Center-Institute, Warsaw, Poland
| | - Janusz Patera
- Department of Pathology, Military Institute of Medicine, Warsaw, Poland
| | - Anton Żawrocki
- Department of Pathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Agnieszka Pliszka
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | - Tomasz Tyszkiewicz
- Laboratory of Molecular Diagnostics and Functional Genomics, Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland
| | - Dagmara Rusinek
- Laboratory of Molecular Diagnostics and Functional Genomics, Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland
| | - Małgorzata Oczko-Wojciechowska
- Laboratory of Molecular Diagnostics and Functional Genomics, Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland
| | - Jacek Jassem
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdańsk, Gdańsk, Poland
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Thangaraj SV, Shyamsundar V, Krishnamurthy A, Ramani P, Ganesan K, Muthuswami M, Ramshankar V. Molecular Portrait of Oral Tongue Squamous Cell Carcinoma Shown by Integrative Meta-Analysis of Expression Profiles with Validations. PLoS One 2016; 11:e0156582. [PMID: 27280700 PMCID: PMC4900586 DOI: 10.1371/journal.pone.0156582] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/17/2016] [Indexed: 12/24/2022] Open
Abstract
Oral Tongue Squamous cell carcinoma (OTSCC), the most frequently affected oral cancer sub-site, is associated with a poor therapeutic outcome and survival despite aggressive multi- modality management. Till date, there are no established biomarkers to indicate prognosis and outcome in patients presenting with tongue cancer. There is an urgent need for reliable molecular prognostic factors to enable identification of patients with high risk of recurrence and treatment failure in OTSCC management. In the current study, we present the meta-analysis of OTSCC microarray based gene expression profiles, deriving a comprehensive molecular portrait of tongue cancer biology, showing the relevant genes and pathways which can be pursued further to derive novel, tailored therapeutics as well as for prognostication. We have studied 5 gene expression profiling data sets available on exclusively oral tongue subsite comprising of sample size; n = 190, consisting of 111 tumors and 79 normals. The meta- analysis results showed 2405 genes differentially regulated comparing OTSCC tumor and normal. The top up regulated genes were found to be involved in Extracellular matrix degradation (ECM) and Epithelial to mesenchymal transition (EMT) pathways. The top down regulated genes were found to be involved in detoxication pathways. We validated the results in clinical samples (n = 206), comprising of histologically normals (n = 10), prospective (n = 29) and retrospective (n = 167) OTSCC by evaluating MMP9 and E-cadherin gene expression by qPCR and immunohistochemistry. Consistent with meta-analysis results, MMP9 mRNA expression was significantly up regulated in OTSCC primary tumors compared to normals. MMP9 protein over expression was found to be a significant predictor of poor prognosis, disease recurrence and poor Disease Free Survival (DFS) in OTSCC patients. Analysis by univariate and multivariate Cox proportional hazard model showed patients with loss of E-cadherin expression in OTSCC tumors having a poorer DFS (HR = 1.566; P value = 0.045) and poorer Overall Survival (OS) (HR = 1.224; P value = 0.003) respectively. Combined over-expression of MMP9 and loss of E-cadherin membrane positivity in the invasive tumor front (ITF) of OTSCC had a significant association with poorer DFS (Log Rank = 16.040; P value = 0.001). These results suggest that along with known clinical indicators of prognosis like occult node positivity, assessment of MMP9 and E-cadherin expression at ITF can be useful to identify patients at high risk and requiring a more intensive treatment strategy for OTSCC. Meta-analysis study of gene expression profiles indicates that OTSCC is a disease of ECM degradation leading to activated EMT processes implying the aggressive nature of the disease. The triggers for these processes should be studied further. Newer clinical application with agents that can inhibit the mediators of ECM degradation may be a key to achieving clinical control of invasion and metastasis of OTSCC.
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Affiliation(s)
| | - Vidyarani Shyamsundar
- Centre for Oral Cancer Prevention Awareness and Research, Sree Balaji Dental College and Hospital, Chennai, India
| | | | - Pratibha Ramani
- Department of Oral and Maxillofacial Pathology, Saveetha Dental College, Saveetha University, Kumanchavadi, Chennai, India
| | - Kumaresan Ganesan
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Muthulakshmi Muthuswami
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Vijayalakshmi Ramshankar
- Department of Preventive Oncology (Research), Cancer Institute (W.I.A.), Chennai, India
- * E-mail:
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12
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Sapkota D, Bruland O, Parajuli H, Osman TA, Teh MT, Johannessen AC, Costea DE. S100A16 promotes differentiation and contributes to a less aggressive tumor phenotype in oral squamous cell carcinoma. BMC Cancer 2015; 15:631. [PMID: 26353754 PMCID: PMC4564982 DOI: 10.1186/s12885-015-1622-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 08/21/2015] [Indexed: 02/01/2023] Open
Abstract
Background Altered expression of S100A16 has been reported in human cancers, but its biological role in tumorigenesis is not fully understood. This study aimed to investigate the clinical significance and functional role of S100A16 in oral squamous cell carcinoma (OSCC) suppression. Methods S100A16 mRNA and/or protein levels were examined by quantitative RT-PCR and immunohistochemistry in whole- and laser microdissected-specimens of normal human oral mucosa (NHOM, n = 65), oral dysplastic lesions (ODL, n = 21), OSCCs (n = 132) and positive cervical nodes (n = 17). S100A16 protein expression in OSCC was examined for correlations with clinicopathological variables and patient survival. S100A16 was over-expressed and knocked-down in OSCC-derived (CaLH3 and H357) cells by employing retroviral constructs to investigate its effects on cell proliferation, sphere formation and three dimensional (3D)-organotypic invasive abilities in vitro and tumorigenesis in a mouse xenograft model. Results Both S100A16 mRNA and protein levels were found to be progressively down-regulated from NHOM to ODL and OSCC. Low S100A16 protein levels in OSCC significantly correlated with reduced 10-year overall survival and poor tumor differentiation. Analysis of two external OSCC microarray datasets showed a positive correlation between the mRNA expression levels of S100A16 and keratinocyte differentiation markers. CaLH3 and H357 cell fractions enriched for differentiated cells either by lack of adherence to collagen IV or FACS sorting for low p75NTR expression expressed significantly higher S100A16 mRNA levels than the subpopulations enriched for less differentiated cells. Corroborating these findings, retroviral mediated S100A16 over-expression and knock-down in CaLH3 and H357 cells led to respective up- and down-regulation of differentiation markers. In vitro functional studies showed significant reduction in cell proliferation, sphere formation and 3D-invasive abilities of CaLH3 and H357 cells upon S100A16 over-expression. These functional effects were associated with concomitant down-regulation of self-renewal (Bmi-1 and Oct 4A) and invasion related (MMP1 and MMP9) molecules. S100A16 over-expression also suppressed tumorigenesis of H357 cells in a mouse xenograft model and the resulting tumor xenografts displayed features/expression of increased differentiation and reduced proliferation/self-renewal. Conclusions These results indicate that S100A16 is a differentiation promoting protein and might function as a tumor suppressor in OSCC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1622-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dipak Sapkota
- Department of Clinical Medicine, The Gade Laboratory for Pathology, University of Bergen, Haukeland University Hospital, N-5021, Bergen, Norway. .,Centre for Cancer Biomarkers (CCBIO), Faculty of Medicine and Dentistry, University of Bergen, N-5021, Bergen, Norway.
| | - Ove Bruland
- Center of Medical Genetics and Molecular Medicine, Haukeland University Hospital, University of Bergen, N-5021, Bergen, Norway.
| | - Himalaya Parajuli
- Department of Clinical Medicine, The Gade Laboratory for Pathology, University of Bergen, Haukeland University Hospital, N-5021, Bergen, Norway. .,Centre for Cancer Biomarkers (CCBIO), Faculty of Medicine and Dentistry, University of Bergen, N-5021, Bergen, Norway.
| | - Tarig A Osman
- Department of Clinical Medicine, The Gade Laboratory for Pathology, University of Bergen, Haukeland University Hospital, N-5021, Bergen, Norway. .,Centre for Cancer Biomarkers (CCBIO), Faculty of Medicine and Dentistry, University of Bergen, N-5021, Bergen, Norway.
| | - Muy-Teck Teh
- Centre for Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, England, UK.
| | - Anne C Johannessen
- Department of Clinical Medicine, The Gade Laboratory for Pathology, University of Bergen, Haukeland University Hospital, N-5021, Bergen, Norway. .,Centre for Cancer Biomarkers (CCBIO), Faculty of Medicine and Dentistry, University of Bergen, N-5021, Bergen, Norway. .,Department of Pathology, Haukeland University Hospital, Bergen, Norway.
| | - Daniela Elena Costea
- Department of Clinical Medicine, The Gade Laboratory for Pathology, University of Bergen, Haukeland University Hospital, N-5021, Bergen, Norway. .,Centre for Cancer Biomarkers (CCBIO), Faculty of Medicine and Dentistry, University of Bergen, N-5021, Bergen, Norway. .,Department of Pathology, Haukeland University Hospital, Bergen, Norway.
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13
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Lloyd KL, Cree IA, Savage RS. Prediction of resistance to chemotherapy in ovarian cancer: a systematic review. BMC Cancer 2015; 15:117. [PMID: 25886033 PMCID: PMC4371880 DOI: 10.1186/s12885-015-1101-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/20/2015] [Indexed: 11/17/2022] Open
Abstract
Background Patient response to chemotherapy for ovarian cancer is extremely heterogeneous and there are currently no tools to aid the prediction of sensitivity or resistance to chemotherapy and allow treatment stratification. Such a tool could greatly improve patient survival by identifying the most appropriate treatment on a patient-specific basis. Methods PubMed was searched for studies predicting response or resistance to chemotherapy using gene expression measurements of human tissue in ovarian cancer. Results 42 studies were identified and both the data collection and modelling methods were compared. The majority of studies utilised fresh-frozen or formalin-fixed paraffin-embedded tissue. Modelling techniques varied, the most popular being Cox proportional hazards regression and hierarchical clustering which were used by 17 and 11 studies respectively. The gene signatures identified by the various studies were not consistent, with very few genes being identified by more than two studies. Patient cohorts were often noted to be heterogeneous with respect to chemotherapy treatment undergone by patients. Conclusions A clinically applicable gene signature capable of predicting patient response to chemotherapy has not yet been identified. Research into a predictive, as opposed to prognostic, model could be highly beneficial and aid the identification of the most suitable treatment for patients. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1101-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine L Lloyd
- MOAC DTC, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Ian A Cree
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Richard S Savage
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK. .,Systems Biology Centre, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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14
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Hatzfeld M, Wolf A, Keil R. Plakophilins in Desmosomal Adhesion and Signaling. ACTA ACUST UNITED AC 2014; 21:25-42. [DOI: 10.3109/15419061.2013.876017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Bonin S, Stanta G. Nucleic acid extraction methods from fixed and paraffin-embedded tissues in cancer diagnostics. Expert Rev Mol Diagn 2014; 13:271-82. [DOI: 10.1586/erm.13.14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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16
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Rentoft M, Coates PJ, Loljung L, Wilms T, Laurell G, Nylander K. Expression of CXCL10 is associated with response to radiotherapy and overall survival in squamous cell carcinoma of the tongue. Tumour Biol 2014; 35:4191-8. [PMID: 24395654 PMCID: PMC4009142 DOI: 10.1007/s13277-013-1549-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/12/2013] [Indexed: 12/23/2022] Open
Abstract
Five-year survival for patients with oral cancer has been disappointingly stable during the last decades, creating a demand for new biomarkers and treatment targets. Lately, much focus has been set on immunomodulation as a possible treatment or an adjuvant increasing sensitivity to conventional treatments. The objective of this study was to evaluate the prognostic importance of response to radiotherapy in tongue carcinoma patients as well as the expression of the CXC-chemokines in correlation to radiation response in the same group of tumours. Thirty-eight patients with tongue carcinoma that had received radiotherapy followed by surgery were included. The prognostic impact of pathological response to radiotherapy, N-status, T-stage, age and gender was evaluated using Cox's regression models, Kaplan-Meier survival curves and chi-square test. The expression of 23 CXC-chemokine ligands and their receptors were evaluated in all patients using microarray and qPCR and correlated with response to treatment using logistic regression. Pathological response to radiotherapy was independently associated to overall survival with a 2-year survival probability of 81% for patients showing a complete pathological response, while patients with a non-complete response only had a probability of 42% to survive for 2 years (p = 0.016). The expression of one CXC-chemokine, CXCL10, was significantly associated with response to radiotherapy and the group of patients with the highest CXCL10 expression responded, especially poorly (p = 0.01). CXCL10 is a potential marker for response to radiotherapy and overall survival in patients with squamous cell carcinoma of the tongue.
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Affiliation(s)
- Matilda Rentoft
- Department of Chemistry, Umeå University, 901 85, Umeå, Sweden,
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17
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Jackson AF, Williams A, Moffat I, Phillips SL, Recio L, Waters MD, Lambert IB, Yauk CL. Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform. J Pharmacol Toxicol Methods 2013; 68:260-268. [PMID: 23458726 DOI: 10.1016/j.vascn.2013.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/14/2013] [Accepted: 02/17/2013] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Tissue samples are routinely formalin-fixed and paraffin-embedded (FFPE) for long term preservation. Gene expression analysis of archival FFPE tissues may advance knowledge of the molecular perturbations contributing to disease. However, formalin causes extensive degradation of RNA. METHODS We compared RNA quality/yield from FFPE samples using six commercial FFPE RNA extraction kits. In addition we compared four DNA microarray protocols for the Agilent 8×60K platform using 16year old FFPE mouse liver samples treated with phenobarbital or vehicle. RESULTS Despite low quality RNA, archival phenobarbital samples exhibited strong induction of the positive control genes Cyp2b9 and Cyp2b10 by quantitative real-time PCR (qPCR). We tested one- and two-color microarray designs and evaluated the effects of increasing the amount of hybridized cDNA. Canonical gene responders to phenobarbital were measurably induced under each experimental condition. Increasing the amount of labeled cDNA did not improve the overall signal intensity. One-color experiments yielded larger fold changes than two-color and the number of differentially expressed genes varied between protocols. Gene expression changes were validated by qPCR and literature searches. Individual protocols exhibited high rates of false positives; however, pathway analysis revealed that nine of the top ten canonical pathways were consistent across experiments. Genes that were differentially expressed in more than one experiment were more likely to be validated. Thus, we recommend that experiments on FFPE samples be done in duplicate to reduce false positives. DISCUSSION In this analysis of archival FFPE samples we were able to identify pathways that are consistent with phenobarbital's mechanism of action. Therefore, we conclude that FFPE samples can be used for meaningful microarray gene expression analyses.
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Affiliation(s)
- A Francina Jackson
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Andrew Williams
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
| | - Ivy Moffat
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
| | | | - Leslie Recio
- ILS, Inc., P.O. Box 13501, Research Triangle Park, NC 27709, USA
| | - Michael D Waters
- ILS, Inc., P.O. Box 13501, Research Triangle Park, NC 27709, USA
| | - Iain B Lambert
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Carole L Yauk
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
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18
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Thasler WE, Thasler RMK, Schelcher C, Jauch KW. Biobanking for research in surgery: are surgeons in charge for advancing translational research or mere assistants in biomaterial and data preservation? Langenbecks Arch Surg 2013; 398:487-99. [PMID: 23430290 DOI: 10.1007/s00423-013-1060-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND High-quality biospecimens of human origin with annotated clinical and procedural data are an important tool for biomedical research, not only to map physiology, pathophysiology and aetiology but also to go beyond in translational research. This has opened a new special field of research known as 'biobanking', which focuses on how to collect, store and provide these specimens and data, and which is substantially supported by national and European funding. PURPOSE An overview on biobanking is given, with a closer look on a clinical setting, concerning a necessary distinction from clinical trials and studies as well as a comparison of prospective sample collection with secondary use of archived samples from diagnostics. Based on a summary of possible use and scientific impact of human tissue in research, it is shown how surgical expertise boosts the scientific value of specimens and data. Finally, an assessment of legal and ethical issues especially from a surgical perspective is given, followed by a model of interdisciplinary biobanking within a joint 'centre' that as synergistic structure merges essential input from surgery as well as laboratory medicine, pathology and biometry. CONCLUSION Within the domain of biobanking, surgeons have to develop a better awareness of their role within translational research, not only on the level of medical faculties but also as nationally and internationally funded initiatives. Therefore, the authors suggest a platform for biobanking within the German association of surgeons in analogy to the existing special interest group for clinical trials.
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Affiliation(s)
- Wolfgang E Thasler
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Ludwig Maximilians University, Marchioninistr. 15, 81377 Munich, Germany.
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