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Cai X, Zhang J, Li L, Liu L, Tang M, Zhou X, Peng C, Li X, Chen X, Xu M, Zhang H, Wang J, Huang Y, Li T. Copy Number Alterations Predict Development of OSCC from Oral Leukoplakia. J Dent Res 2024; 103:138-146. [PMID: 38217281 DOI: 10.1177/00220345231217160] [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] [Indexed: 01/15/2024] Open
Abstract
Oral leukoplakia (OLK) is a common type of potentially malignant disorder. Early identification of the malignancy potential leads to a better management of OLK and prediction of development of oral squamous cell carcinoma (OSCC). However, there has been no effective biomarker to assess the risk of malignancy in OLK. Genomic copy number alteration (CNA) is a complex chromosomal structural variation in the genome and has been identified as a potential biomarker in multiple cancers. This study aimed to develop a predictive model for the malignant transformation risk of OLK by copy number analysis. A total of 431 OLK samples with long-term follow-up (median follow-up of 67 mo) from multiple academic centers were analyzed for CNAs. CNA events increased with the severity of hyperplasia, mild dysplasia, moderate dysplasia, and severe dysplasia. More CNA events were present in patients with OLK who later developed OSCC than in those with OLK who did not. By multivariate Cox regression analysis, the OLK of the CNA scorehigh group showed an increased risk of malignant transformation than the CNA scorelow group (P < 0.001). A CNA score model was developed to accurately predict the prognosis (area under the receiver operating characteristic curve [AUC] = 0.879; 95% confidence interval [CI], 0.799-0.959) and was validated using data from 2 external centers (AUC = 0.836, 95% CI, 0.683-0.989; AUC = 0.876, 95% CI, 0.682-1.000), and all of them showed better prediction performances than histopathological grade in assessing the transformation risk of OLK. Furthermore, we performed CNA models among 4 subgroups of OLK with hyperplasia, mild dysplasia, moderate dysplasia, and severe dysplasia and found that CNA score can accurately predict malignant transformation of different subgroups. CNA score may be a useful biomarker to predict malignant transformation of OLK. Subtyping of OLK by the CNA score could contribute to better management of OLK and predicting development of OSCC.
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Affiliation(s)
- X Cai
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - J Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - L Li
- Hunan Key Laboratory of Oral Health Research & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - L Liu
- Changping Laboratory, Beijing, China
| | - M Tang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - X Zhou
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - C Peng
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
| | - X Li
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - X Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - M Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - H Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - J Wang
- School of Life Sciences, Tsinghua University, Beijing, China, Tsinghua University, Beijing, China
| | - Y Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - T Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China
- Laboratory of Oral Biomedicine, Henan University School of Stomatology, Kaifeng, Henan, China
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Wei K, Zhang X, Yang D. Identification and validation of prognostic and tumor microenvironment characteristics of necroptosis index and BIRC3 in clear cell renal cell carcinoma. PeerJ 2023; 11:e16643. [PMID: 38130918 PMCID: PMC10734432 DOI: 10.7717/peerj.16643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/19/2023] [Indexed: 12/23/2023] Open
Abstract
Background Necroptosis is a form of programmed cell death; it has an important role in tumorigenesis and metastasis. However, details of the regulation and function of necroptosis in clear cell renal cell carcinoma (ccRCC) remain unclear. It is necessary to explore the significance of necroptosis in ccRCC. Methods Necroptosis-related clusters were discerned through the application of Consensus Clustering. Based on the TCGA and GEO databases, we identified prognostic necroptosis-related genes (NRGs) with univariate COX regression analysis. The necroptosis-related model was constructed through the utilization of LASSO regression analysis, and the immune properties, tumor mutation burden, and immunotherapy characteristics of the model were assessed using multiple algorithms and datasets. Furthermore, we conducted comprehensive GO, KEGG, and GSVA analyses to probe into the functional aspects of biological pathways. To explore the expression and of hub gene (BIRC3) in different ccRCC cell types and cell lines, single-cell sequencing data was analysed and we performed Quantitative Real-time PCR to detect the expression of BIRC3 in ccRCC cell lines. Function of BIRC3 in ccRCC was assessed through Cell Counting Kit-8 (CCK8) assay (for proliferation), transwell and wound healing assays (for migration and invasion). Results Distinct necroptosis-related clusters exhibiting varying prognostic implications, and enrichment pathways were identified in ccRCC. A robust necroptosis-related model formulated based on the expression of six prognostic NRGs, presented substantial predictive capabilities of overall survival and was shown to be related with patients' immune profiles, tumor mutation burden, and response to immunotherapy. Notably, the hub gene BIRC3 was markedly upregulated in both ccRCC tissues and cell lines, and showed significant correlations with immunosuppressive cells, immune checkpoints, and oncogenic pathways. Downregulation of BIRC3 demonstrated a negative regulatory effect on ccRCC cell proliferation migration and invasion. Conclusion The necroptosis-related model assumed a pivotal role in determining the prognosis, tumor mutation burden, immunotherapy response, and immune cell infiltration characteristics among ccRCC patients. BIRC3 exhibited significant correlations with the immunosuppressive microenvironment, which highlighted its potential for informing the design of innovative immunotherapies for ccRCC patients.
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Affiliation(s)
- Kai Wei
- Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xi Zhang
- Urology, The State Key Lab of Reproductive; The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dongrong Yang
- Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Zhang M, Li Q, Zhang W, Yang Y, Gu J, Dong Q. Identification and validation of genes associated with copper death in oral squamous cell carcinoma based on machine learning and weighted gene co-expression network analysis. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2023; 124:101561. [PMID: 37451513 DOI: 10.1016/j.jormas.2023.101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
OBJECTIVE To identify copper-induced death-associated hub genes in oral squamous cell carcinoma (OSCC) and understand their functional and biological significance using machine learning and Weighted Gene Co-expression Network Analysis (WGCNA). METHODS OSCC transcriptomic data from GEO and TCGA databases were subjected to data integration, batch effect removal, background correction, and quantile normalization to select cuproptosis-associated genes using Spearman's correlation analysis. The 'limma' R package was used to filter differentially expressed genes (DEGs). Core module genes selected using gene co-expression network analysis with R package 'WGCNA' were screened using Support Vector Machine (SVM), LASSO regression, and Random Forest (RF) machine learning algorithms and validated using TCGA database samples. Core gene expression variations between OSCC and adjacent normal tissues were validated using immunohistochemistry. Immune infiltration analysis using package 'CIBERSORT' correlated hub genes with immune cells. RESULTS From 19 cuproptosis-related genes (identified from literature), 2382 cuproptosis-related mRNA were obtained through Spearman's correlation analysis; 112 DEGs using 'limma' R package and 32 hub genes using WGCNA were obtained. Hub genes TMPRSS11B, SERPINH1, and CDH3 were identified using machine learning algorithms. TCGA validation showed that TMPRSS11B significantly underexpressed (P < 0.001) but SERPINH1 and CDH3 significantly overexpressed (P < 0.001) in tumor samples. The AUC for TMPRSS11B, SERPINH1, and CDH3 in ROC curve analysis were 78.1%, 95.6%, and 87.5%, respectively. CONCLUSION TMPRSS11B, SERPINH1, and CDH3 may be pivotal for OSCC development and progression and potential targets for new therapeutic and predictive strategies. However, their specific functions and mechanisms underlying OSCC remain to be elucidated.
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Affiliation(s)
- Mingrui Zhang
- School of Stomatology, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qingxia Li
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Wu Zhang
- Graduate School, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yuanbo Yang
- Department of Stomatology, Tangshan Workers Hospital, Tangshan, Hebei, China
| | - Jianqi Gu
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Qing Dong
- School of Stomatology, North China University of Science and Technology, Tangshan, Hebei, China.
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Brennan K, Espín-Pérez A, Chang S, Bedi N, Saumyaa S, Shin JH, Plevritis SK, Gevaert O, Sunwoo JB, Gentles AJ. Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer. Genome Med 2023; 15:98. [PMID: 37978395 PMCID: PMC10656821 DOI: 10.1186/s13073-023-01236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The prognosis for patients with head and neck cancer (HNC) is poor and has improved little in recent decades, partially due to lack of therapeutic options. To identify effective therapeutic targets, we sought to identify molecular pathways that drive metastasis and HNC progression, through large-scale systematic analyses of transcriptomic data. METHODS We performed meta-analysis across 29 gene expression studies including 2074 primary HNC biopsies to identify genes and transcriptional pathways associated with survival and lymph node metastasis (LNM). To understand the biological roles of these genes in HNC, we identified their associated cancer pathways, as well as the cell types that express them within HNC tumor microenvironments, by integrating single-cell RNA-seq and bulk RNA-seq from sorted cell populations. RESULTS Patient survival-associated genes were heterogenous and included drivers of diverse tumor biological processes: these included tumor-intrinsic processes such as epithelial dedifferentiation and epithelial to mesenchymal transition, as well as tumor microenvironmental factors such as T cell-mediated immunity and cancer-associated fibroblast activity. Unexpectedly, LNM-associated genes were almost universally associated with epithelial dedifferentiation within malignant cells. Genes negatively associated with LNM consisted of regulators of squamous epithelial differentiation that are expressed within well-differentiated malignant cells, while those positively associated with LNM represented cell cycle regulators that are normally repressed by the p53-DREAM pathway. These pro-LNM genes are overexpressed in proliferating malignant cells of TP53 mutated and HPV + ve HNCs and are strongly associated with stemness, suggesting that they represent markers of pre-metastatic cancer stem-like cells. LNM-associated genes are deregulated in high-grade oral precancerous lesions, and deregulated further in primary HNCs with advancing tumor grade and deregulated further still in lymph node metastases. CONCLUSIONS In HNC, patient survival is affected by multiple biological processes and is strongly influenced by the tumor immune and stromal microenvironments. In contrast, LNM appears to be driven primarily by malignant cell plasticity, characterized by epithelial dedifferentiation coupled with EMT-independent proliferation and stemness. Our findings postulate that LNM is initially caused by loss of p53-DREAM-mediated repression of cell cycle genes during early tumorigenesis.
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Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Almudena Espín-Pérez
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Serena Chang
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Nikita Bedi
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Saumyaa Saumyaa
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - June Ho Shin
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John B Sunwoo
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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Shang Q, Peng J, Jiang Y, Qing M, Zhou Y, Xu H, Chen Q. SNAI2 promotes the malignant transformation of oral leukoplakia by modulating p-EMT. Oral Dis 2023; 29:3232-3242. [PMID: 35894087 DOI: 10.1111/odi.14321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Snail family transcriptional repressor 2 (SNAI2) is a key regulator of partial epithelial-mesenchymal transition (p-EMT) and is associated with tumorigenesis. Whether SNAI2 promotes oral leukoplakia (OLK) malignant transformation by modulating p-EMT is unclear. MATERIALS AND METHODS This study utilized two clinical datasets (GSE26549 and GSE85195) from the Gene Expression Omnibus database, cytological experiments, and a 4-nitroquinoline 1-oxide-induced mice model to explore the role of SNAI2 in OLK malignant transformation. RESULTS The clinical cohort found SNAI2, as a risk factor (HR = 2.50, 95% CI: 1.08-5.79, p = 0.033), could promote OLK malignant transformation (p = 0.012). Cytological experiments indicated that SNAI2 overexpression promoted DOK cell proliferation, invasion, migration, and increase the protein expression of p-EMT relative signatures, whereas SNAI2 silencing has opposite effects. Furthermore, the mice model and clinical datasets demonstrated the expression of SNAI2 and p-EMT relative signatures were increased with OLK malignant transformation. And SNAI2 was strongly correlated with p-EMT. Besides, co-expressed genes of SNAI2 were also enriched in p-EMT relative biological processes and signaling pathways. CONCLUSIONS p-EMT plays a significant role in promoting the OLK malignant transformation. As an important regulator of p-EMT, SNAI2 could be a target to block the OLK malignant transformation.
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Affiliation(s)
- Qianhui Shang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Jiakuan Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Yuchen Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Maofeng Qing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Hao Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
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Inchanalkar M, Srivatsa S, Ambatipudi S, Bhosale PG, Patil A, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers. Clin Epigenetics 2023; 15:93. [PMID: 37245006 DOI: 10.1186/s13148-023-01510-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/21/2023] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Gingivobuccal complex oral squamous cell carcinoma (GBC-OSCC) is an aggressive malignancy with high mortality often preceded by premalignant lesions, including leukoplakia. Previous studies have reported genomic drivers in OSCC, but much remains to be elucidated about DNA methylation patterns across different stages of oral carcinogenesis. RESULTS There is a serious lack of biomarkers and clinical application of biomarkers for early detection and prognosis of gingivobuccal complex cancers. Hence, in search of novel biomarkers, we measured genome-wide DNA methylation in 22 normal oral tissues, 22 leukoplakia, and 74 GBC-OSCC tissue samples. Both leukoplakia and GBC-OSCC had distinct methylation profiles as compared to normal oral tissue samples. Aberrant DNA methylation increases during the different stages of oral carcinogenesis, from premalignant lesions to carcinoma. We identified 846 and 5111 differentially methylated promoters in leukoplakia and GBC-OSCC, respectively, with a sizable fraction shared between the two sets. Further, we identified potential biomarkers from integrative analysis in gingivobuccal complex cancers and validated them in an independent cohort. Integration of genome, epigenome, and transcriptome data revealed candidate genes with gene expression synergistically regulated by copy number and DNA methylation changes. Regularised Cox regression identified 32 genes associated with patient survival. In an independent set of samples, we validated eight genes (FAT1, GLDC, HOXB13, CST7, CYB5A, MLLT11, GHR, LY75) from the integrative analysis and 30 genes from previously published reports. Bisulfite pyrosequencing validated GLDC (P = 0.036), HOXB13 (P < 0.0001) promoter hypermethylation, and FAT1 (P < 0.0001) hypomethylation in GBC-OSCC compared to normal controls. CONCLUSIONS Our findings identified methylation signatures associated with leukoplakia and gingivobuccal complex cancers. The integrative analysis in GBC-OSCC identified putative biomarkers that enhance existing knowledge of oral carcinogenesis and may potentially help in risk stratification and prognosis of GBC-OSCC.
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Affiliation(s)
- Mayuri Inchanalkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sumana Srivatsa
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Srikant Ambatipudi
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Priyanka G Bhosale
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Centre for Gene Therapy and Regenerative Medicine, Guy's Hospital, King's College London, Tower Wing, London, UK
| | - Asawari Patil
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Manoj B Mahimkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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Labat-de-Hoz L, Rubio-Ramos A, Correas I, Alonso MA. The MAL Family of Proteins: Normal Function, Expression in Cancer, and Potential Use as Cancer Biomarkers. Cancers (Basel) 2023; 15:2801. [PMID: 37345137 DOI: 10.3390/cancers15102801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/06/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
The MAL family of integral membrane proteins consists of MAL, MAL2, MALL, PLLP, CMTM8, MYADM, and MYADML2. The best characterized members are elements of the machinery that controls specialized pathways of membrane traffic and cell signaling. This review aims to help answer the following questions about the MAL-family genes: (i) is their expression regulated in cancer and, if so, how? (ii) What role do they play in cancer? (iii) Might they have biomedical applications? Analysis of large-scale gene expression datasets indicated altered levels of MAL-family transcripts in specific cancer types. A comprehensive literature search provides evidence of MAL-family gene dysregulation and protein function repurposing in cancer. For MAL, and probably for other genes of the family, dysregulation is primarily a consequence of gene methylation, although copy number alterations also contribute to varying degrees. The scrutiny of the two sources of information, datasets and published studies, reveals potential prognostic applications of MAL-family members as cancer biomarkers-for instance, MAL2 in breast cancer, MAL2 and MALL in pancreatic cancer, and MAL and MYADM in lung cancer-and other biomedical uses. The availability of validated antibodies to some MAL-family proteins sanctions their use as cancer biomarkers in routine clinical practice.
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Affiliation(s)
- Leticia Labat-de-Hoz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Armando Rubio-Ramos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Isabel Correas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Miguel A Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Cai X, Zhang J, Zhang H, Li T. Biomarkers of malignant transformation in oral leukoplakia: from bench to bedside. J Zhejiang Univ Sci B 2023; 24:868-882. [PMID: 37752089 PMCID: PMC10522567 DOI: 10.1631/jzus.b2200589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/01/2022] [Indexed: 05/16/2023]
Abstract
Oral leukoplakia is a common precursor lesion of oral squamous cell carcinoma, which indicates a high potential of malignancy. The malignant transformation of oral leukoplakia seriously affects patient survival and quality of life; however, it is difficult to identify oral leukoplakia patients who will develop carcinoma because no biomarker exists to predict malignant transformation for effective clinical management. As a major problem in the field of head and neck pathologies, it is imperative to identify biomarkers of malignant transformation in oral leukoplakia. In this review, we discuss the potential biomarkers of malignant transformation reported in the literature and explore the translational probabilities from bench to bedside. Although no single biomarker has yet been applied in the clinical setting, profiling for genomic instability might be a promising adjunct.
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Affiliation(s)
- Xinjia Cai
- Department of Oral Pathology, Peking University School and Hospital of Stomatology / National Center of Stomatology / National Clinical Research Center for Oral Diseases / National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing 100081, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing 100081, China
| | - Jianyun Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology / National Center of Stomatology / National Clinical Research Center for Oral Diseases / National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing 100081, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing 100081, China
| | - Heyu Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing 100081, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing 100081, China.
| | - Tiejun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology / National Center of Stomatology / National Clinical Research Center for Oral Diseases / National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing 100081, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing 100081, China.
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Harris A, Andl T. Precancerous Lesions of the Head and Neck Region and Their Stromal Aberrations: Piecemeal Data. Cancers (Basel) 2023; 15:cancers15082192. [PMID: 37190121 DOI: 10.3390/cancers15082192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Head and neck squamous cell carcinomas (HNSCCs) develop through a series of precancerous stages from a pool of potentially malignant disorders (PMDs). Although we understand the genetic changes that lead to HNSCC, our understanding of the role of the stroma in the progression from precancer to cancer is limited. The stroma is the primary battleground between the forces that prevent and promote cancer growth. Targeting the stroma has yielded promising cancer therapies. However, the stroma at the precancerous stage of HNSCCs is poorly defined, and we may miss opportunities for chemopreventive interventions. PMDs already exhibit many features of the HNSCC stroma, such as inflammation, neovascularization, and immune suppression. Still, they do not induce cancer-associated fibroblasts or destroy the basal lamina, the stroma's initial structure. Our review aims to summarize the current understanding of the transition from precancer to cancer stroma and how this knowledge can reveal opportunities and limitations for diagnostic, prognostic, and therapeutic decisions to benefit patients. We will discuss what may be needed to fulfill the promise of the precancerous stroma as a target to prevent progression to cancer.
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Affiliation(s)
- Ashlee Harris
- Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Pkwy, Orlando, FL 32826, USA
| | - Thomas Andl
- Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Pkwy, Orlando, FL 32826, USA
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10
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Yao L, Guo B, Wang J, Wu J. Analysis of transcriptome expression profiling data in oral leukoplakia and early and late‑stage oral squamous cell carcinoma. Oncol Lett 2023; 25:156. [PMID: 36936021 PMCID: PMC10017914 DOI: 10.3892/ol.2023.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 09/20/2022] [Indexed: 03/06/2023] Open
Abstract
The present study screened, potential prognostic biomarkers for oral carcinogenesis. The GSE85195 dataset, which consisted of oral leukoplakia (OL) and early and late-stage oral squamous cell carcinoma (OSCC) samples, was used. The differentially expressed genes (DEGs) in early OSCC vs. OL, late OSCC vs. OL and late OSCC vs. early OSCC groups were screened using the limma package in R. The Short Time-series Expression Miner software package was used to cluster DEGs with similar expression patterns in the course of disease progression (from OL to early and then late-stage OSCC). Moreover, the Database for Annotation, Visualization and Integrated Discovery online analysis tool was used to perform Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. A protein-protein interaction (PPI) network was also constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Reverse transcription-quantitative PCR was performed to assess the mRNA expression levels of hub node genes in clinical samples, and receiver operating characteristic curve analysis was performed to assess the prognostic value of the hub genes. A total of 4,595, 6,042 and 2,738 DEGs were screened in the early OSCC vs. OL, late OSCC vs. OL and late OSCC vs. early OSCC groups, respectively. A total of 665 overlapping genes were identified when the screened DEGs were compared. Cluster 1 and cluster 7 were identified as the significant clusters, which contained 496 and 341 DEGs, respectively. A PPI network was constructed with 440 interaction pairs. There were five differentially expressed hub nodes identified in different stages from OL to OSCC. The results of the present study indicated that fibronectin 1, signal transducer and activator of transcription 1, collagen type II α1 chain, collagen type X α1 chain and collagen type IV α6 chain might serve as independent diagnostic factors for OL and OSCC, and as prognostic biomarkers for OL carcinogenesis.
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Affiliation(s)
- Lihui Yao
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
- Correspondence to: Dr Lihui Yao, Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, Henan 450000, P.R. China, E-mail:
| | - Bin Guo
- Department of Stomatology, The People's Liberation Army Hong Kong Garrison Hospital, Hong Kong SAR 999077, P.R. China
| | - Jiannan Wang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Jiale Wu
- School of Stomatology, Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
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11
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Anne A, Kumar L, Salavadi RK, Anand PS, Nuguri S, Bindra S, Reddy KVR, Gummanur MR, Mohan KN. Somatic Variants and Exon-Level Copy Number Changes in Five Hyperplastic Oral Leukoplakias. Cytogenet Genome Res 2023; 162:560-569. [PMID: 36630923 DOI: 10.1159/000528890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Oral leukoplakia (OL), an oral potentially malignant disorder, begins with a hyperplastic/hyperkeratotic stage at which no genome-scale somatic single nucleotide variant profiles have been described so far. We performed exome sequencing of five cases at this stage with no evidence of dysplasia to identify genetic alterations (exon-level copy number alterations, indels, and single nucleotide variants), their association with transcript levels, and relationship with oral cancer susceptibility. Pathway enrichment analysis of genes associated with tobacco chewing and age-related mutation signatures, transcripts with variants predicted to be functionally damaging and those with significantly altered levels all indicated the involvement of focal adhesion, ECM-receptor interactions, regulation of cytoskeleton, and DNA repair. Two novel mutations identified in FAT1 tumor suppressor gene were associated with decreased transcript levels. In addition, 16 expressed cancer driver genes contained functionally damaging variants. Many of the affected genes were also reported in dysplastic OL lesions. The presence of variants in cancer driver genes and those shared with oral dysplasias possibly provides a basis for further progression and increased susceptibility to oral cancer.
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Affiliation(s)
- Anuhya Anne
- Molecular Biology and Genetics Laboratory, BITS Pilani Hyderabad Campus, Hyderabad, India
- Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad, India
| | - Lov Kumar
- Computer Science and Information Systems, BITS Pilani Hyderabad Campus, Hyderabad, India
| | | | | | | | | | | | | | - Kommu N Mohan
- Molecular Biology and Genetics Laboratory, BITS Pilani Hyderabad Campus, Hyderabad, India
- Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad, India
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12
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Poonia S, Goel A, Chawla S, Bhattacharya N, Rai P, Lee YF, Yap YS, West J, Bhagat AA, Tayal J, Mehta A, Ahuja G, Majumdar A, Ramalingam N, Sengupta D. Marker-free characterization of full-length transcriptomes of single live circulating tumor cells. Genome Res 2023; 33:80-95. [PMID: 36414416 PMCID: PMC9977151 DOI: 10.1101/gr.276600.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022]
Abstract
The identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor in the enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypes relative to the primary tumor. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from peripheral blood. Most CTC detection methods based on single-cell RNA sequencing (scRNA-seq) use a mix of size selection, marker-based white blood cell (WBC) depletion, and antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analyses. These include a novel method of scRNA-seq clustering, named deep dictionary learning using k-means clustering cost (DDLK), expression-based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell FX and Polaris workflow that works by the principles of size-based separation of CTCs and marker-based WBC depletion.
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Affiliation(s)
- Sarita Poonia
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Anurag Goel
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Department of Computer Science and Engineering, Delhi Technological University, New Delhi 110042, India
| | - Smriti Chawla
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Namrata Bhattacharya
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Priyadarshini Rai
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Yi Fang Lee
- Biolidics Limited, Singapore 118257, Singapore
| | - Yoon Sim Yap
- National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Jay West
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | | | - Juhi Tayal
- Department of Research, Rajiv Gandhi Cancer Institute and Research Centre-Delhi (RGCIRC-Delhi), New Delhi 110085, India
| | - Anurag Mehta
- Department of Laboratory Services and Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre-Delhi (RGCIRC-Delhi), New Delhi 110085, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Angshul Majumdar
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Department of Electronics & Communications Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | | | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
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13
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Screening for Biomarkers for Progression from Oral Leukoplakia to Oral Squamous Cell Carcinoma and Evaluation of Diagnostic Efficacy by Multiple Machine Learning Algorithms. Cancers (Basel) 2022; 14:cancers14235808. [PMID: 36497288 PMCID: PMC9738227 DOI: 10.3390/cancers14235808] [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: 10/31/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
The aim of the study is to identify key genes during the progression from oral leukoplakia (OL) to oral squamous cell carcinoma (OSCC) and predict effective diagnoses. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to identify seven genes associated with the progression from OL to OSCC. Twelve machine learning algorithms including k-nearest neighbor (KNN), neural network (NNet), and extreme gradient boosting (XGBoost) were used to construct multi-gene models, which revealed that each model had good diagnostic efficacy. The functional mechanism or the pathways associated with these genes were evaluated using enrichment analysis, subtype clustering, and immune infiltration analysis. The enrichment analysis revealed that the genes enriched were associated with the cell cycle, cell division, and intracellular energy metabolism. The immunoassay results revealed that the genes primarily affected the infiltration of proliferating T cells and macrophage polarization. Finally, a nomogram and Kaplan-Meier survival analysis were used to predict the prognostic efficacy of key genes in OSCC patients. The results showed that genes could predict the prognosis of the patients, and patients in the high-risk group had a poor prognosis. Our study identified that the seven key genes, including DHX9, BCL2L12, RAD51, MELK, CDC6, ANLN, and KIF4A, were associated with the progression from OL to OSCC. These genes had good diagnostic efficacy and could be used as potential biomarkers for the prognosis of OSCC patients.
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14
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de Avila JG, Redondo CS, Alviz-Amador A. Bioinformatic Analysis of Plus Gene Expression Related to Progression from Leukoplakia to Oral Squamous Cell Carcinoma. Asian Pac J Cancer Prev 2022; 23:3833-3842. [PMID: 36444596 PMCID: PMC9930946 DOI: 10.31557/apjcp.2022.23.11.3833] [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: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Leukoplakia is one of the most frequently found lesions in the oral cavity, with a probability of 17 to 24% of becoming malignant cells in a period of 30 years. OBJECTIVE To identify differentially expressed gene profiles of leukoplakia and its progression to oral squamous cell carcinoma, essential for the discovery of new biomarkers to predict and prevent the presence of diseases in the oral cavity. METHODS Initially, gene profiles of GSE85514 and GSE160042 from the Gene Expression Omnibus database were used. Differentially expressed genes were identified using GEO2R. The CLUEGO plugin in Cytoscape was used for DEG functionality and enrichment analysis. Finally, a protein-protein interaction (PPI) network was constructed using Cytoscape from data collected online from the STRING server. RESULTS According to the MCC algorithm, the 10 most found gene sequences were HNRNPU, SMC1A, PAFAH1B1, EHMT1, SPTBN4, OLFM1, NCAM1, SF3B3, FGF2, and UBE2I; with HNRNPU, SMC1A, and PAFAH1B1 being the most representative of the modules. CONCLUSIONS We were able to describe the gene sequences that promote the progression from leukoplakia to oral squamous cell carcinoma. Within these genes, the HNRNPU, SMC1A, and PAFAH1B1 constitute the main promising therapeutic targets to counteract the progression of oral cancer, they could also be important biomarkers for the diagnosis and classification of the disease.
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Affiliation(s)
- Jaime Guzman de Avila
- Department of Oral Medicine, School of Dentistry, University of Cartagena Cartagena, Colombia.
| | | | - Antistio Alviz-Amador
- Pharmacology and Therapeutic Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Health Science Campus, Colombia. ,For Correspondence:
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15
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Elevated Expression of miR-200c/141 in MDA-MB-231 Cells Suppresses MXRA8 Levels and Impairs Breast Cancer Growth and Metastasis In Vivo. Genes (Basel) 2022; 13:genes13040691. [PMID: 35456497 PMCID: PMC9032019 DOI: 10.3390/genes13040691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/28/2022] [Accepted: 04/09/2022] [Indexed: 02/06/2023] Open
Abstract
Breast cancer cells with mesenchymal characteristics, particularly the claudin-low subtype, express extremely low levels of miR-200s. Therefore, this study examined the functional impact of restoring miR-200 expression in a human claudin-low breast cancer cell line MDA-MB-231. MDA-MB-231 cells were stably transfected with a control vector (MDA-231EV) or the miR-200c/141 cluster (MDA-231c141). Injection of MDA-231c141 cells into the 4th mammary gland of NCG mice produced tumors that developed significantly slower than tumors produced by MDA-231EV cells. Spontaneous metastasis to the lungs was also significantly reduced in MDA-231c141 cells compared to MDA-231EV cells. RNA sequencing of MDA-231EV and MDA-231c141 tumors identified genes including MXRA8 as being downregulated in the MDA-231c141 tumors. MXRA8 was further investigated as elevated levels of MXRA8 were associated with reduced distant metastasis free survival in breast cancer patients. Quantitative RT-PCR and Western blotting confirmed that MXRA8 expression was significantly higher in mammary tumors induced by MDA-231EV cells compared to those induced by MDA-231c141 cells. In addition, MXRA8 protein was present at high levels in metastatic tumor cells found in the lungs. This is the first study to implicate MXRA8 in human breast cancer, and our data suggests that miR-200s inhibit growth and metastasis of claudin-low mammary tumor cells in vivo through downregulating MXRA8 expression.
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16
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Truchard E, Bertolus C, Martinez P, Thomas E, Saintigny P, Foy JP. Identification of a Gene-Expression-Based Surrogate of Genomic Instability during Oral Carcinogenesis. Cancers (Basel) 2022; 14:cancers14030834. [PMID: 35159101 PMCID: PMC8834046 DOI: 10.3390/cancers14030834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary New personalized cancer prevention strategies may decrease the mortality of oral cancer that can arise from oral potentially malignant disorders (OPMD). A major cancer hallmark is the acquisition of multiple deletions or amplifications of genomic material fragments leading to genomic instability (GI). Our goal was to identify a set of genes whose expression was associated with GI. A total of 20 genes correlated with GI were identified in two independent datasets of head and neck cancer (including oral cancer). We computed a score of those genes, referred to as the GIN score, in with each sample from multiple validation datasets. We show that the GIN score: (i) was correlated with GI, (ii) increased at different stages of oral carcinogenesis from normal mucosa to oral cancer, and (iii) was associated with malignant transformation of OPMD. The GIN score is a promising biomarker for identifying patients suffering from OPMD with high risk of oral cancer. Abstract Background: Our goal was to identify a gene-expression-based surrogate of genomic instability (GI) associated with the transformation of oral potentially malignant disorder (OPMD) into oral squamous cell carcinoma (OSCC). Methods: GI was defined as the fraction of genome altered (FGA). Training sets included the CCLE and TCGA databases. The relevance of the enrichment score of the top correlated genes, referred to as the GIN score, was evaluated in eight independent public datasets from the GEO repository, including a cohort of patients with OPMD with available outcome. Results: A set of 20 genes correlated with FGA in head and neck SCC were identified. A significant correlation was found between the 20-gene based GIN score and FGA in 95 esophagus SCC (r = 0.59) and 501 lung SCC (r = 0.63), and in 33 OPMD/OSCC (r = 0.38). A significantly increased GIN score was observed at different stages of oral carcinogenesis (normal–dysplasia –OSCC) in five independent datasets. The GIN score was higher in 10 OPMD that transformed into oral cancer compared to 10 nontransforming OPMD (p = 0.0288), and was associated with oral-cancer-free survival in 86 patients with OPMD (p = 0.0081). Conclusions: The GIN score is a gene-expression surrogate of GI, and is associated with oral carcinogenesis and OPMD malignant transformation.
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Affiliation(s)
- Eléonore Truchard
- Sorbonne Université, Department of Maxillo-Facial Surgery, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France; (E.T.); (C.B.)
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
| | - Chloé Bertolus
- Sorbonne Université, Department of Maxillo-Facial Surgery, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France; (E.T.); (C.B.)
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
| | - Pierre Martinez
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
| | - Emilie Thomas
- Synergie Lyon Cancer-Platform of Bioinformatics Gilles Thomas, 69008 Lyon, France;
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
- Department of Medical Oncology, Centre Léon Bérard, 69008 Lyon, France
| | - Jean-Philippe Foy
- Sorbonne Université, Department of Maxillo-Facial Surgery, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France; (E.T.); (C.B.)
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
- Correspondence: ; Tel.: +33-(0)1421-61448; Fax: +33-(0)1421-61449
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Identification of Biomarkers Associated with Cancerous Change in Oral Leukoplakia Based on Integrated Transcriptome Analysis. JOURNAL OF ONCOLOGY 2022; 2022:4599305. [PMID: 35096060 PMCID: PMC8791753 DOI: 10.1155/2022/4599305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/04/2022] [Indexed: 12/21/2022]
Abstract
Objective Oral leukoplakia (OLK) is the most common precancerous lesion in the oral cavity. This study aimed to explore key biomarkers for monitoring OLK for early diagnosis of oral squamous cell carcinoma (OSCC) and screen small-molecule drugs for the prevention of OSCC. Method The Gene Expression Omnibus (GEO) database was explored to extract two microarray datasets, namely, GSE85195 and GSE25099. The data of the normal group, OLK group, and OSCC group were analyzed by weighted gene coexpression network analysis (WGCNA) to identify the most significant gene module and differentially expressed genes (DEGs). The intersection genes were extracted as the key genes of OLK carcinogenesis. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed in the module. Connectivity Map and molecular docking were used to screen small-molecule drugs. The diagnostic values of four key genes were identified and verified in the GSE26549 dataset. Results WGCNA obtained the red module (r = −0.91, p < 0.05) with the strongest correlation with cancerous phenotype. GO enrichment analysis showed 60 pathways, including 28 biological processes, 11 cell components, and 21 molecular functions, and KEGG enrichment analysis showed 4 pathways (p < 0.05). In the differential expression analysis, there was no intersection between the upregulated genes and the red module genes. However, the intersection of the downregulated genes and the red module genes yielded 4 key genes: dopachrome tautomerase (DCT), keratin 3 (KRT3), keratin 76 (KRT76), and FAM3 metabolic regulation signal molecule B (FAM3B). The area under the curve of the diagnostic model constructed by these four genes was 0.963 (CI = 0.913–1.000). The sensitivity was 0.933, and the specificity was 0.923. The diagnostic model was successfully verified in GSE26549 (AUC = 0.745, CI = 0.638–0.851). Compared with the diagnostic models of the previous studies, the diagnostic efficiency of this model was the highest. The small-molecule drugs, selumetinib and benidipine, were selected according to the gene expression profile and showed binding activity when docking with the above molecules. Conclusions This study provides new targets and drugs for OLK. These targets could be used as the key diagnostic molecules for long-term follow-up of OLK. The small-molecule drugs selumetinib and benidipine could be used for the prevention and treatment of OSCC.
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Mizuki H, Shimoyama Y, Ishikawa T, Sasaki M. A genomic sequence of the type II-A clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system in Mycoplasma salivarium strain ATCC 29803. J Oral Microbiol 2022; 14:2008153. [PMID: 34992734 PMCID: PMC8725752 DOI: 10.1080/20002297.2021.2008153] [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] [Indexed: 10/26/2022] Open
Abstract
Introduction Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated systems are RNA-mediated adaptive immune systems that actagainst invading genetic elements such as phages or plasmids. CRISPR/Cas systems exist in nearly half of bacteria. Mycoplasma salivarium is a commensal species of the oropharynx. The American Type Culture Collection maintains five M. salivarium strains: ATCC 14277, 23064, 23557, 29803, and 33130. The genome sequence of ATCC 23064 revealed that it has an incomplete CRISPR/Cas system. However, the genome sequences of the remaining strains have not been analyzed. Methods We performed polymerase chain reaction-amplicon sequencing and de novo genome sequencing to evaluate the presence of the CRISPR/Cas system in four strains. Results Only ATCC 29803 possessed cas1, cas2, cas9, and csn2 genes, a CRISPR array, and tracrRNA. The sequences of most components were identical between the CRISPR/Cas systems of ATCC 29803 and ATCC 23064, whereas the spacer sequences and a region of the cas9 gene were different. Unlike the CRISPR/Cas system of ATCC 23064, the cas9 gene of ATCC 29803 was not disrupted by the presence of stop codons. Conclusion ATCC 29803 possesses genomic components required to express the type II-A CRISPR/Cas system, which potentially functions as an RNA-guided endonuclease.
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Affiliation(s)
- Harumi Mizuki
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
| | - Yu Shimoyama
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
| | - Taichi Ishikawa
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
| | - Minoru Sasaki
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
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Bardhan A, Banerjee A, Basu K, Pal DK, Ghosh A. PRNCR1: a long non-coding RNA with a pivotal oncogenic role in cancer. Hum Genet 2021; 141:15-29. [PMID: 34727260 PMCID: PMC8561087 DOI: 10.1007/s00439-021-02396-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been gaining importance in the field of cancer research in recent years. PRNCR1 (prostate cancer-associated non-coding RNA1) is a 12.7 kb, intron-less lncRNA found to play an oncogenic role in malignancy of diverse organs including prostate, breast, lung, oral cavity, colon and rectum. Single-nucleotide polymorphisms (SNPs) of PRNCR1 locus have been found to be associated with cancer susceptibility in different populations. In this review, an attempt has been made for the first time to summarize all sorts of available data on PRNCR1 to date from relevant databases (GeneCard, LncExpDB, Ensembl genome browser, and PubMed). As functional roles of PRNCR1, miRNA (microRNA) sponging was mostly highlighted in the pathogenesis of different cancer; in addition, an association of the lncRNA with chromatin-modifying complex to enhance androgen receptor-mediated gene transcription was reported in prostate cancer. Diagnostic and prognostic importance of PRNCR1 was found in some malignancies suggesting potency of the lncRNA to serve as a clinical biomarker. For PRNCR1 SNPs, although cancer susceptibility of the risk alleles/genotypes was reported in different populations, majorities of the findings were not replicated and underlying molecular mechanisms remained unexplored. Therapeutic implication of PRNCR1 was not studied well and future research may come up in this direction for intervening novel strategies to fight against cancer.
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Affiliation(s)
- Abhishek Bardhan
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Anwesha Banerjee
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Keya Basu
- Department of Pathology, IPGME&R, Kolkata, West Bengal, India
| | | | - Amlan Ghosh
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
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20
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Cai X, Zhang H, Li T. The role of SPP1 as a prognostic biomarker and therapeutic target in head and neck squamous cell carcinoma. Int J Oral Maxillofac Surg 2021; 51:732-741. [PMID: 34489157 DOI: 10.1016/j.ijom.2021.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/05/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies and has a low 5-year survival rate. Mounting evidence suggests that oral potentially malignant disorders, such as oral leukoplakia (OLK), may progress to HNSCC. Given that OLK and HNSCC are often insidious and asymptomatic, the identification of markers of OLK malignant transformation and therapeutic targets in HNSCC is critical. Using various online tools and publicly available gene expression datasets, the secreted phosphoprotein 1 gene (SPP1) was identified as a significant differentially expressed gene among OLK, HNSCC, and non-cancerous tissues. SPP1 mRNA levels were elevated in HNSCC tissues and were associated with cancer stage, tumor grade, and human papillomavirus infection status. High SPP1 mRNA levels were correlated with poor overall survival of HNSCC patients. In contrast, SPP1 mutations were not significantly associated with overall survival, although their frequency in HNSCC was very low (0.6%). Furthermore, SPP1 expression levels in HNSCC were positively correlated with the infiltration of CD4+ cells, macrophages, neutrophils, and dendritic cells. The study results suggest that SPP1 may represent a diagnostic and prognostic biomarker, as well as a potential therapeutic target in HNSCC.
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Affiliation(s)
- X Cai
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Haidian District, Beijing, People's Republic of China; Research Unit of Precision Pathological Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, People's Republic of China
| | - H Zhang
- Research Unit of Precision Pathological Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, People's Republic of China; Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China.
| | - T Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Haidian District, Beijing, People's Republic of China; Research Unit of Precision Pathological Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, People's Republic of China.
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21
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Li X, Liu L, Zhang J, Ma M, Sun L, Li X, Zhang H, Wang J, Huang Y, Li T. Improvement in the risk assessment of oral leukoplakia through morphology-related copy number analysis. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1379-1391. [PMID: 34351567 DOI: 10.1007/s11427-021-1965-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/08/2021] [Indexed: 10/20/2022]
Abstract
Oral leukoplakia is the most common type of oral potentially malignant disorders and considered a precursor lesion to oral squamous cell carcinoma. However, a predictor of oral leukoplakia prognosis has not yet been identified. We investigated whether copy number alteration patterns may effectively predict the prognostic outcomes of oral leukoplakia using routinely processed paraffin sections. Comparison of copy number alteration patterns between oral leukoplakia with hyperplasia (HOL, n=22) and dysplasia (DOL, n=21) showed that oral leukoplakia with dysplasia had a higher copy number alteration rate (86%) than oral leukoplakia with hyperplasia (46%). Oral leukoplakia with dysplasia exhibited a wider range of genomic variations across all chromosomes compared with oral leukoplakia with hyperplasia. We also examined a retrospective cohort of 477 patients with oral leukoplakia with hyperplasia with detailed follow-up information. The malignant transformation (MT, n=19) and leukoplakia recurrence (LR, n=253) groups had higher frequencies of aneuploidy events and copy number loss rate than the free of disease (FD, n=205) group. Together, our results revealed the association between the degree of copy number alterations and the histological grade of oral leukoplakia and demonstrated that copy number alteration may be effective for prognosis prediction in oral leukoplakia patients with hyperplasia.
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Affiliation(s)
- Xiaotian Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Lu Liu
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jianyun Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Ming Ma
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Lisha Sun
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Xuefen Li
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Heyu Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China. .,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China.
| | - Jianbin Wang
- School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China. .,College of Chemistry and Molecular Engineering and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China. .,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, 528107, China.
| | - Tiejun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China. .,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China.
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22
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Rubio-Ramos A, Labat-de-Hoz L, Correas I, Alonso MA. The MAL Protein, an Integral Component of Specialized Membranes, in Normal Cells and Cancer. Cells 2021; 10:1065. [PMID: 33946345 PMCID: PMC8145151 DOI: 10.3390/cells10051065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
The MAL gene encodes a 17-kDa protein containing four putative transmembrane segments whose expression is restricted to human T cells, polarized epithelial cells and myelin-forming cells. The MAL protein has two unusual biochemical features. First, it has lipid-like properties that qualify it as a member of the group of proteolipid proteins. Second, it partitions selectively into detergent-insoluble membranes, which are known to be enriched in condensed cell membranes, consistent with MAL being distributed in highly ordered membranes in the cell. Since its original description more than thirty years ago, a large body of evidence has accumulated supporting a role of MAL in specialized membranes in all the cell types in which it is expressed. Here, we review the structure, expression and biochemical characteristics of MAL, and discuss the association of MAL with raft membranes and the function of MAL in polarized epithelial cells, T lymphocytes, and myelin-forming cells. The evidence that MAL is a putative receptor of the epsilon toxin of Clostridium perfringens, the expression of MAL in lymphomas, the hypermethylation of the MAL gene and subsequent loss of MAL expression in carcinomas are also presented. We propose a model of MAL as the organizer of specialized condensed membranes to make them functional, discuss the role of MAL as a tumor suppressor in carcinomas, consider its potential use as a cancer biomarker, and summarize the directions for future research.
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Affiliation(s)
- Armando Rubio-Ramos
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
| | - Leticia Labat-de-Hoz
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
| | - Isabel Correas
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Miguel A. Alonso
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.R.-R.); (L.L.-d.-H.); (I.C.)
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23
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Fang R, Lu Q, Xu B. hsa‑miR‑5580‑3p inhibits oral cancer cell viability, proliferation and migration by suppressing LAMC2. Mol Med Rep 2021; 23:453. [PMID: 33880581 PMCID: PMC8072311 DOI: 10.3892/mmr.2021.12092] [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: 02/28/2020] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
The present study aimed to explore whether and how microRNA-5580-3p (miR-5580-3p) affected oral cancer (OC) cell phenotypes via regulation of laminin subunit γ2 (LAMC2). Bioinformatics analysis was used to identify miR-5580-3p/LAMC2, a novel interactome that, to the best of our knowledge, has not been studied previously in OC. In the present study, the expression levels of miR-5580-3p and LAMC2 were detected by reverse transcription-quantitative PCR, while the protein expression levels of LAMC2 were identified using western blotting. To determine the effects of miR-5580-3p and LAMC2 in OC, a number of experiments, including Cell Counting Kit-8, 5-bromo-2′-deoxyuridine cell proliferation and wound healing migration assays, were performed using OC SCC-4 and Cal-27 cell lines. Additionally, luciferase reporter assays were employed to examine the interaction between miR-5580-3p and LAMC2 mRNA. The results demonstrated that miR-5580-3p expression was downregulated, while LAMC2 expression was upregulated in OC tissues and cell lines. In addition to the observation that miR-5580-3p promoted the malignant phenotypes of OC, it was also revealed that miR-5580-3p inhibited OC cell viability, proliferation and migration by suppressing LAMC2. Therefore, the present study suggested that miR-5580-3p and LAMC2 may be potential biomarkers and therapeutic targets for OC diagnosis and therapies in the future.
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Affiliation(s)
- Rong Fang
- Department of Gastroenterology, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430033, P.R. China
| | - Qian Lu
- Department of Stomatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430015, P.R. China
| | - Bo Xu
- Department of Gastroenterology, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430033, P.R. China
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Abstract
BACKGROUND The evasion from apoptosis is a common strategy adopted by most tumors, and inhibitors of apoptosis proteins (IAPs) are among the most studied molecular and therapeutic targets. BIRC3 (cellular IAP2) and BIRC5 (survivin) are two of the eight members of the human IAPs family. This family is characterized by the presence of the baculoviral IAP repeat (BIR) domains, involved in protein-protein interactions. In addition to the BIR domains, IAPs also contain other important domains like the C-terminal ubiquitin-conjugating (UBC) domain, the caspase recruitment (CARD) domain and the C-terminal Ring zinc-finger (RING) domain. MAIN BODY BIRC3 and BIRC5 have been characterized in some solid and hematological tumors and are therapeutic targets for the family of drugs called "Smac mimetics". Many evidences point to the pro-survival and antiapoptotic role of BIRC3 in cancer cells, however, not all the data are consistent and the resulting picture is heterogeneous. For instance, BIRC3 genetic inactivation due to deletions or point mutations is consistently associated to shorter progression free survival and poor prognosis in chronic lymphocytic leukemia patients. BIRC3 inactivation has also been associated to chemoimmunotherapy resistance. On the contrary, the progression from low grade gliomas to high grade gliomas is accompanied by BIRC3 expression increase, which bears relevant prognostic consequences. Due to the relationship between BIRC3, MAP3K14 and the non-canonical NF-kB pathway, BIRC3 inactivation bears consequences also on the tumor cells relying on NF-kB pathway to survive. BIRC5, on the contrary, is commonly considered an anti-apoptotic molecule, promoting cell division and tumor progression and it is widely regarded as potential therapeutic target. CONCLUSIONS The present manuscript collects and reviews the most recent literature concerning the role played by BIRC3 and BIRC5 in cancer cells, providing useful information for the choice of the best therapeutic targets.
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Affiliation(s)
- Raffaele Frazzi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, Reggio Emilia, Italy.
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25
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Zhang W, Xu S, Shi L, Zhu Z, Xie X. Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma. PLoS One 2020; 15:e0238420. [PMID: 32931492 PMCID: PMC7491744 DOI: 10.1371/journal.pone.0238420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 08/17/2020] [Indexed: 11/18/2022] Open
Abstract
Background Patients diagnosed with Oral Floor Squamous Cell Carcinoma (OFSCC) face considerable challenges in physiology and psychology. This study explored prognostic signatures to predict prognosis in OFSCC through a detailed transcriptomic analysis. Method We built an interactive competing endogenous RNA (ceRNA) network that included lncRNAs, miRNAs and mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to predict the gene functions and regulatory pathways of mRNAs. Least absolute shrinkage and selection operator algorithm (LASSO) analysis and Cox regression analysis were used to screen prognosis factors. The Kaplan-Meier method was used to analyze the survival rate of prognosis factors. Risk score was used to assess the reliability of the prediction model. Results A specific ceRNA network consisting of 56 mRNAs, 16 miRNAs and 31 lncRNAs was established. Three key genes (HOXC13, TGFBR3, KLHL40) and 4 clinical factors (age, gender, TNM, and clinical stage) were identified and effectively predicted the for survival time. The expression of a gene signature was validated in two external validation cohorts. The signature (areas under the curve of 3 and 5 years were 0.977 and 0.982, respectively) showed high prognostic accuracy in the complete TCGA cohort. Conclusions Our study successfully developed an extensive ceRNA network for OFSCC and further identified a 3-mRNA and 4-clinical-factor signature, which may serve as a biomarker.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/mortality
- Databases, Nucleic Acid
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Gene Ontology
- Gene Regulatory Networks
- Homeodomain Proteins/genetics
- Humans
- Kaplan-Meier Estimate
- Male
- MicroRNAs/genetics
- Middle Aged
- Mouth Floor
- Mouth Neoplasms/genetics
- Mouth Neoplasms/mortality
- Muscle Proteins/genetics
- Prognosis
- Proteoglycans/genetics
- RNA, Long Noncoding/genetics
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Receptors, Transforming Growth Factor beta/genetics
- Risk Factors
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Affiliation(s)
- Wenjing Zhang
- Department of Health Management Center, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of First College of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Shuai Xu
- Endocrine Department, Shenzhen Bao'an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Laner Shi
- Department of First College of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhangzhi Zhu
- Endocrine Department, Guangzhou University of Traditional Chinese Medicine First Affiliated Hospital, Guangzhou, Guangdong, China
- * E-mail: (ZZ); (XX)
| | - Xinying Xie
- General Department, Guangzhou University of Traditional Chinese Medicine First Affiliated Hospital, Guangzhou, Guangdong, China
- * E-mail: (ZZ); (XX)
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26
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Identification of oncogenic long noncoding RNAs CASC9 and LINC00152 in oral carcinoma through genome-wide comprehensive analysis. Anticancer Drugs 2020; 30:356-362. [PMID: 30543527 DOI: 10.1097/cad.0000000000000725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Oral carcinoma (OC) is the major cancer type in the head and neck region; however, the molecular mechanisms of its pathogenesis and progression remain poorly understood. In recent years, the long noncoding RNAs (lncRNAs) have been uncovered as critical regulators in the development and progression of multiple human cancers, but most of the lncRNAs expression patterns, clinical relevance, and biological functions in OC are still unclear. To better understand the significance of lncRNAs in OC carcinogenesis, we analyzed the expression levels of lncRNAs between OC and healthy oral mucosa using The Cancer Genome Atlas Cancer Genome RNA sequencing data and another three independent microarray datasets from Gene Expression Omnibus. As a result, we found that thousands of lncRNAs expression are dysregulated in OC, and further somatic copy number variation analyses showed that some of these lncRNAs alterations are associated with copy number amplification or loss in OC. Moreover, lots of lncRNAs expression levels are associated with OC patients' overall survival and recurrence-free survival; for example, higher CASC9, LINC01232, and MIR4435-1HG expression levels are related to shorter overall survival and recurrence-free survival in OC patients. Finally, the potential function of two lncRNAs (CASC9 and LINC00152) that were upregulated in OC tissues and associated with patients' survival time was verified by loss-of-function assays in OC cells. Our findings indicate that these altered lncRNAs might play important roles in the development of OC, and our data can provide a valuable list of lncRNAs candidates for further investigation of their function and mechanisms in OC.
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27
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Zhao L, Xu L, Hemmerich A, Ferguson NL, Guy CD, McCall SJ, Cardona DM, Westerhoff M, Pai RK, Xiao SY, Liu B, Green CL, Hart J, Zhang X. Reduced MFAP5 expression in stroma of gallbladder adenocarcinoma and its potential diagnostic utility. Virchows Arch 2020; 478:427-434. [PMID: 32895766 DOI: 10.1007/s00428-020-02925-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 11/28/2022]
Abstract
The diagnosis of invasive adenocarcinoma of the gallbladder can sometimes be challenging. The presence of true desmoplastic reaction facilitates the diagnosis of invasion. However, desmoplasia-like changes can be observed in benign gallbladder conditions, and recognition of desmoplasia may be challenging based on morphology. In this study, we tested the expression pattern of microfibril-associated protein 5 (MFAP5), a promising immunohistochemical marker for desmoplasia, in benign gallbladders with desmoplasia-like reaction and gallbladders with invasive adenocarcinoma. We also evaluated the diagnostic utility of MFAP5 in challenging cases with an interobserver agreement study. The results showed that all benign cases retained intact/positive MFAP5 staining pattern in periglandular connective tissue, whereas 79.3% (23 out of 29) of cases of adenocarcinomas demonstrated diffuse and complete loss of MFAP5 staining in the tumor stroma. Interobserver agreement was improved by 2.66 times when images of MFAP5 immunohistochemistry were provided. In conclusion, MFAP5 expression is downregulated in the desmoplastic stroma of gallbladder adenocarcinoma and may provide a useful diagnostic marker in difficult cases.
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Affiliation(s)
- Lei Zhao
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Liyan Xu
- Department of Pathology, St. Luke's University Health Network, Bethlehem, PA, USA
| | - Amanda Hemmerich
- Department of Pathology, Foundation Medicine, Inc., Morrisville, NC, USA
| | - N Lynn Ferguson
- Department of Pathology, Foundation Medicine, Inc., Morrisville, NC, USA
| | - Cynthia D Guy
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Shannon J McCall
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Diana M Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Maria Westerhoff
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rish K Pai
- Department of Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Shu-Yuan Xiao
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Beiyu Liu
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Cynthia L Green
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - John Hart
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Xuefeng Zhang
- Department of Pathology, Duke University Medical Center, Durham, NC, USA. .,Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA.
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28
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Gene Expression Clustering and Selected Head and Neck Cancer Gene Signatures Highlight Risk Probability Differences in Oral Premalignant Lesions. Cells 2020; 9:cells9081828. [PMID: 32756466 PMCID: PMC7466020 DOI: 10.3390/cells9081828] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Oral premalignant lesions (OPLs) represent the most common oral precancerous conditions. One of the major challenges in this field is the identification of OPLs at higher risk for oral squamous cell cancer (OSCC) development, by discovering molecular pathways deregulated in the early steps of malignant transformation. Analysis of deregulated levels of single genes and pathways has been successfully applied to head and neck squamous cell cancers (HNSCC) and OSCC with prognostic/predictive implications. Exploiting the availability of gene expression profile and clinical follow-up information of a well-characterized cohort of OPL patients, we aim to dissect tissue OPL gene expression to identify molecular clusters/signatures associated with oral cancer free survival (OCFS). MATERIALS AND METHODS The gene expression data of 86 OPL patients were challenged with: an HNSCC specific 6 molecular subtypes model (Immune related: HPV related, Defense Response and Immunoreactive; Mesenchymal, Hypoxia and Classical); one OSCC-specific signature (13 genes); two metabolism-related signatures (3 genes and signatures raised from 6 metabolic pathways associated with prognosis in HNSCC and OSCC, respectively); a hypoxia gene signature. The molecular stratification and high versus low expression of the signatures were correlated with OCFS by Kaplan-Meier analyses. The association of gene expression profiles among the tested biological models and clinical covariates was tested through variance partition analysis. RESULTS Patients with Mesenchymal, Hypoxia and Classical clusters showed an higher risk of malignant transformation in comparison with immune-related ones (log-rank test, p = 0.0052) and they expressed four enriched hallmarks: "TGF beta signaling" "angiogenesis", "unfolded protein response", "apical junction". Overall, 54 cases entered in the immune related clusters, while the remaining 32 cases belonged to the other clusters. No other signatures showed association with OCFS. Our variance partition analysis proved that clinical and molecular features are able to explain only 21% of gene expression data variability, while the remaining 79% refers to residuals independent of known parameters. CONCLUSIONS Applying the existing signatures derived from HNSCC to OPL, we identified only a protective effect for immune-related signatures. Other gene expression profiles derived from overt cancers were not able to identify the risk of malignant transformation, possibly because they are linked to later stages of cancer progression. The availability of a new well-characterized set of OPL patients and further research is needed to improve the identification of adequate prognosticators in OPLs.
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29
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Zhu L, Yan D, Chen Y, Chen S, Chen N, Han J. The identification of autophagy-related genes in the prognosis of oral squamous cell carcinoma. Oral Dis 2020; 26:1659-1667. [PMID: 32558072 DOI: 10.1111/odi.13492] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/24/2022]
Abstract
OBJECTIVES The aim of this study was to identify prognostic autophagy-related genes and assess the ability of these genes to predict clinical outcomes in oral squamous cell carcinoma (OSCC). SUBJECTS AND METHODS The details of the human autophagy-related genes were obtained from the Human Autophagy Database. The Cancer Genome Atlas database was used to obtain the gene expression profiles and clinical data of patients. Prediction of biological functions of differentially expressed genes was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Prognosis-related genes were identified by Cox regression analysis, and the coefficient was applied to construct a prognostic risk score model. The median of the risk score was applied to distinguish between high- and low-risk groups. The Gene Expression Omnibus database, qRT-PCR and immunohistochemistry were used to validate the expression of key genes. RESULTS KEGG analyses revealed that differentially expressed genes were mainly enriched in autophagy-related pathways and virus infection. BAK1, BID, NKX2-3 and SPHK1 were identified. The risk score model showed that the high-risk score had poorer overall survival (Kaplan-Meier analysis, p = 1.79 × 10-7 ). SPHK1 was upregulated in OSCC tissues and cells, and NXK2-3 was downregulated. CONCLUSIONS Autophagy-related gene expression profiles may be a potential biomarker for OSCC prognosis.
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Affiliation(s)
- Longbiao Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Donglin Yan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yan Chen
- Jiangsu Cancer Centre, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Sheng Chen
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Ning Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jing Han
- Jiangsu Cancer Centre, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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Immune Checkpoint Inhibitors in Oral Cavity Squamous Cell Carcinoma and Oral Potentially Malignant Disorders: A Systematic Review. Cancers (Basel) 2020; 12:cancers12071937. [PMID: 32708945 PMCID: PMC7409293 DOI: 10.3390/cancers12071937] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/12/2020] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Cancers of the oral cavity cause significant cancer-related death worldwide. While survival rates have improved in recent years, new methods of treatment are being investigated to limit disease progression and to improve outcomes, particularly in oral cavity squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMD). The emerging treatment modality of immunotherapy targets immune checkpoint molecules including PD-1 and its ligand PD-L1, CTLA-4, LAG-3, and TIM-3 to enhance the host immune response against tumours, and to limit the growth and progression of cancer cells. In this systematic review, we searched five databases for keywords pertaining to oral cancers and OPMDs, along with immune checkpoint inhibitors, in order to summarize the current status of their use and efficacy in these diseases. A total of 644 different articles were identified between 2004 and 2019, with 76 deemed suitable for inclusion in the study, providing a total of 8826 samples. Combined results show expression of PD-1 and PD-L1 in the majority of OPMD and OSCC samples, with expression correlating with increased progression and decreased survival rates. Immunotherapy agents pembrolizumab and nivolumab target PD-1 and have been shown to prolong survival rates and improve disease outcomes, especially in combination with chemotherapy or radiotherapy. Despite the equivocal nature of current evidence, there is support for the prognostic and predictive value of immune checkpoint molecules, especially PD-L1, and many studies provide support for the effective use of immune checkpoint inhibitors in the management of OSCC. Limited data is available for OPMD, therefore this should be the focus of future research.
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Prognostic and clinicopathological values of tissue expression of MFAP5 and ITM2A in triple-negative breast cancer: an immunohistochemical study. Contemp Oncol (Pozn) 2020; 24:87-95. [PMID: 32774133 PMCID: PMC7403766 DOI: 10.5114/wo.2020.97520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
Introduction Triple-negative breast cancer (TNBC) is a markedly aggressive molecular subtype of breast cancer; there is an urgent need to clarify the molecular mechanisms underlying the progression and metastases of BLBC, in order to find a novel targeted therapy. Microfibrillar-associated protein 5 (MFAP5) plays an essential role in the regulation of cell behaviour and survival. Integral membrane protein 2A (ITM2A) is a type II transmembrane protein, which is a member of a family of autophagy related proteins. The aim of this study was to assess the expression of MFAP5 and ITM2A proteins in tissues of BLBC using immunohistochemistry, in order to correlate the expression with clinicopathological and prognostic parameters of such aggressive cancer. Material and methods The present study included sections from archived paraffin blocks retrieved from 120 patients with TNBC. We collected cases from three years, i.e. from 2016 to 2019. We assessed expression of MFAP5 and ITM2A using immunohistochemistry. Results High expression of MFAP5 and low expression of ITM2A was associated with advanced stage (p = 0.007), higher grade of tumour (p = 0.005 and p = 0.004, respectively), the presence of lymph nodes metastases (p < 0.001 and p = 0.002, respectively), lower three-year RFS rate (p < 0.001 and p = 0.016, respectively), and lower three-year OS rate (p < 0.001). Conclusions MFAP5 and ITM2A are novel prognostic biomarkers for breast cancer and might be considered as promising therapeutic targets for patients with breast cancer, particularly TNBC molecular subtype, in the future.
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Lin YM, Chen ML, Chen CL, Yeh CM, Sung WW. Overexpression of EIF5A2 Predicts Poor Prognosis in Patients with Oral Squamous Cell Carcinoma. Diagnostics (Basel) 2020; 10:diagnostics10070436. [PMID: 32605067 PMCID: PMC7400414 DOI: 10.3390/diagnostics10070436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common epithelial malignancy affecting the oral cavity, and it is especially significant in Asian countries. Patients diagnosed with OSCC have an unfavorable prognosis and additional prognostic markers would help improve therapeutic strategies. We sought to investigate the association between eukaryotic translation initiation factor 5A2 (EIF5A2) and epithelial–mesenchymal transition (EMT) markers as well as the prognostic significance of EIF5A2 in OSCC. The expression of EIF5A2 and EMT markers was measured through the immunohistochemical staining of specimens from 272 patients with OSCC. In addition, the correlation between different clinicopathological factors and EIF5A2 expression was analyzed. The prognostic role of EIF5A2 was then analyzed via Kaplan–Meier analysis and Cox proportional hazard models. Among the 272 patients, high EIF5A2 expression was significantly associated with an advanced N value (p = 0.008). High tumor expression of EIF5A2 was prone to the expression of low E-cadherin and high beta-catenin (p = 0.046 and p = 0.020, respectively). Patients with high EIF5A2 expression had unfavorable five-year survival rates as compared with those with low expression (49.7% and 67.3%, respectively). The prognostic role of EIF5A2 was further confirmed through multivariate analysis (hazard ratio = 1.714, 95% confidence interval: 1.134–2.590, p = 0.011). High EIF5A2 expression is associated with an advanced N value and EMT markers and may serve as a marker for an unfavorable prognosis in patients with OSCC.
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Affiliation(s)
- Yueh-Min Lin
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (Y.-M.L.); (M.-L.C.); (C.-L.C.)
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua 50006, Taiwan;
| | - Mei-Ling Chen
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (Y.-M.L.); (M.-L.C.); (C.-L.C.)
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua 50006, Taiwan;
| | - Chia-Lo Chen
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (Y.-M.L.); (M.-L.C.); (C.-L.C.)
| | - Chung-Min Yeh
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua 50006, Taiwan;
- Department of Medical Technology, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 35664, Taiwan
| | - Wen-Wei Sung
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (Y.-M.L.); (M.-L.C.); (C.-L.C.)
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
- Department of Urology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
- Correspondence: ; Tel.: +886-4-24739595 (ext.*10646)
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Liu J, Lian X, Liu F, Yan X, Cheng C, Cheng L, Sun X, Shi Z. Identification of Novel Key Targets and Candidate Drugs in Oral Squamous Cell Carcinoma. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191127101836] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background:
Oral Squamous Cell Carcinoma (OSCC) is the most common malignant
epithelial neoplasm. It is located within the top 10 ranking incidence of cancers with a poor
prognosis and low survival rates. New breakthroughs of therapeutic strategies are therefore needed
to improve the survival rate of OSCC harboring patients.
Objective:
Since targeted therapy is considered as the most promising therapeutic strategies in
cancer, it is of great significance to identify novel targets and drugs for the treatment of OSCC.
Methods:
A series of bioinformatics approaches were launched to identify the hub proteins and
their potential agents. Microarray analysis and several online functional activity network analysis
were firstly utilized to recognize drug targets in OSCC. Subsequently, molecular docking was used
to screen their potential drugs from the specs chemistry database. At the same time, the assessment
of ligand-based virtual screening model was also evaluated.
Results:
In this study, two microarray data (GSE31056, GSE23558) were firstly selected and
analyzed to get consensus candidate genes including 681 candidate genes. Additionally, we
selected 33 candidate genes based on whether they belong to the kinases and transcription factors
and further clustered candidate hub targets based on functions and signaling pathways with
significant enrichment analysis by using DAVID and STRING online databases. Then, core PPI
network was then identified and we manually selected GRB2 and IGF1 as the key drug targets
according to the network analysis and previous references. Lastly, virtual screening was performed
to identify potential small molecules which could target these two targets, and such small
molecules can serve as the promising candidate agents for future drug development.
Conclusion:
In summary, our study might provide novel insights for understanding of the
underlying molecular events of OSCC, and our discovered candidate targets and candidate agents
could be used as the promising therapeutic strategies for the treatment of OSCC.
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Affiliation(s)
- Juan Liu
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xinjie Lian
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Feng Liu
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xueling Yan
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Chunyan Cheng
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Lijia Cheng
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xiaolin Sun
- Department of Radiotherapy, the Central Hospital of Xuzhou, Xuzhou 221000, China
| | - Zheng Shi
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
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Das D, Ghosh S, Maitra A, Biswas NK, Panda CK, Roy B, Sarin R, Majumder PP. Epigenomic dysregulation-mediated alterations of key biological pathways and tumor immune evasion are hallmarks of gingivo-buccal oral cancer. Clin Epigenetics 2019; 11:178. [PMID: 31796082 PMCID: PMC6889354 DOI: 10.1186/s13148-019-0782-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/17/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Gingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the most common cancer among men in India and is associated with high mortality. Although OSCC-GB is known to be quite different from tongue cancer in its genomic presentation and its clinical behavior, it is treated identically as tongue cancer. Predictive markers of prognosis and therapy that are specific to OSCC-GB are, therefore, required. Although genomic drivers of OSCC-GB have been identified by whole exome and whole genome sequencing, no epigenome-wide study has been conducted in OSCC-GB; our study has filled this gap, and has discovered and validated epigenomic hallmarks of gingivobuccal oral cancer. METHODS We have carried out integrative analysis of epigenomic (n = 87) and transcriptomic (n = 72) profiles of paired tumor-normal tissues collected from OSCC-GB patients from India. Genome-wide DNA methylation assays and RNA-sequencing were performed on high-throughput platforms (Illumina) using a half-sample of randomly selected patients to discover significantly differentially methylated probes (DMPs), which were validated on the remaining half-sample of patients. RESULTS About 200 genes showed significant inverse correlation between promoter methylation and expression, of which the most significant genes included genes that act as transcription factors and genes associated with other cancer types. Novel findings of this study include identification of (a) potential immunosuppressive effect in OSCC-GB due to significant promoter hypomethylation driven upregulation of CD274 and CD80, (b) significant dysregulation by epigenetic modification of DNMT3B (upregulation) and TET1 (downregulation); and (c) known drugs that can reverse the direction of dysregulation of gene expression caused by promoter methylation. CONCLUSIONS In OSCC-GB patients, there are significant alterations in expression of key genes that (a) regulate normal cell division by maintenance of balanced DNA methylation and transcription process, (b) maintain normal physiological signaling (PPAR, B cell receptor) and metabolism (arachidonic acid) pathways, and (c) provide immune protection against antigens, including tumor cells. These findings indicate novel therapeutic targets, including immunotherapeutic, for treatment of OSCC-GB.
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Affiliation(s)
- Debodipta Das
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | | | - Bidyut Roy
- Indian Statistical Institute, Kolkata, India
| | - Rajiv Sarin
- Advanced Centre for Treatment Research and Education in Cancer, Mumbai, India
| | - Partha P Majumder
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India. .,Indian Statistical Institute, Kolkata, India.
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Immunohistochemical Expression of Microfibrillar-associated Protein 5 (MFAP5) in Invasive Breast Carcinoma of No Special Type. Appl Immunohistochem Mol Morphol 2019; 27:649-657. [DOI: 10.1097/pai.0000000000000686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Loss of microfibril-associated protein 5 (MFAP5) expression in colon cancer stroma. Virchows Arch 2019; 476:383-390. [DOI: 10.1007/s00428-019-02649-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/31/2019] [Accepted: 08/13/2019] [Indexed: 11/26/2022]
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Oliva J, Larque A, Marti C, Bodalo‐Torruella M, Nonell L, Nadal A, Castillo P, Sieira R, Ferrer A, Garcia‐Diez E, Alos L. Oral premalignant lesions of smokers and non‐smokers show similar carcinogenic pathways and outcomes. A clinicopathological and molecular comparative analysis. J Oral Pathol Med 2019; 50:280-286. [DOI: 10.1111/jop.12864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Jorge Oliva
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Ana‐Belen Larque
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Carles Marti
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Marta Bodalo‐Torruella
- Microarray Analysis Service Institut Hospital del Mar d’InvestigacionsMèdiques (IMIM) Barcelona Spain
| | - Lara Nonell
- Microarray Analysis Service Institut Hospital del Mar d’InvestigacionsMèdiques (IMIM) Barcelona Spain
| | - Alfons Nadal
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Paola Castillo
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Ramón Sieira
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Ada Ferrer
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Eloy Garcia‐Diez
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Llucia Alos
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
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Meng QB, Peng JJ, Qu ZW, Zhu XM, Wen Z, Kang WM. Eukaryotic initiation factor 5A2 and human digestive system neoplasms. World J Gastrointest Oncol 2019; 11:449-458. [PMID: 31236196 PMCID: PMC6580320 DOI: 10.4251/wjgo.v11.i6.449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/17/2019] [Accepted: 05/04/2019] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic initiation factor 5A2 (eIF5A2), as one of the two isoforms in the family, is reported to be a novel oncogenic protein that is involved in multiple aspects of many types of human cancer. Overexpression or gene amplification of EIF5A2 has been demonstrated in many cancers. Accumulated evidence shows that eIF5A2 initiates tumor formation, enhances cancer cell growth, increases cancer cell metastasis, and promotes treatment resistance through multiple means, including inducing epithelial–mesenchymal transition, cytoskeletal rearrangement, angiogenesis, and metabolic reprogramming. Expression of eIF5A2 in cancer correlates with poor survival, advanced disease stage, as well as metastasis, suggesting that eIF5A2 function is crucial for tumor development and maintenance but not for normal tissue homeostasis. All these studies suggest that eIF5A2 is a useful biomarker in the prediction of cancer prognosis and serves as an anticancer molecular target. This review focuses on the expression, subcellular localization, post-translational modifications, and regulatory networks of eIF5A2, as well as its biochemical functions and evolving clinical applications in cancer, especially in human digestive system neoplasms.
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Affiliation(s)
- Qing-Bin Meng
- Department of Gastrointestinal Surgery, the First Hospital of Wuhan City, Wuhan 430022, Hubei Province, China
| | - Jing-Jing Peng
- Department of Gastroenterology, General Hospital of the Yangtze River Shipping, Wuhan 430015, Hubei Province, China
| | - Zi-Wei Qu
- Department of Gastrointestinal Surgery, the First Hospital of Wuhan City, Wuhan 430022, Hubei Province, China
| | | | - Zhang Wen
- Department of Hepato-Biliary-Pancreatic Surgery and Liver Transplantation, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Wei-Ming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Driehuis E, Kolders S, Spelier S, Lõhmussaar K, Willems SM, Devriese LA, de Bree R, de Ruiter EJ, Korving J, Begthel H, van Es JH, Geurts V, He GW, van Jaarsveld RH, Oka R, Muraro MJ, Vivié J, Zandvliet MMJM, Hendrickx APA, Iakobachvili N, Sridevi P, Kranenburg O, van Boxtel R, Kops GJPL, Tuveson DA, Peters PJ, van Oudenaarden A, Clevers H. Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy. Cancer Discov 2019; 9:852-871. [PMID: 31053628 DOI: 10.1158/2159-8290.cd-18-1522] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Previous studies have described that tumor organoids can capture the diversity of defined human carcinoma types. Here, we describe conditions for long-term culture of human mucosal organoids. Using this protocol, a panel of 31 head and neck squamous cell carcinoma (HNSCC)-derived organoid lines was established. This panel recapitulates genetic and molecular characteristics previously described for HNSCC. Organoids retain their tumorigenic potential upon xenotransplantation. We observe differential responses to a panel of drugs including cisplatin, carboplatin, cetuximab, and radiotherapy in vitro. Additionally, drug screens reveal selective sensitivity to targeted drugs that are not normally used in the treatment of patients with HNSCC. These observations may inspire a personalized approach to the management of HNSCC and expand the repertoire of HNSCC drugs. SIGNIFICANCE: This work describes the culture of organoids derived from HNSCC and corresponding normal epithelium. These tumoroids recapitulate the disease genetically, histologically, and functionally. In vitro drug screening of tumoroids reveals responses to therapies both currently used in the treatment of HNSCC and those not (yet) used in clinical practice.See related commentary by Hill and D'Andrea, p. 828.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Else Driehuis
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sigrid Kolders
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sacha Spelier
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kadi Lõhmussaar
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lot A Devriese
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emma J de Ruiter
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeroen Korving
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Johan H van Es
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Veerle Geurts
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gui-Wei He
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, Utrecht, the Netherlands
| | - Mauro J Muraro
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Judith Vivié
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Maurice M J M Zandvliet
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nino Iakobachvili
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Priya Sridevi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Onno Kranenburg
- Utrecht Platform for Organoid Technology (U-PORT), Utrecht Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Peter J Peters
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands. .,Princess Maxima Center, Utrecht, the Netherlands
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Yu B, Ding Y, Liao X, Wang C, Wang B, Chen X. Overexpression of TONSL might be an independent unfavorable prognostic indicator in hepatocellular carcinoma. Pathol Res Pract 2019; 215:939-945. [PMID: 30723051 DOI: 10.1016/j.prp.2019.01.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/17/2019] [Accepted: 01/29/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND TONSL has been suggested to function as an oncogene in lung, esophageal and cervical cancer. This study was aimed to identify the expression of TONSL and its role in hepatocellular carcinoma (HCC). METHODS By data mining in the Cancer Genome Atlas (TCGA) and Human Protein Atlas (HPA) databases, the expression profile of TONSL, its clinical significance, the potential mechanisms of its dysregulation and its underlying biological function in HCC were investigated. RESULTS TONSL was significantly upregulated in HCC tissues relative to normal liver tissues (P < 0.05). High TONSL expression was significantly correlated with advanced TNM stage, poorly differentiated tumors, vascular invasion, elevated serum alpha-fetoprotein expression and a worse prognosis (all P < 0.05). Multivariate analysis further confirmed that TONSL overexpression was an independent risk factor for poor overall survival (OS) and recurrence-free survival (RFS) in HCC (all P < 0.05). Additionally, 16% of HCC cases (n = 370) had TONSL DNA amplification. The total methylation level of TONSL was moderately and negatively correlated with its mRNA expression (P < 0.05). TONSL was predictively targeted by miR-133b, which was downregulated in HCC and negatively related to TONSL mRNA expression (all P < 0.05). Kaplan-Meier analyses demonstrated that low miR-133b expression was significantly associated with poor OS and RFS (all P < 0.05). Moreover, gene set enrichment analysis revealed that cases with TONSL overexpression were enriched in cell cycle regulation pathways (all P < 0.05). CONCLUSIONS TONSL holds promise for serving as a prognostic biomarker for HCC. DNA amplification, hypomethylation and miR-133b downregulation could be the mechanisms associated with TONSL upregulation in HCC. TONSL might function as an oncogene via cell cycle regulation pathways in HCC.
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Affiliation(s)
- Bin Yu
- Department of Hepatobiliary & Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, PR China
| | - Youming Ding
- Department of Hepatobiliary & Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, PR China.
| | - Xiaofeng Liao
- Department of General Surgery, Xiangyang Central Hospital, Xiangyang, 441021, Hubei Province, PR China
| | - Changhua Wang
- Department of Pathology & Pathophysiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, PR China
| | - Bin Wang
- Department of Hepatobiliary & Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, PR China
| | - Xiaoyan Chen
- Department of Hepatobiliary & Laparoscopic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, PR China
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Costa RL, Boroni M, Soares MA. Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer. Sci Rep 2018; 8:15254. [PMID: 30323202 PMCID: PMC6189122 DOI: 10.1038/s41598-018-33498-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/19/2018] [Indexed: 12/25/2022] Open
Abstract
The human papillomavirus (HPV) is present in a significant fraction of head-and-neck squamous cell cancer (HNSCC). The main goal of this study was to identify distinct co-expression patterns between HPV+ and HPV- HNSCC and to provide insights into potential regulatory mechanisms/effects within the analyzed networks. We selected cases deposited in The Cancer Genome Atlas database comprising data of gene expression, methylation profiles and mutational patterns, in addition to clinical information. The intersection among differentially expressed and differentially methylated genes showed the negative correlations between the levels of methylation and expression, suggesting that these genes have their expression levels regulated by methylation alteration patterns in their promoter. Weighted correlation network analysis was used to identify co-expression modules and a systematic approach was applied to refine them and identify key regulatory elements integrating results from the other omics. Three distinct co-expression modules were associated with HPV status and molecular signatures. Validation using independent studies reporting biological experimental data converged for the most significant genes in all modules. This study provides insights into complex genetic and epigenetic particularities in the development and progression of HNSCC according to HPV status, and contribute to unveiling specific genes/pathways as novel therapeutic targets in HNSCC.
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Affiliation(s)
- Raquel L Costa
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
- Bioinformatics and Computational Biology Lab, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| | - Mariana Boroni
- Bioinformatics and Computational Biology Lab, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Troiano G, Guida A, Aquino G, Botti G, Losito NS, Papagerakis S, Pedicillo MC, Ionna F, Longo F, Cantile M, Pennella A, Lo Russo L, Di Gioia G, Mariggiò MA, Lo Muzio L, Pannone G. Integrative Histologic and Bioinformatics Analysis of BIRC5/Survivin Expression in Oral Squamous Cell Carcinoma. Int J Mol Sci 2018; 19:ijms19092664. [PMID: 30205554 PMCID: PMC6174346 DOI: 10.3390/ijms19092664] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/02/2018] [Indexed: 12/27/2022] Open
Abstract
Survivin is a well-known protein involved in the inhibition of apoptosis in many different cancer types. The aim of this study was to perform an integrated bioinformatic and histologic analysis in order to study the expression and prognostic role of Survivin and its related gene BIRC5 in oral cancer. Publicly available databases were accessed via Gene Expression Omnibus and Oncomine, in addition raw data from The Cancer Genome Atlas (TCGA) were also obtained in order to analyze the rate of gene mutation, expression and methylation in patients with oral squamous cells carcinoma (OSCC). Immunohistochemistry (IHC) was also performed in order to evaluate the nuclear and cytoplasmic expression of Survivin and their correlation with cell proliferation in samples from OSCC patients. Results of this study revealed that Survivin is rarely mutated in OSCC samples and upregulated when compared to non-cancerous tissue. A negative correlation between the methylation of the island cg25986496 and BIRC5 mRNA expression was detected from TCGA data. IHC staining revealed that cytoplasmic (and not nuclear) expression of Survivin is associated with poor overall survival in OSCC patients, while the nuclear expression correlates with higher proliferation rate. In addition, data from TCGA database revealed that BIRC5 gene expression is an independent prognostic factor for OSCC patients.
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Affiliation(s)
- Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, Foggia 71122, Italy.
| | - Agostino Guida
- Maxillofacial and ENT Surgery Department, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione G. Pascale, IRCCS, Naples 80131, Italy.
| | - Gabriella Aquino
- Pathology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione G. Pascale, IRCCS, Naples 80131, Italy.
| | - Gerardo Botti
- Pathology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione G. Pascale, IRCCS, Naples 80131, Italy.
| | - Nunzia Simona Losito
- Pathology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione G. Pascale, IRCCS, Naples 80131, Italy.
| | - Silvana Papagerakis
- Department of Surgery, Cancer Research Cluster, Room 4D10.2, Health Sciences Building, Saskatchewan University, Saskatoon, SKS7N5E5, Canada.
| | - Maria Carmela Pedicillo
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, Foggia 71122, Italy.
| | - Franco Ionna
- Maxillofacial and ENT Surgery Department, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione G. Pascale, IRCCS, Naples 80131, Italy.
| | - Francesco Longo
- Maxillofacial and ENT Surgery Department, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione G. Pascale, IRCCS, Naples 80131, Italy.
| | - Monica Cantile
- Pathology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, Fondazione G. Pascale, IRCCS, Naples 80131, Italy.
| | - Antonio Pennella
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, Foggia 71122, Italy.
| | - Lucio Lo Russo
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, Foggia 71122, Italy.
| | - Giovanni Di Gioia
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, Foggia 71122, Italy.
| | - Maria Addolorata Mariggiò
- Department of Biomedical Sciences and Human Oncology, University of Bari. Piazza Giulio Cesare 11, Bari 70124, Italy.
| | - Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, Foggia 71122, Italy.
| | - Giuseppe Pannone
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, Foggia 71122, Italy.
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43
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Wu Z, Wang T, Fang M, Huang W, Sun Z, Xiao J, Yan W. MFAP5 promotes tumor progression and bone metastasis by regulating ERK/MMP signaling pathways in breast cancer. Biochem Biophys Res Commun 2018. [PMID: 29526753 DOI: 10.1016/j.bbrc.2018.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Breast cancer accounts for about 30% of all cancers in women, while approximately 70% breast cancer patients developed bone metastases throughout the course of their disease, highlighting the importance of exploring new therapeutic targets. Microfibrillar-associated protein 5 (MFAP5) is a component of extracellular elastic microfibril which has been confirmed to function in tissue development and cancer progression. But the role of MFAP5 in breast cancer remains unclear. The present study demonstrated that MFAP5 was up-regulated in breast cancers compared with that in normal breast tissues, and further increased in breast cancer bone metastasis. Functionally, MFAP5 overexpression accelerated breast cancer cell proliferation and migration, while an opposite effect was observed when MFAP5 was knocked down. In addition, up-regulation of MFAP5 increased the expression of MMP2 and MMP9 and activated the ERK signaling pathway. Conversely, inhibition of MFAP5 suppressed the expression of MMP2, MMP9, p-FAK, p-Erk1/2 and p-cJun. These findings may provide a better understanding about the mechanism of breast cancer and suggest that MFAP5 may be a potential prognostic biomarker and therapeutic target for breast cancer, especially for bone metastasis of breast cancer.
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Affiliation(s)
- Zhiqiang Wu
- Department of Musculoskeletal Tumor, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ting Wang
- Department of Orthopaedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Meng Fang
- Department of Musculoskeletal Tumor, Shanghai Cancer Center, Fudan University, Shanghai, China; Department of Orthopaedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wending Huang
- Department of Musculoskeletal Tumor, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhengwang Sun
- Department of Musculoskeletal Tumor, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jianru Xiao
- Department of Orthopaedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai, China.
| | - Wangjun Yan
- Department of Musculoskeletal Tumor, Shanghai Cancer Center, Fudan University, Shanghai, China; Department of Orthopaedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai, China.
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Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC. Sci Rep 2017; 7:16051. [PMID: 29167558 PMCID: PMC5700126 DOI: 10.1038/s41598-017-16247-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
A key feature in the pathogenesis of OSCC is genetic instability, which results in altered expression of genes located in amplified/deleted chromosomal regions. In a previous study we have shown that the amplification of the 11q22.1-q22.2 region, encoding cIAP1 and cIAP2, is associated with lymph node metastasis and poor clinical outcome in OSCC. Here, we validate the aCGH results by nuc ish and detect a weak amplification at the 11q22.1-q22.2 locus in 37% of the 182 samples tested. We find positive correlation of 11q22.1-q22.2 amplification with lymph node metastasis, reduced survival, and increased cancer recurrence, and we observe that patients with 11q22.1-q22.2 amplification fail to respond to radiotherapy. We confirm the concurrent overexpression of cIAP1 and cIAP2 and observe differential subcellular localization of the two proteins in OSCC. To ascertain the roles of cIAP1/cIAP2 in lymph node metastasis and radioresistance, we use an in vitro pre-clinical model and confirm the role of cIAP1 in invasion and the role of cIAP2 in invasion and migration. Studies of other tumor types in which cIAP1 is overexpressed suggest that multi-regimen treatments including SMAC mimetics may be effective. Thus, the evaluation of 11q22.1-q22.2 amplifications in OSCC patients may help choose the most effective treatment.
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