A 3-gene signature comprising CDH4, STAT4 and EBV-encoded LMP1 for early diagnosis and predicting disease progression of nasopharyngeal carcinoma
Purpose Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies. Methods The transcriptomic data of primary NPC cell strains were use...
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Published in | Discover. Oncology Vol. 14; no. 1; pp. 119 - 14 |
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Main Authors | , , , , , |
Format | Journal Article |
Language | English |
Published |
New York
Springer US
01.07.2023
Springer Nature B.V Springer |
Subjects | |
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Abstract | Purpose
Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies.
Methods
The transcriptomic data of primary NPC cell strains were used as a discovery tool. Linear regression approach was used to define signatures distinctive between early and late stage of NPC. Expressions of candidates were validated with an independent set of biopsies (n = 39). Leave-one-out cross-validation technique was employed to estimate the prediction accuracy on stage classification. The clinical relevance of marker genes was verified using NPC bulk RNA sequencing data and IHC analysis.
Results
Three genes comprising CDH4, STAT4, and CYLD were found to have a significant differentiating power to separate NPC from normal nasopharyngeal samples and predicting disease malignancy. IHC analyses showed stronger CDH4, STAT4, and CYLD immunoreactivity in adjacent basal epithelium compared with that in tumor cells (
p
< 0.001). EBV-encoded LMP1 was exclusively expressed in NPC tumors. Using an independent set of biopsies, we showed that a model combining CDH4, STAT4, and LMP1 had a 92.86% of diagnostic accuracy, whereas a combination of STAT4 and LMP1 had a 70.59% accuracy for predicting advanced disease. Mechanistic studies suggested that promoter methylation, loss of DNA allele, and LMP1 contributed to the suppressive expression of CDH4, CYLD, and STAT4, respectively.
Conclusion
A model combining CDH4 and STAT4 and LMP1 was proposed to be a feasible model for diagnosing NPC and predicting late stage of NPC. |
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AbstractList | Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies.PURPOSENasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies.The transcriptomic data of primary NPC cell strains were used as a discovery tool. Linear regression approach was used to define signatures distinctive between early and late stage of NPC. Expressions of candidates were validated with an independent set of biopsies (n = 39). Leave-one-out cross-validation technique was employed to estimate the prediction accuracy on stage classification. The clinical relevance of marker genes was verified using NPC bulk RNA sequencing data and IHC analysis.METHODSThe transcriptomic data of primary NPC cell strains were used as a discovery tool. Linear regression approach was used to define signatures distinctive between early and late stage of NPC. Expressions of candidates were validated with an independent set of biopsies (n = 39). Leave-one-out cross-validation technique was employed to estimate the prediction accuracy on stage classification. The clinical relevance of marker genes was verified using NPC bulk RNA sequencing data and IHC analysis.Three genes comprising CDH4, STAT4, and CYLD were found to have a significant differentiating power to separate NPC from normal nasopharyngeal samples and predicting disease malignancy. IHC analyses showed stronger CDH4, STAT4, and CYLD immunoreactivity in adjacent basal epithelium compared with that in tumor cells (p < 0.001). EBV-encoded LMP1 was exclusively expressed in NPC tumors. Using an independent set of biopsies, we showed that a model combining CDH4, STAT4, and LMP1 had a 92.86% of diagnostic accuracy, whereas a combination of STAT4 and LMP1 had a 70.59% accuracy for predicting advanced disease. Mechanistic studies suggested that promoter methylation, loss of DNA allele, and LMP1 contributed to the suppressive expression of CDH4, CYLD, and STAT4, respectively.RESULTSThree genes comprising CDH4, STAT4, and CYLD were found to have a significant differentiating power to separate NPC from normal nasopharyngeal samples and predicting disease malignancy. IHC analyses showed stronger CDH4, STAT4, and CYLD immunoreactivity in adjacent basal epithelium compared with that in tumor cells (p < 0.001). EBV-encoded LMP1 was exclusively expressed in NPC tumors. Using an independent set of biopsies, we showed that a model combining CDH4, STAT4, and LMP1 had a 92.86% of diagnostic accuracy, whereas a combination of STAT4 and LMP1 had a 70.59% accuracy for predicting advanced disease. Mechanistic studies suggested that promoter methylation, loss of DNA allele, and LMP1 contributed to the suppressive expression of CDH4, CYLD, and STAT4, respectively.A model combining CDH4 and STAT4 and LMP1 was proposed to be a feasible model for diagnosing NPC and predicting late stage of NPC.CONCLUSIONA model combining CDH4 and STAT4 and LMP1 was proposed to be a feasible model for diagnosing NPC and predicting late stage of NPC. Purpose Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies. Methods The transcriptomic data of primary NPC cell strains were used as a discovery tool. Linear regression approach was used to define signatures distinctive between early and late stage of NPC. Expressions of candidates were validated with an independent set of biopsies (n = 39). Leave-one-out cross-validation technique was employed to estimate the prediction accuracy on stage classification. The clinical relevance of marker genes was verified using NPC bulk RNA sequencing data and IHC analysis. Results Three genes comprising CDH4, STAT4, and CYLD were found to have a significant differentiating power to separate NPC from normal nasopharyngeal samples and predicting disease malignancy. IHC analyses showed stronger CDH4, STAT4, and CYLD immunoreactivity in adjacent basal epithelium compared with that in tumor cells ( p < 0.001). EBV-encoded LMP1 was exclusively expressed in NPC tumors. Using an independent set of biopsies, we showed that a model combining CDH4, STAT4, and LMP1 had a 92.86% of diagnostic accuracy, whereas a combination of STAT4 and LMP1 had a 70.59% accuracy for predicting advanced disease. Mechanistic studies suggested that promoter methylation, loss of DNA allele, and LMP1 contributed to the suppressive expression of CDH4, CYLD, and STAT4, respectively. Conclusion A model combining CDH4 and STAT4 and LMP1 was proposed to be a feasible model for diagnosing NPC and predicting late stage of NPC. Abstract Purpose Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies. Methods The transcriptomic data of primary NPC cell strains were used as a discovery tool. Linear regression approach was used to define signatures distinctive between early and late stage of NPC. Expressions of candidates were validated with an independent set of biopsies (n = 39). Leave-one-out cross-validation technique was employed to estimate the prediction accuracy on stage classification. The clinical relevance of marker genes was verified using NPC bulk RNA sequencing data and IHC analysis. Results Three genes comprising CDH4, STAT4, and CYLD were found to have a significant differentiating power to separate NPC from normal nasopharyngeal samples and predicting disease malignancy. IHC analyses showed stronger CDH4, STAT4, and CYLD immunoreactivity in adjacent basal epithelium compared with that in tumor cells (p < 0.001). EBV-encoded LMP1 was exclusively expressed in NPC tumors. Using an independent set of biopsies, we showed that a model combining CDH4, STAT4, and LMP1 had a 92.86% of diagnostic accuracy, whereas a combination of STAT4 and LMP1 had a 70.59% accuracy for predicting advanced disease. Mechanistic studies suggested that promoter methylation, loss of DNA allele, and LMP1 contributed to the suppressive expression of CDH4, CYLD, and STAT4, respectively. Conclusion A model combining CDH4 and STAT4 and LMP1 was proposed to be a feasible model for diagnosing NPC and predicting late stage of NPC. Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies. The transcriptomic data of primary NPC cell strains were used as a discovery tool. Linear regression approach was used to define signatures distinctive between early and late stage of NPC. Expressions of candidates were validated with an independent set of biopsies (n = 39). Leave-one-out cross-validation technique was employed to estimate the prediction accuracy on stage classification. The clinical relevance of marker genes was verified using NPC bulk RNA sequencing data and IHC analysis. Three genes comprising CDH4, STAT4, and CYLD were found to have a significant differentiating power to separate NPC from normal nasopharyngeal samples and predicting disease malignancy. IHC analyses showed stronger CDH4, STAT4, and CYLD immunoreactivity in adjacent basal epithelium compared with that in tumor cells (p < 0.001). EBV-encoded LMP1 was exclusively expressed in NPC tumors. Using an independent set of biopsies, we showed that a model combining CDH4, STAT4, and LMP1 had a 92.86% of diagnostic accuracy, whereas a combination of STAT4 and LMP1 had a 70.59% accuracy for predicting advanced disease. Mechanistic studies suggested that promoter methylation, loss of DNA allele, and LMP1 contributed to the suppressive expression of CDH4, CYLD, and STAT4, respectively. A model combining CDH4 and STAT4 and LMP1 was proposed to be a feasible model for diagnosing NPC and predicting late stage of NPC. PurposeNasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular diagnostic method for early detection of NPC in clinical biopsies.MethodsThe transcriptomic data of primary NPC cell strains were used as a discovery tool. Linear regression approach was used to define signatures distinctive between early and late stage of NPC. Expressions of candidates were validated with an independent set of biopsies (n = 39). Leave-one-out cross-validation technique was employed to estimate the prediction accuracy on stage classification. The clinical relevance of marker genes was verified using NPC bulk RNA sequencing data and IHC analysis.ResultsThree genes comprising CDH4, STAT4, and CYLD were found to have a significant differentiating power to separate NPC from normal nasopharyngeal samples and predicting disease malignancy. IHC analyses showed stronger CDH4, STAT4, and CYLD immunoreactivity in adjacent basal epithelium compared with that in tumor cells (p < 0.001). EBV-encoded LMP1 was exclusively expressed in NPC tumors. Using an independent set of biopsies, we showed that a model combining CDH4, STAT4, and LMP1 had a 92.86% of diagnostic accuracy, whereas a combination of STAT4 and LMP1 had a 70.59% accuracy for predicting advanced disease. Mechanistic studies suggested that promoter methylation, loss of DNA allele, and LMP1 contributed to the suppressive expression of CDH4, CYLD, and STAT4, respectively.ConclusionA model combining CDH4 and STAT4 and LMP1 was proposed to be a feasible model for diagnosing NPC and predicting late stage of NPC. |
ArticleNumber | 119 |
Author | Tsang, Ngan-Ming Juang, Jyh-Lyh Sui, Yun-Hua Liu, Tzu-Tung Liu, Shu-Chen Wang, Chun-I |
Author_xml | – sequence: 1 givenname: Shu-Chen surname: Liu fullname: Liu, Shu-Chen email: jennyliu66@gmail.com organization: Department of Biomedical Sciences and Engineering, National Central University – sequence: 2 givenname: Chun-I surname: Wang fullname: Wang, Chun-I organization: Department of Biochemistry, School of Medicine, China Medical University – sequence: 3 givenname: Tzu-Tung surname: Liu fullname: Liu, Tzu-Tung organization: Department of Biomedical Sciences and Engineering, National Central University – sequence: 4 givenname: Ngan-Ming surname: Tsang fullname: Tsang, Ngan-Ming organization: Department of Radiation Oncology, China Medical University Hsinchu Hospital – sequence: 5 givenname: Yun-Hua surname: Sui fullname: Sui, Yun-Hua organization: Department of Biomedical Sciences and Engineering, National Central University – sequence: 6 givenname: Jyh-Lyh surname: Juang fullname: Juang, Jyh-Lyh email: juang@nhri.edu.tw organization: Institute of Molecular and Genomic Medicine, National Health Research Institutes |
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Keywords | Nasopharyngeal carcinoma STAT4 EBV-encoded LMP1 CYLD CDH4 |
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Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient... Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient molecular... PurposeNasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly efficient... Abstract Purpose Nasopharyngeal carcinoma is highly metastatic but difficult to detect in its early stages. It is critical to develop a simple and highly... |
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SubjectTerms | Accuracy Biopsy Cancer Cancer Research CDH4 CYLD Discriminant analysis EBV-encoded LMP1 Epstein-Barr virus Genes Infections Internal Medicine Lymphoma Medical diagnosis Medical prognosis Medicine Medicine & Public Health Molecular Medicine Nasopharyngeal carcinoma Oncology Pathogenesis Patients Proteins Radiotherapy Regression analysis STAT4 Surgical Oncology Throat cancer Tumorigenesis Tumors Viral infections |
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Title | A 3-gene signature comprising CDH4, STAT4 and EBV-encoded LMP1 for early diagnosis and predicting disease progression of nasopharyngeal carcinoma |
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