The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers
The oral microbiome can play a role in the instigation and progression of oral diseases that can manifest into other systemic conditions. These associations encourage the exploration of oral dysbiosis leading to the pathogenesis of cancers. In this study, oral rinse was used to characterize the oral...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2018-08-01
|
| Series: | Frontiers in Cellular and Infection Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fcimb.2018.00267/full |
| _version_ | 1828519085645758464 |
|---|---|
| author | Yenkai Lim Yenkai Lim Naoki Fukuma Makrina Totsika Liz Kenny Mark Morrison Chamindie Punyadeera Chamindie Punyadeera |
| author_facet | Yenkai Lim Yenkai Lim Naoki Fukuma Makrina Totsika Liz Kenny Mark Morrison Chamindie Punyadeera Chamindie Punyadeera |
| author_sort | Yenkai Lim |
| collection | DOAJ |
| description | The oral microbiome can play a role in the instigation and progression of oral diseases that can manifest into other systemic conditions. These associations encourage the exploration of oral dysbiosis leading to the pathogenesis of cancers. In this study, oral rinse was used to characterize the oral microbiome fluctuation associated with oral cavity cancer (OCC) and oropharyngeal cancers (OPC). The study cohort consists of normal healthy controls (n = 10, between 20 and 30 years of age; n = 10, above 50 years of age), high-risk individuals (n = 11, above 50 years of age with bad oral hygiene and/or oral diseases) and OCC and OPC patients (n = 31, HPV-positive; n = 21, HPV-negative). Oral rinse samples were analyzed using 16S rRNA gene amplicon sequencing on the MiSeq platform. Kruskal–Wallis rank test was used to identify genera associated with OCC and OPC. A logistic regression analysis was carried out to determine the performance of these genera as a biomarker panel to predict OCC and OPC. In addition, a two-fold cross-validation with a bootstrap procedure was carried out in R to investigate how well the panel would perform in an emulated clinical scenario. Our data indicate that the oral microbiome is able to predict the presence of OCC and OPC with sensitivity and specificity of 100 and 90%, respectively. With further validation, the panel could potentially be implemented into clinical diagnostic and prognostic workflows for OCC and OPC. |
| first_indexed | 2024-12-11T19:06:02Z |
| format | Article |
| id | doaj.art-c81570a79c8a41f69bc551b5a06c0938 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-12-11T19:06:02Z |
| publishDate | 2018-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-c81570a79c8a41f69bc551b5a06c09382022-12-22T00:53:53ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882018-08-01810.3389/fcimb.2018.00267390376The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal CancersYenkai Lim0Yenkai Lim1Naoki Fukuma2Makrina Totsika3Liz Kenny4Mark Morrison5Chamindie Punyadeera6Chamindie Punyadeera7The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, AustraliaTranslational Research Institute, Brisbane, QLD, AustraliaThe Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, JapanThe School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, AustraliaThe School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, AustraliaTranslational Research Institute, University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, AustraliaThe School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, AustraliaTranslational Research Institute, Brisbane, QLD, AustraliaThe oral microbiome can play a role in the instigation and progression of oral diseases that can manifest into other systemic conditions. These associations encourage the exploration of oral dysbiosis leading to the pathogenesis of cancers. In this study, oral rinse was used to characterize the oral microbiome fluctuation associated with oral cavity cancer (OCC) and oropharyngeal cancers (OPC). The study cohort consists of normal healthy controls (n = 10, between 20 and 30 years of age; n = 10, above 50 years of age), high-risk individuals (n = 11, above 50 years of age with bad oral hygiene and/or oral diseases) and OCC and OPC patients (n = 31, HPV-positive; n = 21, HPV-negative). Oral rinse samples were analyzed using 16S rRNA gene amplicon sequencing on the MiSeq platform. Kruskal–Wallis rank test was used to identify genera associated with OCC and OPC. A logistic regression analysis was carried out to determine the performance of these genera as a biomarker panel to predict OCC and OPC. In addition, a two-fold cross-validation with a bootstrap procedure was carried out in R to investigate how well the panel would perform in an emulated clinical scenario. Our data indicate that the oral microbiome is able to predict the presence of OCC and OPC with sensitivity and specificity of 100 and 90%, respectively. With further validation, the panel could potentially be implemented into clinical diagnostic and prognostic workflows for OCC and OPC.https://www.frontiersin.org/article/10.3389/fcimb.2018.00267/fulloral canceroral rinsesalivabiomarkeroral microbiome |
| spellingShingle | Yenkai Lim Yenkai Lim Naoki Fukuma Makrina Totsika Liz Kenny Mark Morrison Chamindie Punyadeera Chamindie Punyadeera The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers Frontiers in Cellular and Infection Microbiology oral cancer oral rinse saliva biomarker oral microbiome |
| title | The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers |
| title_full | The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers |
| title_fullStr | The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers |
| title_full_unstemmed | The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers |
| title_short | The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers |
| title_sort | performance of an oral microbiome biomarker panel in predicting oral cavity and oropharyngeal cancers |
| topic | oral cancer oral rinse saliva biomarker oral microbiome |
| url | https://www.frontiersin.org/article/10.3389/fcimb.2018.00267/full |
| work_keys_str_mv | AT yenkailim theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT yenkailim theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT naokifukuma theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT makrinatotsika theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT lizkenny theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT markmorrison theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT chamindiepunyadeera theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT chamindiepunyadeera theperformanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT yenkailim performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT yenkailim performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT naokifukuma performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT makrinatotsika performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT lizkenny performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT markmorrison performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT chamindiepunyadeera performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers AT chamindiepunyadeera performanceofanoralmicrobiomebiomarkerpanelinpredictingoralcavityandoropharyngealcancers |