High-throughput nucleotide sequencing for bacteriome studies in oral squamous cell carcinoma: a systematic review

Ramos, Rudnei O.; Sodré, Camila Stofella; Rodrigues, Paulo M. G.; Silva, Alexandre Marques Paes da; Fuly, Milenna Silva; Santos, Henrique F.; Gonçalves, Lúcio Souza; Ferreira, Dennis de Carvalho; Ribeiro, Márcia Gonçalves

doi:10.1007/s10006-020-00873-4

Cited by 7 publications

(31 citation statements)

References 52 publications

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“…Overall, the study design seems to be lacking in rationale, with widespread variances in selection of the 16S hypervariable region for sequencing, DNA extraction methods and sampling method for OSCC lesions. Such differences can impact the overall microbiome under study, thus causing a misinterpretation of the oral microbial community, as evidenced by previous systematic reviews (10, 13). A key aim of this study was to identify potential biomarker organisms in OSCC, which could help map early development of the disease as an aid to diagnosis, as evidenced by previous studies conducted with the gut (31).…”

Section: Discussionmentioning

confidence: 99%

“…Despite these advancements, the future of oral microbiome research in OSCC is highly dependent on study design characterization. Several systematic reviews conducted over the past few years have concluded that oral microbiome studies must widely focus on a standard study design, collect essential and adequate metadata, and follow proper pipelines for analyses of the data (10,13). We have determined that it may be difficult to rely upon microbiome studies for this purpose, due to a lack of specificity, and wide variation between individual study design and outcomes.…”

Section: Discussionmentioning

confidence: 99%

“…Studies have also found that tobacco consumption in the form of chewing and smoking could alter the oral microbiome, leading to tumour progression. These parameters are extremely important and need to be included during patient data collection, which seemed to be lacking among most studies (13). Five of 11 studies had included information about smokers and alcoholics, however, it was only 4% and 10% of the overall sample size included in our meta‐analysis.…”

Section: Discussionmentioning

confidence: 99%

“…These 'intratumoural' bacteria play a key role in modulating immune-related changes leading to a more aggressive, enhanced tumour form (15,16). Several studies have been published utilizing amplicon sequencing of the oral microbiome in OSCC, however, wide-scale variances in study design including sampling technique, nucleic acid extraction methods, sequencing technique and region of 16S rRNA selected for analysis vary dramatically between studies, ultimately hindering the ability to compare findings (13,14,17). However, it is now thought that specific members of the oral microbial community promote genetic instability, tumour proliferation and changes to the host metabolism contributing to resistance to therapy (18).…”

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confidence: 99%

“…Studies have implicated the role of Fusobacterium, Pseudomonas, Porphyromonas, Provotella, Campylobacter, Rothia and Leptotrichia in the progression of OSCC (10,11,13). These bacteria are often present in the surrounding tumour environment, however recent evidence has shown that a few species, such as Fusobacterium nucleatum and Porphyromonas.…”

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confidence: 99%

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Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma

Delaney

Veena

Butcher

et al. 2023

APMIS

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A new era of next‐generation sequencing has changed our perception of the oral microbiome in health and disease, and with this there is a growing understanding that the oral microbiome is a contributing factor to oral squamous cell carcinoma (OSCC), a malignancy of the oral cavity. This study aimed to analyse the trends and relevant literature based on the 16S rRNA oral microbiome in head and neck cancer using next‐generation sequencing technologies, and to conduct a meta‐analysis of the studies with OSCC cases and healthy controls. A literature search using the databases Web of Science and PubMed was conducted in a scoping‐like review to collect information based on the study design, and plots were generated using RStudio. We selected case–control studies using 16S rRNA oral microbiome sequencing analysis in OSCC cases versus healthy controls for re‐analysis. Statistical analyses were conducted using R. Out of 916 original articles, we filtered and selected 58 studies for review, and 11 studies for meta‐analysis. Differences between sampling type, DNA extraction methods, next‐generation sequencing technology and region of the 16S rRNA were identified. No significant differences in the α‐ and β‐diversity between health and oral squamous cell carcinoma were observed (p < 0.05). Random Forest classification marginally improved predictability of four studies (training set) when split 80/20. We found an increase in Selenomonas, Leptotrichia and Prevotella species to be indicative of disease. A number of technological advances have been accomplished to study oral microbial dysbiosis in oral squamous cell carcinoma. There is a clear need for standardization of study design and methodology to ensure 16S rRNA outputs are comparable across the discipline in the hope of identifying ‘biomarker’ organisms for designing screening or diagnostic tools.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma

Delaney

Veena

Butcher

et al. 2023

APMIS

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Identification of consensus head and neck cancer-associated microbiota signatures: a systematic review and meta-analysis of 16S rRNA and The Cancer Microbiome Atlas datasets

Yeo,

Li,

et al. 2024

Journal of Medical Microbiology

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Introduction. Multiple reports have attempted to describe the tumour microbiota in head and neck cancer (HNSC). Gap statement. However, these have failed to produce a consistent microbiota signature, which may undermine understanding the importance of bacterial-mediated effects in HNSC. Aim. The aim of this study is to consolidate these datasets and identify a consensus microbiota signature in HNSC. Methodology. We analysed 12 published HNSC 16S rRNA microbial datasets collected from cancer, cancer-adjacent and non-cancer tissues to generate a consensus microbiota signature. These signatures were then validated using The Cancer Microbiome Atlas (TCMA) database and correlated with the tumour microenvironment phenotypes and patient’s clinical outcome. Results. We identified a consensus microbial signature at the genus level to differentiate between HNSC sample types, with cancer and cancer-adjacent tissues sharing more similarity than non-cancer tissues. Univariate analysis on 16S rRNA datasets identified significant differences in the abundance of 34 bacterial genera among the tissue types. Paired cancer and cancer-adjacent tissue analyses in 16S rRNA and TCMA datasets identified increased abundance in Fusobacterium in cancer tissues and decreased abundance of Atopobium , Rothia and Actinomyces in cancer-adjacent tissues. Furthermore, these bacteria were associated with different tumour microenvironment phenotypes. Notably, high Fusobacterium signature was associated with high neutrophil (r=0.37, P<0.0001), angiogenesis (r=0.38, P<0.0001) and granulocyte signatures (r=0.38, P<0.0001) and better overall patient survival [continuous: HR 0.8482, 95 % confidence interval (CI) 0.7758–0.9273, P=0.0003]. Conclusion. Our meta-analysis demonstrates a consensus microbiota signature for HNSC, highlighting its potential importance in this disease.

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Biological biomarkers of oral cancer

Radaic,

Kamarajan,

Cho

et al. 2023

Periodontology 2000

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The oral squamous cell carcinoma (OSCC) 5 year survival rate of 41% has marginally improved in the last few years, with less than a 1% improvement per year from 2005 to 2017, with higher survival rates when detected at early stages. Based on histopathological grading of oral dysplasia, it is estimated that severe dysplasia has a malignant transformation rate of 7%–50%. Despite these numbers, oral dysplasia grading does not reliably predict its clinical behavior. Thus, more accurate markers predicting oral dysplasia progression to cancer would enable better targeting of these lesions for closer follow‐up, especially in the early stages of the disease. In this context, molecular biomarkers derived from genetics, proteins, and metabolites play key roles in clinical oncology. These molecular signatures can help predict the likelihood of OSCC development and/or progression and have the potential to detect the disease at an early stage and, support treatment decision‐making and predict treatment responsiveness. Also, identifying reliable biomarkers for OSCC detection that can be obtained non‐invasively would enhance management of OSCC. This review will discuss biomarkers for OSCC that have emerged from different biological areas, including genomics, transcriptomics, proteomics, metabolomics, immunomics, and microbiomics.

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High-throughput nucleotide sequencing for bacteriome studies in oral squamous cell carcinoma: a systematic review

Cited by 7 publications

References 52 publications

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma

Identification of consensus head and neck cancer-associated microbiota signatures: a systematic review and meta-analysis of 16S rRNA and The Cancer Microbiome Atlas datasets

Biological biomarkers of oral cancer

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