16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, Human Papilloma Virus infection and surgical treatment

Guerrero-Preston, Rafael; Godoy-Vitorino, Filipa; Jedlicka, Anne; Rodríguez, Angélica Rodríguez; González, Herminio; Bondy, Jessica; Lawson, Fahcina; Folawiyo, Oluwasina; Michailidi, M.; Dziedzic, Amanda; Thangavel, Rajagowthamee R.; Hadar, Tal; Noordhuis, Maartje; Westra, W. H.; Koch, Wayne M.; Sidransky, David

doi:10.1016/j.toxlet.2016.07.133

Cited by 10 publications

(9 citation statements)

References 41 publications

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“…In the present study, Firmicutes and Bacteriodetes were the most common phyla, which is in accord with studies of the oral microbiome in health and disease (Guerrero-Preston et al 2016). In addition, Prevotella, Veillonella, and Streptococcus Figure 1.…”

Section: Discussionsupporting

confidence: 91%

“…*P < 0.05 (Differences did not reach false discovery rate [FDR] adjusted statistical significance). were the most frequently detected genera, which is in line with the literature (Al-Hebshi et al 2015;Guerrero-Preston et al 2016). FA patients showed VPI (31.3%) and GBI (34.2%) levels that are higher than the recommended levels.…”

Section: Discussionsupporting

confidence: 89%

“…Its open-ended character allows for the discovery of new taxa potentially related to disease, and its culture-independent nature does not exclude species and phylotypes that are difficult to grow or currently uncultivated but that might have a role in disease initiation. The most recent studies of the association between the oral microbiome and OSCC have used 454 pyrosequencing (Schmidt et al 2014;Guerrero-Preston et al 2016). However, this form of sequencing has recently been outperformed by MiSeq Illumina sequencing (Caporaso et al 2012), which has a lower error rate and generates over 10 times more reads (Nelson et al 2014) and has thus become the leading sequencing platform for human microbiome studies (Amarasekara et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia

et al. 2016

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Fanconi anemia (FA) is a rare genetic disease characterized by chromosomal instability and impaired DNA damage repair. FA patients develop oral squamous cell carcinoma (OSCC) earlier and more frequently than the general population, especially after hematopoietic stem cell transplantation (HSCT). Although evidence of an etiological role of the local microbiome and carcinogenesis has been mounting, no information exists regarding the oral microbiome of FA patients. The aim of this study was to explore the salivary microbiome of 61 FA patients regarding their oral health status and OSCC risk factors. After answering a questionnaire and receiving clinical examination, saliva samples were collected and analyzed using 16S rRNA sequencing of the V3-V4 hypervariable region. The microbial profiles associated with medical and clinical parameters were analyzed using general linear models. Patients were young (mean age, 22 y) and most had received HSCT (n = 53). The most abundant phyla were Firmicutes [mean relative abundance (SD), 42.1% (10.1%)] and Bacteroidetes [(25.4% (11.4%)]. A history of graft-versus-host disease (GVHD) (n = 27) was associated with higher proportions of Firmicutes (43.8% × 38.5%, P = 0.05). High levels of gingival bleeding were associated with the genera Prevotella (22.25% × 20%), Streptococcus (19.83% × 17.61%), Porphyromonas (3.63% × 1.42%, P = 0.03), Treponema (1.02% × 0.28%, P = 0.009), Parvimonas (0.28% × 0.07%, P = 0.02) and Dialister (0.27% × 0.10%, P = 0.04). Finally, participants transplanted over 11 y ago showed the highest levels of Streptococcus (18.4%), Haemophilus (12.7%) and Neisseria (6.8%). In conclusion, FA patients that showed poor oral hygiene harbored higher proportions of the genera of bacteria compatible with gingival disease. Specific microbial differences were associated with a history of oral GVHD and a history of oral mucositis.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

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The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia

et al. 2016

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“…Recently, a study on HNSCC patients showed a significant loss in diversity of microbiota species compared with healthy controls (82). In addition, bacteria diversity also significantly decreased after surgery (83). Furthermore, it has been noted that mucosal toxicity of different treatments for HNSCC are related to patient overall survival, also including HPV status in the analysis (107).…”

Section: Microbiome Studies In Head and Neck Cancermentioning

confidence: 99%

“…So far, research on microbiome changes associated to HPV infection in HNSCC is limited, but HPV infection has been associated with microbiota changes in HPV related cervical intraepithelial neoplasia (CIN) and cervical cancer (108). There is hint that the abundance of Veillonella, Prevotela and Streptococcus fluctuated when HPV status changed (83). However, all data in HNSCC are still preliminary and the sample sizes are small.…”

Section: Microbiome Studies In Head and Neck Cancermentioning

confidence: 99%

Human Papillomavirus and Potentially Relevant Biomarkers in Tonsillar and Base of Tongue Squamous Cell Carcinoma

Näsman

Bersani

Lindquist

et al. 2017

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Abstract. Human papillomavirus (HPV)-positive tonsillarand base of tongue cancer is increasing epidemically and has much better outcome than corresponding HPV-negativeIn 2007, human papillomavirus (HPV) was recognized as a risk factor for oropharyngeal squamous cell carcinoma (OPSCC) by the International Agency for Research against Cancer (IARC), besides the traditional risk factors smoking and alcohol (1-4). Concurrently, an increased incidence of OPSCC, more specifically tonsillar and base of tongue cancer (TSCC and BOTSCC, the two main HPV-positive OPSCC sites) was described in many developed countries, and found to be due to a sharp rise of HPV-positive cases (5-18). These HPV-positive tumors had a much better clinical outcome than their HPV-negative counterparts and head and neck squamous cell carcinoma (HNSCC) in general when treated with radiotherapy and surgery (1-3, 15-17, 19, 20). Treatment of HNSCC including OPSCC has, however, gradually become more intensified with induction chemotherapy or concurrent chemo-radiotherapy and sometimes the administration of Erbitux, leading to more severe side effects (16, 20, 21). This is likely unnecessary for most HPV-positive TSCC and BOTSCC patients since they generally respond well to less therapy and furthermore, intensified therapy does not improve survival of [15][16][17] 20, 22, 23). It is, therefore, important to identify patients with HPV-positive TSCC and BOTSCC eligible for less treatment or targeted therapy and efforts focus now on finding predictive and targetable markers for these patients (24-39).Here, a short background of the field and an update on recent attempts to find predictive and targetable markers with different methodologies for individualized therapy is presented. Human Papillomavirus in Tonsillar and Base of Tongue Squamous Cell Carcinoma and an Epidemic Increase of these TumorsIn 2000, an association between HPV and OPSCC and TSCC was reported, and with radiotherapy and surgery, these HPVpositive cases had much better outcome than corresponding HPV-negative cases (80% vs. 40-50% 5-year survival) (1, 2). In 2004, a similar relationship of HPV to BOTSCC, but not to mobile tongue cancer was disclosed (40). Based on 5319

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Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma

Al-Hebshi

Nasher

Maryoud

et al. 2017

Sci Rep

218

231

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Studies on the possible association between bacteria and oral squamous cell carcinoma (OSCC) remain inconclusive, largely due to methodological variations/limitations. The objective of this study was to characterize the species composition as well as functional potential of the bacteriome associated with OSCC. DNA obtained from 20 fresh OSCC biopsies (cases) and 20 deep-epithelium swabs (matched control subjects) was sequenced for the V1-V3 region using Illumina’s 2 × 300 bp chemistry. High quality, non-chimeric merged reads were classified to species level using a prioritized BLASTN-algorithm. Downstream analyses were performed using QIIME, PICRUSt, and LEfSe. Fusobacterium nucleatum subsp. polymorphum was the most significantly overrepresented species in the tumors followed by Pseudomonas aeruginosa and Campylobacter sp. Oral taxon 44, while Streptococcus mitis, Rothia mucilaginosa and Haemophilus parainfluenzae were the most significantly abundant in the controls. Functional prediction showed that genes involved in bacterial mobility, flagellar assembly, bacterial chemotaxis and LPS synthesis were enriched in the tumors while those responsible for DNA repair and combination, purine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, ribosome biogenesis and glycolysis/gluconeogenesis were significantly associated with the controls. This is the first epidemiological evidence for association of F. nucleatum and P. aeruginosa with OSCC. Functionally, an “inflammatory bacteriome” is enriched in OSSC.

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16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, Human Papilloma Virus infection and surgical treatment

Cited by 10 publications

References 41 publications

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia

Human Papillomavirus and Potentially Relevant Biomarkers in Tonsillar and Base of Tongue Squamous Cell Carcinoma

Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma

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