Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing

Ganly, Ian; Pei, Zhiheng; Hao, Yuhan; Ma, Yingfei; Rosenthal, Matthew; ZhengLin, Wu; Migliacci, Jocelyn; Huang, Bin; Katabi, Nora; Tseng, Wenzhi; Brown, Stuart M.; Tang, Yi‐Wei; Yang, Liying

doi:10.1038/s41598-021-83197-x

Cited by 6 publications

(9 citation statements)

References 39 publications

(53 reference statements)

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“…In this way, 83 novel HPV genomes were discovered. A non-selective approach that theoretically can identify all HPV types has been recently described [64]. This is based on DNA fragmentation and shotgun metagenomic library preparation followed by sequencing.…”

Section: Known and Novel Hpvsmentioning

confidence: 99%

Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology

et al. 2021

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Oral infection by Human Papillomavirus (HPV) has recently gained great attention because of its involvement in the development of a subset of head and neck squamous cell carcinoma. The role of specific Alpha-HPVs in this regard has been well established, whereas the contribution of other genera is under investigation. Despite their traditional classification as “cutaneous” types, Beta and Gamma HPVs are frequently detected in oral samples. Due to the lack of a standardized protocol, a large variety of methodologies have been used for oral sample collection, DNA extraction, HPV detection and genotyping. Laboratory procedures influence the evaluation of oral HPV prevalence, which largely varies also according to the population characteristics, e.g., age, gender, sexual behavior, Human Immunodeficiency Virus (HIV) status. Nevertheless, oral infection by Beta and Gamma HPVs seems to be even more common than Alpha-HPVs. The latter is 5–7% in the general population, and increases up to 30% approximately in HIV-infected men who have sex with men. Despite major advances in the evaluation of oral HPV prevalence, its natural history is still little understood, especially for Beta and Gamma HPVs. The latest technologies, such as Next Generation Sequencing (NGS), can be exploited to gain new insights into oral HPV, and to improve the identification of novel HPV types.

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Section: Known and Novel Hpvsmentioning

confidence: 99%

Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology

et al. 2021

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“…A case–control study was approved by the Institutional Review Board of Memorial Sloan Kettering Cancer Center (MSK) (IRB 15-256) and New York University School of Medicine (i15-00389), as previously described [ 37 ]. In brief, we recruited 42 OC-SCC cases and 45 non-OC-SCC controls from MSK.…”

Section: Methodsmentioning

confidence: 99%

“…There is no simple mathematic parameter for determining the adequacy of sampling of a complex microbiota. Rather, we empirically estimated the adequacy of sample size based on the findings from our previous study “periodontal pathogens are a risk factor of the oral cavity squamous cell carcinoma” [ 37 ]. The previous study used 18 nonsmoker OC-SCC cases and 12 controls while the current study used 42 OC-SCC cases and 45 controls, more than double the cases and triple the controls.…”

Section: Methodsmentioning

confidence: 99%

Oral Microbiome in Nonsmoker Patients with Oral Cavity Squamous Cell Carcinoma, Defined by Metagenomic Shotgun Sequencing

Ganly

Hao

Rosenthal

et al. 2022

Cancers

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Objectives: Smoking is the commonest cause of oral cavity squamous cell carcinoma (OC-SCC), but the etiology of OC-SCC in nonsmokers is unknown. Our primary goal was to use metagenomic shotgun sequencing (MSS) to define the taxonomic composition and functional potential of oral metagenome in nonsmokers with OC-SCC. Methods: We conducted a case–control study with 42 OC-SCC case and 45 control nonsmokers. MSS was performed on DNA extracted from mouthwash samples. Taxonomic analysis and pathway analysis were done using MetaPhlAn2 and HUMAnN2, respectively. Statistical difference was determined using the Mann–Whitney test controlling false discovery rate. Results: There was no significant difference in age, sex, race, or alcohol consumption between OC-SCC and control patients. There was a significant difference in beta diversity between OC-SCC and controls. At the phylum level, Bacteroidetes and Synergistetes were overly represented in OC-SCC while Actinobacteria and Firmicutes were overly represented in controls. At the genus level, Fusobacterium was overly represented in OC-SCC compared with controls, while Corynebacterium, Streptococcus, Actinomyces, Cryptobacterium, and Selenomonas were overly represented in controls. Bacterial pathway analysis identified overrepresentation in OC-SCC of pathways related to metabolism of flavin, biotin, thiamin, heme, sugars, fatty acids, peptidoglycans, and tRNA and overrepresentation of nucleotides and essential amino acids in controls. Conclusions: The oral microbiome in nonsmoker patients with OC-SCC is significantly different from that of nonsmoker control patients in taxonomic compositions and functional potentials. Our study’s MSS findings matched with previous 16S-based methods in taxonomic differentiation but varied greatly in functional differentiation of microbiomes in OC-SCC and controls.

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“…People living with HIV (PLHIV) have 2-3-fold higher odds of prevalent oral human papillomavirus (HPV) compared to HIV-uninfected individuals [1]. Oncogenic high-risk HPV (hrHPV) types (mostly HPV16, HPV18 and HPV33) [2], have been isolated in 12% -26% of oral samples of PLHIV in previous studies [1].…”

Section: Introductionmentioning

confidence: 99%

“…This puts PLHIV at an increased risk of oral squamous cell carcinomas (OSCCs), particularly of the base of tongue, lingual and palatine tonsils [1,2].…”

Section: Introductionmentioning

confidence: 99%

Xpert® HPV is not a useful screening tool for oral HPV among people living with HIV (PLHIV)

Admase

Joshi²,

Borse³

et al. 2022

Preprint

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Background: Rapid diagnostic tests (RPTs) for high-risk HPV genotypes can help triage people living with HIV (PLHIV), who are at greater risk for oral cancers especially in low-and-middle-income-countries (LMICs), that have a high burden of both HIV and oral cancers. We evaluated the utility of Xpert® HPV, a RPT for oral HPV among PLHIV. Methods: We used data from 429 PLHIV receiving care at a tertiary care hospital affiliated antiretroviral therapy center in Pune, India. Oral HPV was evaluated using oral rinse samples. Samples were classified as usable (if they were successfully processed on Xpert® HPV) or not usable (if they were not successfully processed on Xpert® HPV). Factors associated with non-usability were evaluated using logistic regression. We compared the sensitivity and specificity of the Xpert® HPV for oral samples with conventional polymerase chain reaction (PCR). Results: The Xpert® HPV deemed almost a third (29.8%) of the oral samples not usable for oral HPV detection. We were unable to identify factors associated with non-usability. Compared to conventional polymerase chain reaction (PCR), the sensitivity of Xpert® HPV was 6.2% and specificity 100%, for detection of oral HPV. Conclusions: Xpert® HPV cannot be used for the detection of oral HPV among PLHIV presently. More research to optimize Xpert® HPV for oral samples is required.

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Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing

Cited by 6 publications

References 39 publications

Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology

Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology

Oral Microbiome in Nonsmoker Patients with Oral Cavity Squamous Cell Carcinoma, Defined by Metagenomic Shotgun Sequencing

Xpert® HPV is not a useful screening tool for oral HPV among people living with HIV (PLHIV)

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