Using Formalin Fixed Paraffin Embedded Tissue to Characterize the Microbiota in P16-positive and P16-negative Tongue Squamous Cell Carcinoma: a Pilot Study

Overview

Journal BMC Oral Health

Publisher Biomed Central

Specialty Dentistry

Date 2024 Feb 28

PMID 38419008

Authors

Zhan Yuanbo

Liu Tianyi

Song Xuejing

Liu Xinpeng

Wang Jianqun

Xu Wenxia

Geng Jingshu

Affiliations

Soon will be listed here.

Abstract

Background: Tongue squamous cell carcinoma (TSCC) is the most common oral cavity cancer, and p16 immunohistochemistry is an exact and available tool in the prognostic and predictive characterization of squamous cell cancers in the head and neck. Microorganisms have a close relationship with the development of TSCC. However, the association between oral bacteria and p16 status has not been well defined in the case of TSCC. Compared with traditional clinical microbial collection methods, formalin-fixed paraffin-embedded (FFPE) tissue samples have several advantages.

Methods: To compare the microbiota compositions between p16-positive and p16-negative patients with TSCC, we performed a small pilot study of microbiological studies of TSCC by paraffin tissue. DNA from FFPE tissue blocks were extracted and microbiomes were profiled by sequencing the 16 S-rRNA-encoding gene (V1-V2/V3-V4/V4 regions). Alterations in the functional potential of the microbiome were predicted using PICRUSt, Tax4Fun, and BugBase.

Results: A total of 60 patients with TSCC were enrolled in the study, however, some challenges associated with DNA damage in FFPE tissues existed, and only 27 (15 p16-positive and 12 p16-negative) passed DNA quality control. Nevertheless, we have tentatively found some meaningful results. The p16 status is associated with microbiota diversity, which is significantly increased in p16-positive patients compared with p16-negative patients. Desulfobacteria, Limnochordia, Phycisphaerae, Anaerolineae, Saccharimonadia and Kapabacteria had higher abundances among participants with p16-positive. Moreover, functional prediction revealed that the increase of these bacteria may enhance viral carcinogenesis in p16-positive TSCC.

Conclusions: Bacterial profiles showed a significant difference between p16-positive TSCC and p16-negative TSCC. These findings may provide insights into the relationship between p16 status and the microbial taxa in TSCC, and these bacteria may provide new clues for developing therapeutic targets for TSCC.

Citing Articles

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References

Waite D, Chuvochina M, Pelikan C, Parks D, Yilmaz P, Wagner M . Proposal to reclassify the proteobacterial classes and , and the phylum into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol. 2020; 70(11):5972-6016. DOI: 10.1099/ijsem.0.004213. View

Senel S . An Overview of Physical, Microbiological and Immune Barriers of Oral Mucosa. Int J Mol Sci. 2021; 22(15). PMC: 8346143. DOI: 10.3390/ijms22157821. View

Pande P, Mathur M, Shukla N, Ralhan R . pRb and p16 protein alterations in human oral tumorigenesis. Oral Oncol. 1998; 34(5):396-403. DOI: 10.1016/s1368-8375(98)00024-4. View

Stephen J, Divine G, Chen K, Chitale D, Havard S, Worsham M . Significance of p16 in Site-specific HPV Positive and HPV Negative Head and Neck Squamous Cell Carcinoma. Cancer Clin Oncol. 2013; 2(1):51-61. PMC: 3736998. DOI: 10.5539/cco.v2n1p51. View

Franceschi D, Gupta R, SPIRO R, Shah J . Improved survival in the treatment of squamous carcinoma of the oral tongue. Am J Surg. 1993; 166(4):360-5. DOI: 10.1016/s0002-9610(05)80333-2. View

Scanu T, Spaapen R, Bakker J, Pratap C, Wu L, Hofland I . Salmonella Manipulation of Host Signaling Pathways Provokes Cellular Transformation Associated with Gallbladder Carcinoma. Cell Host Microbe. 2015; 17(6):763-74. DOI: 10.1016/j.chom.2015.05.002. View

Ndiaye C, Mena M, Alemany L, Arbyn M, Castellsague X, Laporte L . HPV DNA, E6/E7 mRNA, and p16INK4a detection in head and neck cancers: a systematic review and meta-analysis. Lancet Oncol. 2014; 15(12):1319-31. DOI: 10.1016/S1470-2045(14)70471-1. View

Charlson E, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R . Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One. 2010; 5(12):e15216. PMC: 3004851. DOI: 10.1371/journal.pone.0015216. View

Kawamoto D, Borges R, Ribeiro R, de Souza R, Amado P, Saraiva L . Oral Dysbiosis in Severe Forms of Periodontitis Is Associated With Gut Dysbiosis and Correlated With Salivary Inflammatory Mediators: A Preliminary Study. Front Oral Health. 2022; 2:722495. PMC: 8757873. DOI: 10.3389/froh.2021.722495. View

10.

Wang P, Dong Y, Jiao J, Zuo K, Han C, Zhao L . Cigarette smoking status alters dysbiotic gut microbes in hypertensive patients. J Clin Hypertens (Greenwich). 2021; 23(7):1431-1446. PMC: 8678690. DOI: 10.1111/jch.14298. View

11.

Marsh P, Head D, Devine D . Ecological approaches to oral biofilms: control without killing. Caries Res. 2015; 49 Suppl 1:46-54. DOI: 10.1159/000377732. View

12.

Jiang Q, Liu J, Chen L, Gan N, Yang D . The Oral Microbiome in the Elderly With Dental Caries and Health. Front Cell Infect Microbiol. 2019; 8:442. PMC: 6328972. DOI: 10.3389/fcimb.2018.00442. View

13.

Zhu A, Yang X, Bai L, Hou Y, Guo C, Zhao D . Analysis of microbial changes in the tonsillar formalin-fixed paraffin-embedded tissue of Chinese patients with IgA nephropathy. Pathol Res Pract. 2020; 216(11):153174. DOI: 10.1016/j.prp.2020.153174. View

14.

Asshauer K, Wemheuer B, Daniel R, Meinicke P . Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. 2015; 31(17):2882-4. PMC: 4547618. DOI: 10.1093/bioinformatics/btv287. View

15.

Stasiewicz M, Kwasniewski M, Karpinski T . Microbial Associations with Pancreatic Cancer: A New Frontier in Biomarkers. Cancers (Basel). 2021; 13(15). PMC: 8345173. DOI: 10.3390/cancers13153784. View

16.

Perez-Sayans M, Suarez-Penaranda J, Gayoso-Diz P, Barros-Angueira F, Gandara-Rey J, Garcia-Garcia A . p16(INK4a)/CDKN2 expression and its relationship with oral squamous cell carcinoma is our current knowledge enough?. Cancer Lett. 2011; 306(2):134-41. DOI: 10.1016/j.canlet.2011.02.039. View

17.

de Abreu P, Co A, Azevedo P, do Valle I, Oliveira K, Gouvea S . Frequency of HPV in oral cavity squamous cell carcinoma. BMC Cancer. 2018; 18(1):324. PMC: 5870524. DOI: 10.1186/s12885-018-4247-3. View

18.

Zhao Q, Yang T, Yan Y, Zhang Y, Li Z, Wang Y . Alterations of Oral Microbiota in Chinese Patients With Esophageal Cancer. Front Cell Infect Microbiol. 2020; 10:541144. PMC: 7609410. DOI: 10.3389/fcimb.2020.541144. View

19.

Warnakulasuriya S . Global epidemiology of oral and oropharyngeal cancer. Oral Oncol. 2008; 45(4-5):309-16. DOI: 10.1016/j.oraloncology.2008.06.002. View

20.

Zhang X, Li C, Cao W, Zhang Z . Alterations of Gastric Microbiota in Gastric Cancer and Precancerous Stages. Front Cell Infect Microbiol. 2021; 11:559148. PMC: 7966516. DOI: 10.3389/fcimb.2021.559148. View