Altered vaginal eukaryotic virome is associated with different cervical disease status

Yanpeng Li; Le Cao; Xiao Han; Yingying Ma; Yanmei Liu; Shujun Gao; Chiyu Zhang

doi:10.1016/j.virs.2022.12.004

April 2023

. doi: 10.1016/j.virs.2022.12.004

Citation: Yanpeng Li, Le Cao, Xiao Han, Yingying Ma, Yanmei Liu, Shujun Gao, Chiyu Zhang. Altered vaginal eukaryotic virome is associated with different cervical disease status .VIROLOGICA SINICA, 2023, 38(2) : 184-197. http://dx.doi.org/10.1016/j.virs.2022.12.004

阴道真核病毒组变化与不同的宫颈疾病状态相关

李龑鹏 ^a ,
曹乐 ^a ,
韩笑 ^b,c ,
马英英 ^a ,
刘艳梅 ^b,c ,
高蜀君 ^b,c,, ,
张驰宇 ^a,,

1 复旦大学附属上海市公共卫生临床中心;
2 复旦大学附属妇产科医院

通讯作者： 高蜀君, 031108282@fudan.edu.cn; 张驰宇, chiyu_zhang1999@163.com
收稿日期： 2022-09-06
录用日期： 2022-12-14

摘要

病毒是人体的重要组成部分，越来越多的证据表明，病毒可参与宿主的生理和疾病状态。尽管阴道细菌微生物组与人乳头瘤病毒（HPV）感染和宫颈癌（CC）进展有关，但对于阴道中病毒组的作用知之甚少。在这项初步的探索研究中，我们利用无偏的病毒宏基因组方法，研究了具有不同程度宫颈病变的女性的阴道真核病毒组，并分析它们与不同宫颈疾病状态的相关性。在具有不同程度宫颈病变和乳酸杆菌组成的阴道样本中观察到了不同的真核病毒组。指环病毒和乳头瘤病毒是阴道病毒组中最常见的真核病毒。更高丰度和多样性的指环病毒以及乳头瘤病毒与低级别鳞状上皮内病变（LSIL）和宫颈癌相关。此外我们也发现，较高的指环病毒丰度与乳酸菌的缺失以及和乳酸杆菌群落类型（CST IV）相关。在宫颈病变严重程度从LSIL到CC的过程中，我们发现了逐渐增加的指环病毒和乳头瘤病毒之间的相关性。这些数据表明不同微生物以及宿主生理状态之间存在的潜在相互作用关系。LSIL和CC具有更高丰度和多样性的指环病毒和乳头瘤病毒类群，暗示了这些病毒类群可作为预测HPV持续感染或者宫颈癌风险的潜在辅助生物标志物。该研究也表明，未来需要重点关注指环病毒的丰度与宫颈疾病之间的临床相关性，并评估它们作为预测宫颈癌发展的辅助生物标志物的潜力。
- 阴道病毒组
- , 宫颈癌
- , 指环病毒
- , 乳头瘤病毒

Altered vaginal eukaryotic virome is associated with different cervical disease status

Yanpeng Li ^a ,
Le Cao ^a ,
Xiao Han ^b,c ,
Yingying Ma ^a ,
Yanmei Liu ^b,c ,
Shujun Gao ^b,c,, ,
Chiyu Zhang ^a,,

a. Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China;
b. Center of Diagnosis and Treatment for Cervical Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200080, China;
c. Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Fudan University, Shanghai, 200080, China

Corresponding author: Shujun Gao, 031108282@fudan.edu.cn Chiyu Zhang, chiyu_zhang1999@163.com
Received Date: 06 September 2022
Accepted Date: 14 December 2022

Abstract

Viruses are important components of the human body. Growing evidence suggests that they are engaged in the physiology and disease status of the host. Even though the vaginal microbiome is involved in human papillomavirus (HPV) infection and cervical cancer (CC) progression, little is known about the role of the vaginal virome. In this pilot exploratory study, using unbiased viral metagenomics, we aim to investigate the vaginal eukaryotic virome in women with different levels of cervical lesions, and examine their associations with different cervical disease status. An altered eukaryotic virome was observed in women with different levels of lesions and Lactobacillus profiles. Anelloviruses and papillomaviruses are the most commonly detected eukaryotic viruses of the vaginal virome. Higher abundance and richness of anelloviruses and papillomaviruses were associated with low-grade squamous intraepithelial lesion (LSIL) and CC. Besides, higher anellovirus abundance was also associated with lactobacillus-depleted microbiome profiles and bacterial community state (CST) type IV. Furthermore, increased correlations between Anelloviridae and Papillomaviridae occurred in the women with increased cervical disease severity level from LSIL to CC. These data suggest underlying interactions between different microbes as well as the host physiology. Higher abundance and diversity of both anelloviruses and papillomaviruses shared by LSIL and CC suggest that anellovirus may be used as a potential adjunct biomarker to predict the risk of HPV persistent infection and/or CC. Future studies need to focus on the clinical relevance of anellovirus abundance with cervical disease status, and the evaluation of their potential as a new adjunct biomarker for the prediction and prognoses of CC.
- Vaginal virome
- , Cervical cancer
- , Anellovirus
- , Papillomavirus

References
1. Audirac-Chalifour A, Torres-Poveda K, Bahena-Román M, Téllez-Sosa J, Martínez-Barnetche J, Cortina-Ceballos B, López-Estrada G, Delgado-Romero K, Burguete-García AI, Cantú D, García-Carrancá A, Madrid-Marina V. 2016. Cervical microbiome and cytokine profile at various stages of cervical cancer:A pilot study. PLoS One, 11:e0153274.
2. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic:A flexible trimmer for illumina sequence data. Bioinformatics, 30:2114-2120.
3. Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using diamond. Nat Methods, 12:59-60.
4. Cao Z, Sugimura N, Burgermeister E, Ebert MP, Zuo T, Lan P. 2022. The gut virome:A new microbiome component in health and disease. EBioMedicine, 81:104113.
5. Carroll D, Daszak P, Wolfe ND, Gao GF, Morel CM, Morzaria S, Pablos-Méndez A, Tomori O, Mazet JAK. 2018. The global virome project. Science, 359:872-874.
6. Castanheira CP, Sallas ML, Nunes RAL, Lorenzi NPC, Termini L. 2021. Microbiome and cervical cancer. Pathobiology, 88:187-197.
7. Castellsagué X. 2008. Natural history and epidemiology of hpv infection and cervical cancer. Gynecol Oncol, 110:S4-7.
8. Champer M, Wong AM, Champer J, Brito IL, Messer PW, Hou JY, Wright JD. 2018. The role of the vaginal microbiome in gynaecological cancer. Bjog, 125:309-315.
9. Chase D, Goulder A, Zenhausern F, Monk B, Herbst-Kralovetz M. 2015. The vaginal and gastrointestinal microbiomes in gynecologic cancers:A review of applications in etiology, symptoms and treatment. Gynecol Oncol, 138:190-200.
10. Curty G, de Carvalho PS, Soares MA. 2019. The role of the cervicovaginal microbiome on the genesis and as a biomarker of premalignant cervical intraepithelial neoplasia and invasive cervical cancer. Int J Mol Sci, 21:222.
11. da Costa AC, Moron AF, Forney LJ, Linhares IM, Sabino E, Costa SF, Mendes-Correa MC, Witkin SS. 2021. Identification of bacteriophages in the vagina of pregnant women:A descriptive study. Bjog, 128:976-982.
12. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, Okamoto J, Snyder TM, Cornfield DN, Nicolls MR, Weill D, Bernstein D, Valantine HA, Quake SR. 2013. Temporal response of the human virome to immunosuppression and antiviral therapy. Cell, 155:1178-1187.
13. Eskew AM, Stout MJ, Bedrick BS, Riley JK, Omurtag KR, Jimenez PT, Odem RR, Ratts VS, Keller SL, Jungheim ES, Wylie KM. 2020. Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation:A prospective exploratory study. Bjog, 127:208-216.
14. Fernández-Ruiz M, Albert E, Giménez E, Ruiz-Merlo T, Parra P, López-Medrano F, San Juan R, Polanco N, Andrés A, Navarro D, Aguado JM. 2019. Monitoring of alphatorquevirus DNA levels for the prediction of immunosuppression-related complications after kidney transplantation. Am J Transplant, 19:1139-1149.
15. Gardella B, Pasquali MF, La Verde M, Cianci S, Torella M, Dominoni M. 2022. The complex interplay between vaginal microbiota, hpv infection, and immunological microenvironment in cervical intraepithelial neoplasia:A literature review. Int J Mol Sci, 23:7174.
16. Geoghegan JL, Di Giallonardo F, Wille M, Ortiz-Baez AS, Costa VA, Ghaly T, Mifsud JCO, Turnbull OMH, Bellwood DR, Williamson JE, Holmes EC. 2021. Virome composition in marine fish revealed by meta-transcriptomics. Virus Evol, 7:veab005.
17. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. 2018. Current understanding of the human microbiome. Nat Med, 24:392-400.
18. Graham SV. 2017. The human papillomavirus replication cycle, and its links to cancer progression:A comprehensive review. Clin Sci (Lond), 131:2201-2221.
19. Hoek RA, Verschuuren EA, de Vries RD, Vonk JM, van Baarle D, van der Heiden M, van Gemert JP, Gore EJ, Niesters HG, Erasmus M, Hellemons ME, Scherbeijn SM, Wijbenga N, Mahtab EAF, GeurtsvanKessel CH, Buter CVL. 2022. High torque tenovirus (ttv) load before first vaccine dose is associated with poor serological response to covid-19 vaccination in lung transplant recipients. J Heart Lung Transplant, 41:765-772.
20. Hudelist G, Manavi M, Pischinger KI, Watkins-Riedel T, Singer CF, Kubista E, Czerwenka KF. 2004. Physical state and expression of hpv DNA in benign and dysplastic cervical tissue:Different levels of viral integration are correlated with lesion grade. Gynecol Oncol, 92:873-880.
21. Jakobsen RR, Haahr T, Humaidan P, Jensen JS, Kot WP, Castro-Mejia JL, Deng L, Leser TD, Nielsen DS. 2020. Characterization of the vaginal DNA virome in health and dysbiosis. Viruses, 12:1143.
22. Kaczorowska J, van der Hoek L. 2020. Human anelloviruses:Diverse, omnipresent and commensal members of the virome. FEMS Microbiol Rev, 44:305-313.
23. Kaelin EA, Skidmore PT, Łaniewski P, Holland LA, Chase DM, Herbst-Kralovetz MM, Lim ES. 2022. Cervicovaginal DNA virome alterations are associated with genital inflammation and microbiota composition. mSystems, 7:e0006422.
24. Kandathil AJ, Cox AL, Page K, Mohr D, Razaghi R, Ghanem KG, Tuddenham SA, Hsieh YH, Evans JL, Coller KE, Timp W, Celentano DD, Ray SC, Thomas DL. 2021. Plasma virome and the risk of blood-borne infection in persons with substance use disorder. Nat Commun, 12:6909.
25. Katoh K, Rozewicki J, Yamada KD. 2019. Mafft online service:Multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform, 20:1160-1166.
26. Klaes R, Woerner SM, Ridder R, Wentzensen N, Duerst M, Schneider A, Lotz B, Melsheimer P, von Knebel Doeberitz M. 1999. Detection of high-risk cervical intraepithelial neoplasia and cervical cancer by amplification of transcripts derived from integrated papillomavirus oncogenes. Cancer Res, 59:6132-6136.
27. Kyrgiou M, Mitra A, Moscicki AB. 2017. Does the vaginal microbiota play a role in the development of cervical cancer? Transl Res, 179:168-182.
28. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with bowtie 2. Nat Methods, 9:357-359.
29. Łaniewski P, Ilhan ZE, Herbst-Kralovetz MM. 2020. The microbiome and gynaecological cancer development, prevention and therapy. Nat Rev Urol, 17:232-250.
30. Li D, Liu CM, Luo R, Sadakane K, Lam TW. 2015. Megahit:An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph. Bioinformatics, 31:1674-1676.
31. Li Y, Altan E, Reyes G, Halstead B, Deng X, Delwart E. 2021. Virome of bat guano from nine northern california roosts. J Virol, 95:e01713-01720.
32. Li Y, Altan E, Pilcher C, Hartogensis W, Hecht FM, Deng X, Delwart E. 2020a. Semen virome of men with hiv on or off antiretroviral treatment. Aids, 34:827-832.
33. Li Y, Gordon E, Idle A, Altan E, Seguin MA, Estrada M, Deng X, Delwart E. 2020b. Virome of a feline outbreak of diarrhea and vomiting includes bocaviruses and a novel chapparvovirus. Viruses, 12:506.
34. Li Y, Cao L, Ye M, Xu R, Chen X, Ma Y, Tian RR, Liu FL, Zhang P, Kuang YQ, Zheng YT, Zhang C. 2022. Plasma virome reveals blooms and transmission of anellovirus in intravenous drug users with hiv-1, hcv, and/or hbv infections. Microbiol Spectr:e0144722.
35. Li Y, Fu X, Ma J, Zhang J, Hu Y, Dong W, Wan Z, Li Q, Kuang YQ, Lan K, Jin X, Wang JH, Zhang C. 2019. Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children. Nat Commun, 10:2288.
36. Liang G, Bushman FD. 2021. The human virome:Assembly, composition and host interactions. Nat Rev Microbiol, 19:514-527.
37. Liu K, Li Y, Xu R, Zhang Y, Zheng C, Wan Z, Li H, Yang Z, Jin X, Hao P, Zhao J, Zhang C. 2021. Hiv-1 infection alters the viral composition of plasma in men who have sex with men. mSphere, 6:e00081-00021.
38. Madere FS, Monaco CL. 2022. The female reproductive tract virome:Understanding the dynamic role of viruses in gynecological health and disease. Curr Opin Virol, 52:15-23.
39. Mantovani A, Allavena P, Sica A, Balkwill F. 2008. Cancer-related inflammation. Nature, 454:436-444.
40. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. Iq-tree 2:New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol, 37:1530-1534.
41. Mitra A, MacIntyre DA, Marchesi JR, Lee YS, Bennett PR, Kyrgiou M. 2016. The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia:What do we know and where are we going next? Microbiome, 4:58.
42. Mitra A, MacIntyre DA, Lee YS, Smith A, Marchesi JR, Lehne B, Bhatia R, Lyons D, Paraskevaidis E, Li JV, Holmes E, Nicholson JK, Bennett PR, Kyrgiou M. 2015. Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity. Sci Rep, 5:16865.
43. Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW. 2015. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell, 160:447-460.
44. Organization GWH. 2008. Iarc monographs on the evaluation of carcinogenic risks to humans. Volume 97. IARC Monogr Eval Carcinog Risks Hum, 97:3-471.
45. Parks DH, Beiko RG. 2010. Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26:715-721.
46. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The silva ribosomal rna gene database project:Improved data processing and web-based tools. Nucleic Acids Res, 41:D590-596.
47. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. 2011a. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A, 108 Suppl 1:4680-4687.
48. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. 2011b. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A, 108 Suppl 1:4680-4687.
49. Redondo N, Navarro D, Aguado JM, Fernández-Ruiz M. 2022. Viruses, friends, and foes:The case of torque teno virus and the net state of immunosuppression. Transpl Infect Dis, 24:e13778.
50. Ren NJ WS, Shi CY, Yu P, Zhao L, Huang DD, Ma HX, Xiao SQ, Wang F, Yuan ZM, Xia H. 2021. Dynamic surveillance of mosquitoes and their viromes in wuhan during 2020. Zoonoses, 1:8.
51. Schiffman M, Wentzensen N, Perkins RB, Guido RS. 2020. An introduction to the 2019 asccp risk-based management consensus guidelines. J Low Genit Tract Dis, 24:87-89.
52. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. 2011. Metagenomic biomarker discovery and explanation. Genome Biol, 12:R60.
53. Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. 2018. Complex virome in feces from amerindian children in isolated amazonian villages. Nat Commun, 9:4270.
54. Siqueira JD, Curty G, Xutao D, Hofer CB, Machado ES, Seuánez HN, Soares MA, Delwart E, Soares EA. 2019. Composite analysis of the virome and bacteriome of hiv/hpv co-infected women reveals proxies for immunodeficiency. Viruses, 11:422.
55. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. 2021. Global cancer statistics 2020:Globocan estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin, 71:209-249.
56. Szládek G, Juhász A, Kardos G, Szoke K, Major T, Sziklai I, Tar I, Márton I, Kónya J, Gergely L, Szarka K. 2005. High co-prevalence of genogroup 1 tt virus and human papillomavirus is associated with poor clinical outcome of laryngeal carcinoma. J Clin Pathol, 58:402-405.
57. Taylo LJ, Keeler EL, Bushman FD, Collman RG. 2022. The enigmatic roles of anelloviridae and redondoviridae in humans. Curr Opin Virol, 55:101248.
58. Thijssen M, Tacke F, Beller L, Deboutte W, Yinda KC, Nevens F, Laleman W, Van Ranst M, Pourkarim MR. 2020. Clinical relevance of plasma virome dynamics in liver transplant recipients. EBioMedicine, 60:103009.
59. Tozetto-Mendoza TR, Mendes-Correa MC, Moron AF, Forney LJ, Linhares IM, Ribeiro da Silva A, Jr., Honorato L, Witkin SS. 2022. The vaginal torquetenovirus titer varies with vaginal microbiota composition in pregnant women. PLoS One, 17:e0262672.
60. Tozetto-Mendoza TR, Bongiovanni AM, Minis E, Linhares IM, Boester A, Freire WS, Lima SH, de Oliveira NPG, Mendes-Correa MC, Forney LJ, Witkin SS. 2020. Torquetenovirus titer in vaginal secretions from pregnant and postpartum women:Association with absence of lactobacillus crispatus and levels of lactic acid and matrix metalloproteinase-8. Reprod Sci, 27:2075-2081.
61. Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M, Burk RD. 2020. Cervicovaginal microbiome and natural history of hpv in a longitudinal study. PLoS Pathog, 16:e1008376.
62. Virgin HW. 2014. The virome in mammalian physiology and disease. Cell, 157:142-150.
63. Wylie KM, Wylie TN, Cahill AG, Macones GA, Tuuli MG, Stout MJ. 2018. The vaginal eukaryotic DNA virome and preterm birth. Am J Obstet Gynecol, 219:189.e181-189.e112.
64. Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z, Zhang C. 2021. Temporal association between human upper respiratory and gut bacterial microbiomes during the course of covid-19 in adults. Commun Biol, 4:240.
65. Zhang HT, Wang H, Wu HS, Zeng J, Yang Y. 2021. Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis. Virol J, 18:11.
66. Zhang Y, Xu X, Yu L, Shi X, Min M, Xiong L, Pan J, Zhang Y, Liu P, Wu G, Gao G. 2022. Vaginal microbiota changes caused by hpv infection in chinese women. Front Cell Infect Microbiol, 12:814668.
67. Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D. 2017. Virusseeker, a computational pipeline for virus discovery and virome composition analysis. Virology, 503:21-30.
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