Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition

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Reviewed Marked as Reviewed by Fatima on 2022/03/12
Quality issues
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Liu J, Luo M, Zhang Y, Cao G, Wang S
Journal
Annals of translational medicine
Year
2020
Keywords:
Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota
Background: Cervical cancer is reportedly caused by the synergistic effects of persistent high-risk human papillomavirus (HPV) infection. Cervical microbiota represent a unique and dynamically changing microecological system that is directly exposed to the vagina. The relationship between HPV and the composition of the cervical microbiome has long been a primary focus of research. Methods: To determine the specific differential florae throughout the process of cervical cancer development, in the present study, 16S rRNA sequencing was combined with KEGG pathway enrichment analysis to analyse five groups of cervical scraping samples with increasing durations of HPV infection and cervical intraepithelial neoplasia pathological classification. Results: The findings revealed that decreasing levels of probiotics, including Shuttleworthia, Prevotella, Lactobacillus, and Sneathia, and increasing levels of pathogenic bacteria, including Dispar, Streptococcus, and Faecalibacterium prausnitzii, could be the direct result of early HPV infection. Other pathogenic bacteria, such as Bifidobacteriaceae, might represent key factors in cancer progression. Additionally, KEGG pathway enrichment analysis indicated that HPV infection directly inhibits multiple pathways, including those of sporulation, porphyrin and chlorophyll metabolism, arginine and proline metabolism, isoquinoline alkaloid biosynthesis, and ansamycin biosynthesis, which may lead to the development of early symptoms of cervical cancer. Biomarkers were predicted based on operational taxonomic unit (OTU) abundance data, and OTU851726 and OTU715913 were undoubtedly the best potential indicators of cervical cancer. Conclusions: The findings of the present study could assist with the development of a guideline for screening new clinical drugs for cervical cancer.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/18

Curator: Cynthia Anderson

Revision editor(s): Fatima, Cynthia Anderson, WikiWorks, Peace Sandy

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
Group 0 name Corresponds to the control (unexposed) group for case-control studies
persistent HPV+ with LSIL
Group 1 name Corresponds to the case (exposed) group for case-control studies
persistent HPV+ with HSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
ANOVA
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes


Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/18

Curator: Cynthia Anderson

Revision editor(s): Fatima, Cynthia Anderson

Source: Figure 3A

Description: Differential florae types in the comparison of the microbiota between high-risk human papillomavirus (HPV) persistent infection higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group

Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL

NCBI Quality ControlLinks
Achromobacter
Comamonas
Commensalibacter
Gallicola
Halomonas
Lactococcus
Leuconostoc
Lysobacter
Massilia
Methylobacterium
Nocardioides
Paracoccus
Phascolarctobacterium
Pseudoduganella
Pseudomonas
Solirubrobacter
Stappia
Syntrophococcus
Thermus

Revision editor(s): Fatima, Cynthia Anderson

Experiment 2


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/18

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
transient HPV+ with LSIL
Group 1 name Corresponds to the case (exposed) group for case-control studies
transient HPV+ with HSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-risk HPV transient infection (HPV has regressed within 1 year) with high grade squamus intraepithelial lesion

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
Not specified


Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 3B

Description: comparison of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group

Abundance in Group 1: decreased abundance in transient HPV+ with HSIL

NCBI Quality ControlLinks
Xanthomonadaceae
[Clostridium] innocuum

Revision editor(s): Cynthia Anderson

Experiment 3


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV-
Group 1 name Corresponds to the case (exposed) group for case-control studies
transient HPV+ with LSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-risk HPV transient infection (HPV has regressed within 1 year) with low grade squamus intraepithelial lesion
Group 0 sample size Number of subjects in the control (unexposed) group
31

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 3C

Description: Comparison of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group

Abundance in Group 1: decreased abundance in transient HPV+ with LSIL

NCBI Quality ControlLinks
Sneathia
Shuttleworthia
Veillonella
[Clostridium] innocuum
Megasphaera
Devosia
Xanthomonadaceae
Gardnerella

Revision editor(s): Cynthia Anderson

Experiment 4


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
persistent HPV+ with HSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-risk HPV persistent infection with high grade squamus intraepithelial lesion

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Fatima, Cynthia Anderson

Source: Figure 3D

Description: Comparison of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group

Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL

NCBI Quality ControlLinks
Megasphaera
Peptostreptococcus
Shuttleworthia
Sneathia

Revision editor(s): Fatima, Cynthia Anderson

Experiment 5


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
persistent HPV+ with LSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified

Lab analysis

Statistical Analysis

Statistical test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
Not specified
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Not specified


Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4A

Description: Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group

Abundance in Group 1: increased abundance in persistent HPV+ with HSIL

NCBI Quality ControlLinks
Streptococcus agalactiae

Revision editor(s): Cynthia Anderson

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4A

Description: Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group

Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL

NCBI Quality ControlLinks
Faecalibacterium
Planococcaceae
Corynebacterium tuberculostearicum
Lawsonella
Erysipelotrichales
Micrococcaceae
Pseudarthrobacter oxydans
Corynebacterium aurimucosum
Peptoniphilus
Actinomycetaceae
Anaerococcus
[Ruminococcus] torques
Prevotella disiens
Nocardiaceae
Dialister
Deinococcota
Actinomycetales
Prevotella
Gardnerella
Deinococci
Leuconostoc
Nitrosomonadaceae
Xanthomonadales
Howardella
Finegoldia
Peptoniphilus coxii
Bifidobacterium dentium
Staphylococcus
Staphylococcus aureus
Staphylococcaceae
Bacillales
Enterococcus durans
Enterococcus
Enterococcaceae
Ligilactobacillus salivarius
Dialister micraerophilus
Selenomonadales
Negativicutes
Bifidobacteriaceae
Bifidobacteriales
Streptococcaceae

Revision editor(s): Cynthia Anderson

Experiment 6


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
transient HPV+ with HSIL
Group 1 name Corresponds to the case (exposed) group for case-control studies
persistent HPV+ with LSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-risk HPV persistent infection with low grade squamus intraepithelial lesion

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4B

Description: Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group

Abundance in Group 1: increased abundance in persistent HPV+ with LSIL

NCBI Quality ControlLinks
[Ruminococcus] torques

Revision editor(s): Cynthia Anderson

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4B

Description: Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group

Abundance in Group 1: decreased abundance in persistent HPV+ with LSIL

NCBI Quality ControlLinks
Porphyromonas
Trichinella pseudospiralis
Quinella
Tyzzerella
Flavobacterium gelidilacus
Parabacteroides faecis
Dechloromonas

Revision editor(s): Cynthia Anderson

Experiment 7


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
transient HPV+ with LSIL
Group 1 name Corresponds to the case (exposed) group for case-control studies
transient HPV+ with HSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-risk HPV transient infection with high grade squamus intraepithelial lesion

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4C

Description: Abundance analysis of the microbiota between high-risk HPV transient infection with HSIL group and high-risk HPV transient infection with LSIL group

Abundance in Group 1: increased abundance in transient HPV+ with HSIL

NCBI Quality ControlLinks
Flavobacteriia
Flavobacteriales
Cloacibacterium
Lactobacillus
Dyella koreensis
Flavobacterium gelidilacus
Dyella
Parabacteroides faecis

Revision editor(s): Cynthia Anderson

Experiment 8


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV-
Group 1 name Corresponds to the case (exposed) group for case-control studies
transient HPV+ with LSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-risk HPV transient infection with low grade squamus intraepithelial lesion

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4D

Description: Abundance analysis of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group

Abundance in Group 1: decreased abundance in transient HPV+ with LSIL

NCBI Quality ControlLinks
Devosia riboflavina
Candidatus Saccharibacteria
Sneathia
Lactobacillus
Pseudomonas
Shuttleworthia
Leptotrichiaceae
Oscillospiraceae
Pseudomonadaceae

Revision editor(s): Cynthia Anderson

Experiment 9


Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
persistent HPV+ with HSIL
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-risk HPV persistent infection with low grade squamus intraepithelial lesion

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4E

Description: Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group

Abundance in Group 1: increased abundance in persistent HPV+ with HSIL

NCBI Quality ControlLinks
Solirubrobacterales
Morganella

Revision editor(s): Cynthia Anderson

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/03/19

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 4E

Description: Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group

Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL

NCBI Quality ControlLinks
Prevotella melaninogenica
Dialister
Lactobacillus equicursoris
Prevotella
Sutterella
Peptostreptococcus
Pseudomonas
Peptoniphilus lacrimalis
Prevotella disiens
Oscillospiraceae

Revision editor(s): Cynthia Anderson