TABLE 2.
| Experiment | Groups included | Variable | Variable levels | R2 | P-value | P-value significance |
q-value | q-value significance |
Notes |
|---|---|---|---|---|---|---|---|---|---|
| Experiment 1 | All (infected mice) | Pre- v. Post-Infection | Pre-Infection v. Post-Infection | 0.04829 | 1.30E-02 | * | 0.0303 | * | |
| Experiment 1 | All (infected mice) | Infection Stage (pre-infect v. post-depo v. infection establishment v. early infection v. mid infection) | Pre-Infection, Post-Depoprovera, Infection Establishment, Early Infection, Mid Infection |
0.3 | 1.00E-04 | *** | 0.0004 | *** | |
| Experiment 1 | All (infected mice) | Viral copy number | Low v. High | 0.0573 | 0.0590 | ° | 0.1033 | ns | |
| Experiment 1 | All (infected mice) | Viral Persistence | Persistence | -- | -- | -- | -- | -- | All infected mice had viral persistence |
| Experiment 1 | All (infected mice) | Cervicovaginal Dysplasia Stage | CIN 2, CIN 3, SCC | 0.0777 | 0.2330 | ns | 0.3262 | ns | |
| Experiment 1 | All mice (post infection timepoints only) | Infection Stage (infection establishment v. early infection v. mid infection) | Pre-Infection, Post-Depoprovera, Infection Establishment, Early Infection, Mid Infection | 0.3169 | 1.00E-04 | *** | 0.0004 | *** | |
| Experiment 1 | All mice (post infection timepoints only) | Viral copy number (H vs. L) | Low v. High | 0.0151 | 0.6657 | ns | 0.7767 | ns | |
| Experiment 1 | All mice (post infection timepoints only) | Viral Persistence | Persistence | -- | -- | -- | -- | -- | All infected mice had viral persistence |
| Experiment 1 | All mice (post infection timepoints only) | Cervicovaginal Dysplasia Stage | CIN 2, CIN 3, SCC | 0.0493 | 0.7972 | ns | 0.7972 | ns | |
| Experiment 2 | All mice | Intervention Group | Untreated, Mock Infected, mMUPV1 Infected. | 0.0316 | 0.0293 | * | 0.0553 | ° | |
| Experiment 2 | All mice | Pre- vs. Post-Infection | Pre-Infection v. Post-Infection | 0.04178 | 1.00E-04 | *** | 0.0006 | *** | |
| Experiment 2 | All mice | Pre-Infection vs. Post-infection Untouched, Mock, and Infected | Pre-Infection, Post-Depoprovera, Untouched, Mock, Infected (at post-infection timepoints) | 0.10989 | 1.00E-04 | *** | 0.0006 | *** | |
| Experiment 2 | All mice | Infection Stage | Pre-Infection, Post-Depoprovera, Infection Establishment, Early Infection, Mid Infection | 0.04178 | 1.00E-04 | *** | 0.0006 | *** | |
| Experiment 2 | All mice | Viral copy number | Low v. High | 0.01861 | 0.1981 | ns | 0.2806 | ns | |
| Experiment 2 | All mice | Viral Persistence | Persistence | -- | -- | -- | -- | -- | All infected mice had viral persistence |
| Experiment 2 | All mice | Cervicovaginal Dysplasia Stage | CIN 2, CIN 3 | -- | -- | -- | -- | -- | Only histology from Infected mice was scored. No histology from Untouched or Mock infected mice. |
| Experiment 2 | All mice (post infection timepoints only) | Intervention Group | Untreated, Mock Infected, mMUPV1 Infected. | 0.0599 | 0.0018 | ** | 0.0061 | ** | |
| Experiment 2 | Untreated Mice | Pre- vs. Post-Infection | Pre-Infection v. Post-Infection | 0.0253 | 0.5674 | ns | 0.6029 | ns | |
| Experiment 2 | Untreated Mice | Infection Stage | Pre-Infection, Post-Depoprovera, Infection Establishment, Early Infection, Mid Infection | 0.1288 | 0.5421 | ns | 0.6029 | ns | |
| Experiment 2 | Mock infection mice | Pre- vs. Post-Infection | Pre-Infection v. Post-Infection | 0.0887 | 0.0013 | ** | 0.0055 | ** | |
| Experiment 2 | Mock infection mice | Infection Stage | Pre-Infection, Post-Depoprovera, Infection Establishment, Early Infection, Mid Infection | 0.1751 | 0.0054 | ** | 0.0131 | * | |
| Experiment 2 | Infected Mice | Pre- vs. Post-Infection | Pre-Infection v. Post-Infection | 0.0606 | 0.0031 | ** | 0.0089 | ** | |
| Experiment 2 | Infected Mice | Infection Stage | Pre-Infection, Post-Depoprovera, Infection Establishment, Early Infection, Mid Infection | 0.1483 | 0.0099 | ** | 0.021 | * | |
| Experiment 2 | Infected Mice | Viral copy number | Low v. High | 0.0609 | 0.1925 | ns | 0.2806 | ns | |
| Experiment 2 | Infected Mice | Viral Persistence | Persistence | -- | -- | -- | -- | -- | All infected mice had viral persistence |
| Experiment 2 | Infected Mice | Cervicovaginal Dysplasia Stage | CIN 2, CIN 3 | 0.0945 | 0.683 | ns | 0.683 | ns | |
| Experiment 2 | Infected Mice (post infection Only) | Infection Stage | Infection Establishment, Early Infection, Mid Infection |
0.09341 | 0.3099 | ns | 0.3763 | ns | |
| Experiment 2 | Infected Mice (post infection Only) | Viral copy number | Low v. High | 0.0726 | 0.3099 | ns | 0.3763 | ns | |
| Experiment 2 | Infected Mice (post infection Only) | Viral Persistence | Persistence | -- | -- | -- | -- | -- | All infected mice had viral persistence |
| Experiment 2 | Infected Mice (post infection Only) | Cervicovaginal Dysplasia Stage | CIN 2, CIN 3 | 0.1718 | 0.133 | ns | 0.226 | ns | |
| Experiment 3 (late Infection) |
All | Mock v. Infection | Mock v. MmuPV1 infection | 0.0155 | 0.3943 | ns | 0.4929 | ns | |
| Experiment 3 (late Infection) |
All | Infection Stage | Early Infection, Mid infection, Late Infection | 0.058 | 0.0054 | ** | 0.043 | * | |
| Experiment 3 (late Infection) |
All | Viral copy number | Low v. High | 0.0494 | 0.3046 | ns | 0.4929 | ns | |
| Experiment 3 (late Infection) |
All | Viral Persistence | Persistence v. Clearance | 0.0441 | 0.567 | ns | 0.63 | ns | |
| Experiment 3 (late Infection) |
All | Cervicovaginal Dysplasia Stage | Normal to hyperplasia, CIN 3, CIN 3+ | 0.0382 | 0.141 | ns | 0.3525 | ns | |
| Experiment 3 (late Infection) |
Infected Mice | Infection Stage | Early Infection, Mid infection, Late Infection | 0.0651 | 0.0086 | ** | 0.043 | * | |
| Experiment 3 (late Infection) |
Infected Mice | Viral copy number | Low v. High | 0.0398 | 0.317 | ns | 0.4929 | ns | |
| Experiment 3 (late Infection) |
Infected Mice | Viral Persistence | Persistence v. Clearance | 0.0346 | 0.6952 | ns | 0.6952 | ns | |
| Experiment 3 (late Infection) |
Infected Mice | Cervicovaginal Dysplasia Stage | CIN 3, CIN 3+ | 0.0385 | 0.3735 | ns | 0.4929 | ns | |
| Experiment 3 (late Infection) |
Mock infection mice | Infection Stage | Early Infection, Mid infection, Late Infection | 0.0651 | 0.0666 | ° | 0.222 | ns | |
| Experiment 4 (Viral Dose) |
All | Viral Inoculation Dose | Mock, 10^4, 10^6, 10^8 | 0.165 | 0.0034 | ** | 0.0059 | ** | |
| Experiment 4 (Viral Dose) |
All | Viral copy number | Low v. High | 0.1148 | 0.0044 | ** | 0.0059 | ** | |
| Experiment 4 (Viral Dose) |
All | Viral Persistence | Persistence v. Clearance | 0.1432 | 9.00E-04 | *** | 0.0024 | ** | |
| Experiment 4 (Viral Dose) |
All | Cervicovaginal Dysplasia Stage | Normal, CIN1, CIN2, CIN 3, SCC | 0.13389 | 0.37 | ns | 0.37 | ns | |
| Experiment 4 (Viral Dose) |
Infected Mice | Viral Inoculation Dose | Mock, 10^4, 10^6, 10^8 | 0.1253 | 0.0041 | ** | 0.0059 | ** | |
| Experiment 4 (Viral Dose) |
Infected Mice | Viral copy number | Low v. High | 0.11326 | 1.00E-04 | *** | 0.0008 | *** | |
| Experiment 4 (Viral Dose) |
Infected Mice | Viral Persistence | Persistence v. Clearance | 0.1014 | 4.00E-04 | *** | 0.0016 | ** | |
| Experiment 4 (Viral Dose) |
Infected Mice | Cervicovaginal Dysplasia Stage | Normal, CIN1, CIN2, CIN 3, SCC | 0.1854 | 0.0276 | * | 0.0315 | * | |
| Experiment 5 (LCM) |
All | Group | Mock, Mock + estrogen, Infected, Infected + estrogen |
0.901 | 0.0624 | ° | 0.3266 | ns | |
| Experiment 5 (LCM) |
All | Mock v. Infection | Mock v. MmuPV1 infection | 0.0315 | 0.0994 | ° | 0.3266 | ns | |
| Experiment 5 (LCM) |
All | Estrogen Supplementation | Estrogen v. No Estrogen | 0.0339 | 0.0657 | ° | 0.3266 | ns | |
| Experiment 5 (LCM) |
All | Estrus stage | proestrus, estrus, metestrus, diestrus | 0.1189 | 0.9889 | ns | 0.9911 | ns | |
| Experiment 5 (LCM) |
All | Sampling Location | Ectocervix, Cervicovaginal wall, Vaginal wall | 0.0721 | 0.9844 | ns | 0.9911 | ns | |
| Experiment 5 (LCM) |
All | Cervicovaginal Dysplasia Stage | Normal to hyperplasia, CIN 2, CIN 3, SCC | 0.1054 | 0.2318 | ns | 0.6544 | ns | |
| Experiment 5 (LCM) |
All Mock infected mice | Estrogen Supplementation | Estrogen v. No Estrogen | 0.0473 | 0.6681 | ns | 0.9207 | ns | |
| Experiment 5 (LCM) |
All Mock infected mice | Estrus stage | proestrus, estrus, metestrus, diestrus | 0.2175 | 0.3416 | ns | 0.7163 | ns | |
| Experiment 5 (LCM) |
All Mock infected mice | Sampling Location | Ectocervix, Cervicovaginal wall, Vaginal wall | 0.0553 | 0.3426 | ns | 0.7163 | ns | |
| Experiment 5 (LCM) |
All Infected Mice | Estrogen | Estrogen v. No Estrogen | 0.0702 | 0.0527 | ° | 0.3266 | ns | |
| Experiment 5 (LCM) |
All Infected Mice | Estrus stage | proestrus, estrus, metestrus, diestrus | 0.1743 | 0.897 | ns | 0.9911 | ns | |
| Experiment 5 (LCM) |
All Infected Mice | Sampling Location | Ectocervix, Cervicovaginal wall, Vaginal wall | 0.1449 | 0.4191 | ns | 0.7415 | ns | |
| Experiment 5 (LCM) |
All Infected Mice | Viral copy number | Low v. High | 0.067 | 0.0788 | ° | 0.3266 | ns | |
| Experiment 5 (LCM) |
All Infected Mice | Viral Persistence | Persistence | -- | -- | -- | -- | -- | All infected mice had viral persistence |
| Experiment 5 (LCM) |
All Infected Mice | Cervicovaginal Dysplasia Stage | Normal to hyperplasia, CIN 2, CIN 3, SCC | 0.097 | 0.4064 | ns | 0.7415 | ns | |
| Experiment 5 (LCM) |
No Estrogen Mice | Mock v. Infection | Mock v. MmuPV1 infection | 0.07 | 0.5519 | ns | 0.8772 | ns | |
| Experiment 5 (LCM) |
No Estrogen Mice | Estrus stage | proestrus, estrus, metestrus, diestrus | 0.2264 | 0.9911 | ns | 0.9911 | ns | |
| Experiment 5 (LCM) |
No Estrogen Mice | Sampling Location | Ectocervix, Cervicovaginal wall, Vaginal wall | 0.103 | 0.6805 | ns | 0.9207 | ns | |
| Experiment 5 (LCM) |
No Estrogen + Infected | Viral copy number | Low v. High | 0.1198 | 0.8571 | ns | 0.9911 | ns | note: two had low viral load |
| Experiment 5 (LCM) |
No Estrogen + Infected | Cervicovaginal Dysplasia Stage | CIN 3, CIN 3 | 0.2305 | 0.0952 | ° | 0.3266 | ns | |
| Experiment 5 (LCM) |
Estrogen Mice | Mock v. Infection | Mock v. MmuPV1 infection | 0.0534 | 0.0444 | * | 0.3266 | ns | |
| Experiment 5 (LCM) |
Estrogen Mice | Estrus stage | proestrus, estrus, metestrus, diestrus | 0.1214 | 0.9623 | ns | 0.9911 | ns | |
| Experiment 5 (LCM) |
Estrogen Mice | Sampling Location | Ectocervix, Cervicovaginal wall, Vaginal wall | 0.2215 | 0.5721 | ns | 0.8772 | ns | |
| Experiment 5 (LCM) |
Estrogen + Infection | Viral copy number | Low v. High | -- | -- | -- | -- | -- | Only one had Low viral load so unable to assess |
| Experiment 5 (LCM) |
Estrogen + Infection | Cervicovaginal Dysplasia Stage | CIN 2, CIN 3, SCC | 0.1594 | 0.2561 | ns | 0.6545 | ns |
a
The Bray-Curtis metric was utilized to assess beta-diversity between cervicovaginal microbiome samples for each of the experiments included in this study. Univariate permutation ANOVAS with 9999 permutations were then used to assess whether sample microbial community beta diversity significantly clustered by intervention group (i.e., mock-infected vs MmuPV1-infected) or infection outcomes (i.e., high vs low viral load, cervical dysplasia severity, etc.). The table summarizes the permutation ANOVA results for each analysis within each experiment.
b
To account for multiple comparisons, significance values were corrected with the Benjamini-Hochberg (B-H) Procedure. LCM: Laser capture microdissection.ns: not significant.-- indicates unable to assess. See “Notes” column for details.° indicates the p-value or the B-H adjusted q-value < 0.1, * indicates the p-value or the B-H adjusted q-value < 0.05, ** indicates the p-value or the B-H adjusted q-value < 0.01, *** indicates the p-value or the B-H adjusted q-value < 0.001.