Mechanistic Signatures of Human Papillomavirus Insertions in Anal Squamous Cell Carcinomas
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patients
2.2. Methods
2.2.1. DNA Extraction
2.2.2. HPV Genotyping
2.2.3. DNA Library Preparation
2.2.4. HPV Double Capture Method
2.2.5. HPV Viral Load
2.2.6. Bioinformatics Pipeline for Analysis of HPV Genotypes and Viral–Cellular Junctions
2.3. Statistical Analysis
3. Results
3.1. Patient Characteristics
3.2. HPV Genotype and Mutational Analysis
3.3. HPV Viral Load
3.4. Integration Mechanisms
3.5. Dynamic Evolution of Integration Status in Patients with Matched Samples
3.6. Insertion Sites
3.7. Association between Insertion Mechanisms and Patient Clinicopathological Data
3.8. Response to Treatment and Overall Survival
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Data Access
Abbreviations
2J | Two hybrid junctions |
2J-COL | Two hybrid co-linear junctions |
2J-NL | Two hybrid non-linear junctions |
5FU-CDDP | 5-Fluorouracil-Cisplatin |
5FU-MMC | 5-Fluorouracil-Mitomycin C |
AJCC | American Joint Committee on Cancer |
ASCC | Anal squamous cell carcinoma |
CR | Complete response |
CRT | Chemo-radiotherapy |
EPI | Episomal |
HIV | Human immunodeficiency virus |
HNSCC | Head and neck squamous cell carcinoma |
HPV | Human papillomavirus |
MJ | Multiple hybrid junction |
MJ-CL | Multiple hybrid junctions clustered in one locus |
MJ-SC | Multiple hybrid junctions scattered at distinct loci |
NGS | Next-Generation Sequencing |
NS | Not significant |
OS | Overall survival |
RT | Radiation therapy |
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Heading | Patients (%) | Univariable Analysis | Multivariable Analysis | |||
---|---|---|---|---|---|---|
Patients (%) | Events (%) a | OS (p-Value) a, b | HR f | 95% CI h | p-Value i | |
Total | 93 (100) | 37 (40.9) | ||||
Age (years) <65 ≥65 | 60 (64.5) 33 (35.5) | 24 (40.0) 13 (39.4) | 0.32 (NS) | |||
Gender Male Female | 18 (19.4) 75 (80.6) | 6 (33.3) 31 (41.3) | 0.83 (NS) | |||
Tumor differentiation Well/Moderate Poor | 83 (89.2) 10 (10.8) | 31 (37.3) 6 (60.0) | 0.014 | 0.40 1 | 0.14–1.16 | 0.092 (NS) |
Basaloid contingent Present Absent | 9 (9.7) 84 (90.3) | 2 (22.2) 35 (41.7) | 0.23 (NS) | |||
HPV status Genotype 16 Other genotypes | 85 (91.4) 8 (8.6) | 33 (38.8) 4 (50.0) | 0.005 | 1 6.78 | 1.66–27.8 | 0.008 |
Concomitant HIV infection c Yes No | 8 (8.8) 83 (91.2) | 5 (62.5) 31 (37.3) | 0.099 (NS) | 1.87 1 | 0.57–6.16 | 0.31 (NS) |
Tumor stage (AJCC 2010) a I II IIIA IIIB IV | 8 (8.9) 37 (41.1) 21 (23.3) 20 (22.2) 4 (4.4) | 3 (37.5) 16 (43.2) 4 (19.0) 9 (45.0) 2 (50.0) | 0.088 (NS) | 1 2.49 2.82 8.04 9.07 | 0.49–12.7 0.18–43.5 0.44–146 0.55–148 | 0.048 |
Lymph node invasion c Yes No | 40 (44.0) 51 (56.0) | 15 (37.5) 20 (39.2) | 0.094 (NS) | 0.51 1 | 0.15–1.80 | 0.30 (NS) |
Synchronous metastasis d Yes No | 4 (4.3) 88 (95.7) | 2 (50.0) 34 (38.6) | 0.44 (NS) | |||
Sample status Treatment-naive tumor Tumor recurrence | 54 (58.1) 39 (41.9) | 16 (29.6) 21 (53.8) | 0.45 (NS) | |||
Complete response after RT/CRT e Yes No | 72 (86.7) 11 (13.3) | 25 (34.7) 7 (63.6) | <0.0001 | 0.16 1 | 0.00–0.46 | 0.001 |
PIK3CA mutational status Wild-type Mutated | 71 (76.3) 22 (23.7) | 27 (38.0) 10 (45.5) | 0.57 (NS) |
Patients (%) | Number of Patients (%) | p-Value a | |||
---|---|---|---|---|---|
Heading | EPI | 2J | MJ | ||
Total | 93 (100) | 42 (45.2) | 15 (16.1) | 36 (38.7) | |
Age (years) <65 ≥65 | 60 (64.5) 33 (35.5) | 28 (66.7) 14 (33.3) | 10 (66.7) 5 (33.3) | 22 (61.1) 14 (38.9) | 0.86 (NS) |
Gender Male Female | 18 (19.4) 75 (80.6) | 7 (16.7) 35 (83.3) | 3 (20.0) 12 (80.0) | 8 (22.2) 28 (77.8) | 0.83 (NS) |
Tumor differentiation Well/Moderate Poor | 83 (89.2) 10 (10.8) | 37 (88.1) 5 (11.9) | 14 (93.3) 1 (6.7) | 32 (88.9) 4 (11.1) | 0.85 (NS) |
Basaloid contingent Present Absent | 9 (9.7) 84 (90.3) | 6 (14.3) 36 (85.7) | 0 (0.0) 15 (100.0) | 3 (8.3) 33 (91.7) | 0.26 (NS) |
HPV status Genotype 16 Other genotypes | 85 (91.4) 8 (8.6) | 36 (85.7) 6 (14.3) | 14 (93.3) 1 (6.7) | 35 (97.2) 1 (2.8) | 0.44 (NS) |
Concomitant HIV infection b Yes No | 8 (8.8) 83 (91.2) | 3 (7.3) 38 (92.7) | 2 (13.3) 13 (86.7) | 3 (8.6) 32 (91.4) | 0.92 (NS) |
Tumor stage (AJCC 2010) c I II IIIA IIIB IV | 8 (8.9) 37 (41.1) 21 (23.3) 20 (22.2) 4 (4.4) | 5 (11.9) 18 (42.9) 9 (21.4) 8 (19.0) 2 (4.8) | 1 (6.7) 6 (40.0) 3 (20.0) 4 (26.7) 1 (6.7) | 2 (5.6) 13 (36.1) 9 (25.0) 8 (22.2) 1 (2.8) | 0.98 (NS) |
Lymph node invasion b Yes No | 40 (44.0) 51 (56.0) | 14 (33.3) 28 (66.7) | 8 (53.3) 7 (46.7) | 18 (52.9) 16 (47.1) | 0.17 (NS) |
Synchronous metastasis d Yes No | 4 (4.3) 88 (95.7) | 2 (4.8) 40 (95.2) | 1 (6.7) 14 (93.3) | 1 (2.9) 34 (97.1) | 0.82 (NS) |
Sample status Treatment-naive tumor Tumor recurrence | 54 (58.1) 39 (41.9) | 25 (59.5) 17 (40.5) | 9 (60.0) 6 (40.0) | 20 (55.6) 16 (44.4) | 0.93 (NS) |
Initial therapy Upfront surgery d No Yes RT or CRT b RT CRT With concomitant 5FU-MMC With concomitant 5FU-CDDP With other concomitant CT No RT/CRT | 77 (83.7) 15 (16.3) 22 (24.2) 61 (67.0) 11 (18.0) 44 (77.0) 3 (4.9) 8 (8.8) | 36 (85.7) 6 (14.3) 10 (24.4) 27 (65.9) 5 (18.5) 21 (77.8) 1 (3.7) 4 (9.8) | 12 (80.0) 3 (20.0) 2 (13.3) 11 (73.3) 1 (9.1) 10 (90.9) 0 (0.0) 2 (13.3) | 29 (82.9) 6 (17.1) 10 (27.8) 23 (63.9) 5 (21.7) 16 (69.6) 2 (8.7) 2 (5.6) | 0.86 (NS) 0.76 (NS) |
Complete Response after RT/CRT e Yes No | 72 (86.7) 11 (13.3) | 34 (91.9) 3 (7.1) | 10 (76.9) 3 (23.1) | 28 (84.8) 5 (15.2) | 0.36 (NS) |
PIK3CA mutational status Wild-type Mutated | 71 (76.3) 22 (23.7) | 38 (90.5) 4 (9.5) | 8 (53.3) 7 (46.7) | 25 (69.4) 11 (30.6) | 0.0069 |
HPV viral load Low (<12) High (≥12) | 41 (44.1) 52 (55.9) | 21 (50.0) 21 (50.0) | 10 (66.7) 5 (33.3) | 10 (27.8) 26 (72.2) | 0.022 |
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Morel, A.; Neuzillet, C.; Wack, M.; Lameiras, S.; Vacher, S.; Deloger, M.; Servant, N.; Veyer, D.; Péré, H.; Mariani, O.; et al. Mechanistic Signatures of Human Papillomavirus Insertions in Anal Squamous Cell Carcinomas. Cancers 2019, 11, 1846. https://doi.org/10.3390/cancers11121846
Morel A, Neuzillet C, Wack M, Lameiras S, Vacher S, Deloger M, Servant N, Veyer D, Péré H, Mariani O, et al. Mechanistic Signatures of Human Papillomavirus Insertions in Anal Squamous Cell Carcinomas. Cancers. 2019; 11(12):1846. https://doi.org/10.3390/cancers11121846
Chicago/Turabian StyleMorel, Adeline, Cindy Neuzillet, Maxime Wack, Sonia Lameiras, Sophie Vacher, Marc Deloger, Nicolas Servant, David Veyer, Hélène Péré, Odette Mariani, and et al. 2019. "Mechanistic Signatures of Human Papillomavirus Insertions in Anal Squamous Cell Carcinomas" Cancers 11, no. 12: 1846. https://doi.org/10.3390/cancers11121846
APA StyleMorel, A., Neuzillet, C., Wack, M., Lameiras, S., Vacher, S., Deloger, M., Servant, N., Veyer, D., Péré, H., Mariani, O., Baulande, S., Rouzier, R., Kamal, M., El Alam, E., Jeannot, E., Nicolas, A., Bièche, I., & Cacheux, W. (2019). Mechanistic Signatures of Human Papillomavirus Insertions in Anal Squamous Cell Carcinomas. Cancers, 11(12), 1846. https://doi.org/10.3390/cancers11121846