{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T15:46:36Z","timestamp":1782920796976,"version":"3.54.5"},"reference-count":30,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,1,19]],"date-time":"2025-01-19T00:00:00Z","timestamp":1737244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"MD Anderson Cancer Center HPV-related Cancers Moon Shot"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>Background: To extend the practicality of liquid biopsy beyond the historical HPV circulating tumor DNA (ctDNA) assays, we evaluated the clinical relevance of a novel next-generation sequencing HPV ctDNA assay in patients with locally advanced and metastatic squamous cell cancer of the anal canal (mSCCA). Methods: ctDNA isolated from the plasma of patients with mSCCA was sequenced using a 1.4 Mb hybrid-capture target-enrichment panel covering the whole genome sequences of all 193 HPV types. The HPV type, copy number (CN), and integration sites were determined using a bioinformatic pipeline. Results: A total of 77 plasma samples from 28 patients with HPV-related SCCA were retrospectively analyzed. HPV ctDNA was detected in 26 cases (93%) (including uncommon subtypes). The median HPV CN was higher in metastatic versus locally recurrent\/unresectable SCCA (p = 0.043). Changes in the HPV CN were concordant with the radiographic response (p = 0.027). An integration event was detected in 23 patients (82%), with presumed episomal HPV DNA present in the remaining patients. Higher HPV integration (a mean of \u22651 integration across samples) was associated with a worse overall survival from the start of immunotherapy (13.6 months versus 36.0 months; p = 0.003). Conclusions: Using HPV-informed next-generation sequencing of the ctDNA, we found changes in the HPV CN correlated with the treatment response and that HPV integration detected in the ctDNA is an unfavorable prognostic biomarker.<\/jats:p>","DOI":"10.3390\/cancers17020308","type":"journal-article","created":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T09:11:13Z","timestamp":1737364273000},"page":"308","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["The Clinical Utility of a Next-Generation Sequencing-Based Approach to Detecting Circulating HPV DNA in Patients with Advanced Anal Cancer"],"prefix":"10.3390","volume":"17","author":[{"given":"Deepak","family":"Bhamidipati","sequence":"first","affiliation":[{"name":"Department of Cancer Medicine Fellowship Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"},{"name":"Sarah Cannon Research Institute, Nashville, TN 37203, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay R.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0140-2557","authenticated-orcid":false,"given":"Kangyu","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helene","family":"Pelicano","sequence":"additional","affiliation":[{"name":"Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cathy","family":"Eng","sequence":"additional","affiliation":[{"name":"Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA"},{"name":"Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"Huey","sequence":"additional","affiliation":[{"name":"Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert A.","family":"Wolff","sequence":"additional","affiliation":[{"name":"Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel M.","family":"Halperin","sequence":"additional","affiliation":[{"name":"Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael F.","family":"Frumovitz","sequence":"additional","affiliation":[{"name":"Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacio I.","family":"Wistuba","sequence":"additional","affiliation":[{"name":"Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dzifa Y.","family":"Duose","sequence":"additional","affiliation":[{"name":"Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1230-9942","authenticated-orcid":false,"given":"Saradhi","family":"Mallampati","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajyalakshmi","family":"Luthra","sequence":"additional","affiliation":[{"name":"Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4911-2252","authenticated-orcid":false,"given":"Van K.","family":"Morris","sequence":"additional","affiliation":[{"name":"Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1016\/S1473-3099(17)30653-9","article-title":"Human Papillomavirus Types from Infection to Cancer in the Anus, According to Sex and HIV Status: A Systematic Review and Meta-Analysis","volume":"18","author":"Lin","year":"2018","journal-title":"Lancet Infect Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1093\/jnci\/djz219","article-title":"Recent Trends in Squamous Cell Carcinoma of the Anus Incidence and Mortality in the United States, 2001\u20132015","volume":"112","author":"Deshmukh","year":"2020","journal-title":"J. Natl. Cancer Inst."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1086\/514194","article-title":"Prevalence and Risk Factors for Human Papillomavirus Infection of the Anal Canal in Human Immunodeficiency Virus (HIV)-Positive and HIV-Negative Homosexual Men","volume":"177","author":"Palefsky","year":"1998","journal-title":"J. Infect Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.1200\/JCO.21.02566","article-title":"Anal Cancer: Emerging Standards in a Rare Disease","volume":"40","author":"Eng","year":"2022","journal-title":"JCO"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"16086","DOI":"10.1038\/nrdp.2016.86","article-title":"Carcinogenic Human Papillomavirus Infection","volume":"2","author":"Schiffman","year":"2016","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1158\/2159-8290.CD-22-0900","article-title":"Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration","volume":"13","author":"Akagi","year":"2023","journal-title":"Cancer Discov."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"McBride, A.A., and Warburton, A. (2017). The Role of Integration in Oncogenic Progression of HPV-Associated Cancers. PLoS Pathog., 13.","DOI":"10.1371\/journal.ppat.1006211"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"117269","DOI":"10.1016\/j.cca.2023.117269","article-title":"Circulating HPV DNA in HPV-Associated Cancers","volume":"542","author":"Lin","year":"2023","journal-title":"Clin. Chim. Acta"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5767","DOI":"10.1158\/1078-0432.CCR-18-0922","article-title":"Prognostic Impact of Residual HPV ctDNA Detection after Chemoradiotherapy for Anal Squamous Cell Carcinoma","volume":"24","author":"Cabel","year":"2018","journal-title":"Clin. Cancer Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2109","DOI":"10.1158\/1078-0432.CCR-18-2984","article-title":"Clinical Validity of HPV Circulating Tumor DNA in Advanced Anal Carcinoma: An Ancillary Study to the Epitopes-HPV02 Trial","volume":"25","author":"Jeannot","year":"2019","journal-title":"Clin. Cancer Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5857","DOI":"10.1158\/1078-0432.CCR-19-2384","article-title":"HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA","volume":"27","author":"Leung","year":"2021","journal-title":"Clin. Cancer Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"105469","DOI":"10.1016\/j.jcv.2023.105469","article-title":"The Role of Circulating Viral and Tumour DNA in the Diagnosis and Management of HPV Associated Anogenital Cancers, a Systematic Review and Meta-Analysis","volume":"164","author":"Elasifer","year":"2023","journal-title":"J. Clin. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"104958","DOI":"10.1016\/j.oraloncology.2020.104958","article-title":"cfDNA Detection for HPV+ Squamous Cell Carcinomas","volume":"115","author":"Roche","year":"2021","journal-title":"Oral Oncol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.jmoldx.2023.11.007","article-title":"Comparing the Diagnostic Performance of Quantitative PCR, Digital Droplet PCR, and Next-Generation Sequencing Liquid Biopsies for Human Papillomavirus-Associated Cancers","volume":"26","author":"Naegele","year":"2024","journal-title":"J. Mol. Diagn."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Lee, J.Y., Cutts, R.J., White, I., Augustin, Y., Garcia-Murillas, I., Fenwick, K., Matthews, N., Turner, N.C., Harrington, K., and Gilbert, D.C. (2020). Next Generation Sequencing Assay for Detection of Circulating HPV DNA (cHPV-DNA) in Patients Undergoing Radical (Chemo)Radiotherapy in Anal Squamous Cell Carcinoma (ASCC). Front. Oncol., 10.","DOI":"10.3389\/fonc.2020.00505"},{"key":"ref_16","first-page":"1","article-title":"Detection of Early Human Papillomavirus\u2013Associated Cancers by Liquid Biopsy","volume":"3","author":"Damerla","year":"2019","journal-title":"JCO Pr\u00e9cis. Oncol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Debernardi, A., Meurisse, A., Pr\u00e9tet, J.-L., Guenat, D., Monnien, F., Spehner, L., Vienot, A., Roncarati, P., Andr\u00e9, T., and Abramowitz, L. (2022). Prognostic Role of HPV Integration Status and Molecular Profile in Advanced Anal Carcinoma: An Ancillary Study to the Epitopes-HPV02 Trial. Front. Oncol., 12.","DOI":"10.3389\/fonc.2022.941676"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1158\/1541-7786.MCR-17-0153","article-title":"HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers","volume":"16","author":"Koneva","year":"2018","journal-title":"Mol. Cancer Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3001","DOI":"10.1002\/1878-0261.13219","article-title":"Human Papilloma Virus Integration Sites and Genomic Signatures in Head and Neck Squamous Cell Carcinoma","volume":"16","author":"Vacher","year":"2022","journal-title":"Mol. Oncol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1101\/gr.275911.121","article-title":"Diverse Tumorigenic Consequences of Human Papillomavirus Integration in Primary Oropharyngeal Cancers","volume":"32","author":"Symer","year":"2022","journal-title":"Genome Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"17973","DOI":"10.1007\/s00432-023-05494-4","article-title":"Characteristics of HPV Integration in Cervical Adenocarcinoma and Squamous Carcinoma","volume":"149","author":"Bi","year":"2023","journal-title":"J. Cancer Res. Clin. Oncol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1038\/s41416-020-01153-4","article-title":"Human Papilloma Virus (HPV) Integration Signature in Cervical Cancer: Identification of MACROD2 Gene as HPV Hot Spot Integration Site","volume":"124","author":"Kamal","year":"2021","journal-title":"Br. J. Cancer"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.cell.2016.05.052","article-title":"Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility","volume":"166","author":"Denny","year":"2016","journal-title":"Cell"},{"key":"ref_24","first-page":"902","article-title":"CHRM3 Is a Novel Prognostic Factor of Poor Prognosis in Patients with Endometrial Carcinoma","volume":"7","author":"Wang","year":"2015","journal-title":"Am. J. Transl. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.3346\/jkms.2016.31.10.1586","article-title":"Eukaryotic Translation Initiation Factor 3a (eIF3a) Promotes Cell Proliferation and Motility in Pancreatic Cancer","volume":"31","author":"Wang","year":"2016","journal-title":"J. Korean Med. Sci."},{"key":"ref_26","first-page":"2411","article-title":"Src Kinase-Associated Phosphoprotein2 Expression Is Associated with Poor Prognosis in Non-Small Cell Lung Cancer","volume":"35","author":"Kuranami","year":"2015","journal-title":"Anticancer Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1038\/s41388-021-02153-1","article-title":"SKAP2 Suppresses Inflammation-Mediated Tumorigenesis by Regulating SHP-1 and SHP-2","volume":"41","author":"Takagane","year":"2022","journal-title":"Oncogene"},{"key":"ref_28","first-page":"28","article-title":"Dual Role of GRK5 in Cancer Development and Progression","volume":"14","author":"Gambardella","year":"2016","journal-title":"Transl. Med. UniSa"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Du, R., Li, K., Guo, K., Chen, Z., Zhao, X., Han, L., and Bian, H. (2024). Two Decades of a Protooncogene TBL1XR1: From a Transcription Modulator to Cancer Therapeutic Target. Front. Oncol., 14.","DOI":"10.3389\/fonc.2024.1309687"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"9629","DOI":"10.2147\/IJGM.S341076","article-title":"A Pan-Cancer Analysis of the Oncogenic Role of Integrin Beta4 (ITGB4) in Human Tumors","volume":"14","author":"Huang","year":"2021","journal-title":"Int. J. Gen. Med."}],"container-title":["Cancers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6694\/17\/2\/308\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T10:31:37Z","timestamp":1759919497000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6694\/17\/2\/308"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,19]]},"references-count":30,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,1]]}},"alternative-id":["cancers17020308"],"URL":"https:\/\/doi.org\/10.3390\/cancers17020308","relation":{},"ISSN":["2072-6694"],"issn-type":[{"value":"2072-6694","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,19]]}}}