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Molano M, Machalek DA, Phillips S, Tan G, Garland SM, Hawkes D, Balgovind P, Haqshenas R, Badman SG, Bolnga J, Gabuzzi J, Kombati Z, Munnull GM, Brotherton JM, Saville M, Kaldor JM, Toliman PJ, Vallely AJ, Murray GL. DNA methylation at individual CpG-sites of EPB41L3, HTERT and FAM19A4 are useful for detection of cervical high-grade squamous intraepithelial lesions (HSIL) or worse: Analysis of individual CpG-sites outperforms averaging. Tumour Virus Res 2024; 18:200288. [PMID: 38960143 PMCID: PMC11278974 DOI: 10.1016/j.tvr.2024.200288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/17/2024] [Accepted: 06/23/2024] [Indexed: 07/05/2024] Open
Abstract
Global methylation analysis of gene promoters is promising for detection of high-grade squamous intraepithelial lesions or worse (HSIL+) in high-risk human papillomavirus (hrHPV)-positive women. However, diagnostic performance of methylation data at individual CpG-sites is limited. We explored methylation for predicting HSIL+ in self- and clinician-collected samples from Papua New Guinea. Methylation of EPB41L3 (1-6 CpG-sites), hTERT (1-10 CpG-sites) and FAM19A4 (1-5 CpG-sites) was assessed through pyrosequencing from 44 HPV+ samples (4 cancers, 19 HSIL, 4 low-grade squamous intraepithelial lesions (LSIL), 17 normal). New primers were designed for FAM19A4 directed to the first exon region not explored previously. In clinician-collected samples, methylation at CpG-sites 4 and 5 of EPB41L3 were the best HSIL predictors (AUC >0.83) and CpG-site 4 for cancer (0.925). Combination of EPB41L3 sites 2/4 plus FAM19A4 site 1 were the best HSIL+ markers [100% sensitivity, 63.2% specificity]. Methylation at CpG-site 5 of FAM19A4 was the best HSIL predictor (0.67) in self-collected samples, and CpG-sites 1 and 3 of FAM19A4 for cancer (0.77). Combined, FAM19A4 site 1 plus HPV 16/18 detection yielded sensitivity of 82.6% and specificity of 61.9%. In conclusion, methylation at individual CpG-sites of EPB41L3 and FAM19A4 outperformed global analysis and improved HSIL+ detection, warranting further investigation.
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Affiliation(s)
- Monica Molano
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
| | - Dorothy A Machalek
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Victoria, Australia; The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Samuel Phillips
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Grace Tan
- Australian Centre for the Prevention of Cervical Cancer, Melbourne, Victoria, Australia
| | - Suzanne M Garland
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
| | - David Hawkes
- Australian Centre for the Prevention of Cervical Cancer, Melbourne, Victoria, Australia
| | - Prisha Balgovind
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Reza Haqshenas
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
| | - Steve G Badman
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - John Bolnga
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea; Department of Obstetrics and Gynaecology, Modilon General Hospital, Madang, Papua New Guinea
| | - Josephine Gabuzzi
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea; Department of Obstetrics and Gynaecology, Modilon General Hospital, Madang, Papua New Guinea
| | - Zure Kombati
- Department of Pathology, Mt Hagen Provincial Hospital, WHP 281, Papua New Guinea
| | - Gloria M Munnull
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea; Department of Obstetrics and Gynaecology, Mt Hagen Provincial Hospital, Mount Hagen, Papua New Guinea
| | - Julia Ml Brotherton
- Australian Centre for the Prevention of Cervical Cancer, Melbourne, Victoria, Australia
| | - Marion Saville
- Australian Centre for the Prevention of Cervical Cancer, Melbourne, Victoria, Australia
| | - John M Kaldor
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Pamela J Toliman
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Andrew J Vallely
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Gerald L Murray
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
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Poynten IM, Jin F, Molano M, Machalek DA, Roberts JM, Hillman RJ, Cornall A, Phillips S, Templeton DJ, Law C, Fairley CK, Grulich AE, Garland SM. Comparison of four assays for human papillomavirus detection in the anal canal. Clin Microbiol Infect 2022; 28:1652.e1-1652.e6. [PMID: 35809783 DOI: 10.1016/j.cmi.2022.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Anal cancer is preceded by high-risk human papillomavirus (HRHPV) infection, predominantly HPV16. No HPV assay is licenced for use in anal screening. We aimed to determine the sensitivity and specificity of four anal canal swab HPV assays to predict high grade squamous epithelial lesions (HSIL). METHODS In a cohort of Australian HIV-positive and negative gay and bisexual men, we compared the sensitivity and specificity of detection of 13 anal HRHPV genotypes by Linear Array (LA), Cobas 4800, EuroArray and Anyplex II HPV28 (+ and ++ cut offs), compared their ability to predict prevalent anal HSIL and compared anal canal HRHPV detection with HRHPV isolated from HSIL using laser capture microdissection (LCM). RESULTS A total of 475 participants had baseline results available for all 4 assays (166, 35.0% HIV positive), and 169 participants had a diagnosis of cytological and/or histological HSIL.HPV16 and any HRHPV detection were highest with Anyplex II HPV28 (+) (156, 32.8% 95% CI 28.6-37.2 and 359, 75.6%, 95% CI 71.5-79.4 respectively). For detection of concurrent HSIL and HPV16, the assay sensitivity was similar ranging from 49.1%, 95% CI 41.4-56.9 (Anyplex II HPV28 ++) to 55.0%, 95% CI 47.2-62.7 (Anyplex II HPV28 +). For concurrent HSIL and any HRHPV detection, EuroArray was more specific than Anyplex II HPV28 (+) (45.9% 95% CI 40.2-51.7 vs 36.7%, 95% CI 31.3-42.4, p=0.021) and had comparable specificity with Anyplex II HPV28 (++) (45.9% vs 47.2%, 95% CI 41.5-53.0, p=0.75). All assays had high sensitivities for predicting HPV16 detected on LCM (92.5-97.5%). Anyplex II HPV28 and EuroArray were significantly more sensitive than LA for lesions caused by non-HPV16 HRHPV types on LCM. CONCLUSION Anyplex II HPV28 and EuroArray detected more non-16 HRHPV genotypes than LA. Increasing the Anyplex II HPV28 cut off improved specificity, without compromising sensitivity for detection of concurrent HSIL.
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Affiliation(s)
- I Mary Poynten
- The Kirby Institute, Wallace Wurth Building, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia.
| | - Fengyi Jin
- The Kirby Institute, Wallace Wurth Building, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
| | - Monica Molano
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia; Molecular Microbiology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia
| | - Dorothy A Machalek
- The Kirby Institute, Wallace Wurth Building, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia; Centre for Women's Infectious Diseases, The Royal Women's Hospital, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia; Molecular Microbiology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia
| | - Jennifer M Roberts
- Douglas Hanly Moir Pathology, 14 Giffnock Ave, Macquarie Park, Sydney, New South, Wales 2113, Australia
| | - Richard J Hillman
- St Vincent's Hospital, 390 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Alyssa Cornall
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia; Molecular Microbiology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia
| | - Samuel Phillips
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia; Molecular Microbiology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia
| | - David J Templeton
- Department of Sexual Health Medicine, Sydney Local Health District, 16 Marsden St, Camperdown, Sydney, New South Wales 2050, Australia; Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Carmella Law
- St Vincent's Hospital, 390 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | | | - Andrew E Grulich
- The Kirby Institute, Wallace Wurth Building, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
| | - Suzanne M Garland
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia; Molecular Microbiology, Murdoch Children's Research Institute, Flemington Rd, Parkville, Melbourne, Victoria 3052, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Grattan St, Parkville, Melbourne, Victoria 3052, Australia
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Roberts JM, Poynten IM, Molano M, Machalek DA, Hillman RJ, Guzman P, Jin F, Templeton DJ, Fairley CK, Law C, Garland SM, Grulich AE, Cornall AM. Human Papillomavirus Genotypes in Anal High-Grade Squamous Intraepithelial Lesion (HSIL): Anal Intraepithelial Neoplasia Grades 2 (AIN2) and 3 (AIN3) Are Different. Cancer Epidemiol Biomarkers Prev 2020; 29:2078-2083. [PMID: 32732249 DOI: 10.1158/1055-9965.epi-20-0664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/18/2020] [Accepted: 07/23/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Anal high-grade squamous intraepithelial lesion (HSIL) can be histomorphologically categorized into anal intraepithelial neoplasia (AIN) grade 2 (AIN2) and grade 3 (AIN3). Different risk factors for these two categories have been described. We investigated whether there were also differences in lesion-specific human papillomavirus (HPV) genotypes. METHODS The Study of the Prevention of Anal Cancer (SPANC) recruited 617 gay and bisexual men (GBM); 36% of participants were HIV positive. At baseline, 196 men (31.8%) had histologic HSIL lesions. Tissue was available for genotyping in 171, with a total of 239 HSIL lesions (183 AIN3 and 56 AIN2). Using laser capture microdissection, each lesion revealed a maximum of one genotype. RESULTS High-risk HPV (HR-HPV) genotypes were found in 220 (92.1%) HSIL lesions, with no significant difference between AIN3 (93.4%) and AIN2 (87.5%). AIN3 lesions had significantly more HPV16 (42.1%) than AIN2 lesions (12.5%; P < 0.001) and AIN2 lesions had significantly more non-16 HR-HPV types (75.0%) than AIN3 lesions (51.4%; P = 0.002). These associations were similar for HIV-negative men with HPV16 in 51.1% AIN3 and 18.2% AIN2 (P = 0.001) and non-16 HR-HPV in 40.0% AIN3 and 75.8% AIN2 (P < 0.001). For HIV-positive men, HPV16 remained more frequently detected in AIN3 (33.3% vs. 4.4% for AIN2; P = 0.004), but there was no difference between AIN3 and AIN2 for non-16 HR-HPV (62.4% vs. 73.9%; P = 0.300). CONCLUSIONS As HPV16 has the strongest link with anal cancer, the subcategorization of HSIL may enable stratification of lesions for anal cancer risk and guide anal HSIL management. IMPACT Stratification of anal cancer risk by histologic HSIL grade.
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Affiliation(s)
| | - Isobel M Poynten
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
| | - Monica Molano
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, Melbourne, Victoria, Australia
- Molecular Microbiology, Murdoch Children's Research Institute, Parkville, Melbourne, Victoria, Australia
| | - Dorothy A Machalek
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, Melbourne, Victoria, Australia
- School of Population and Global Health, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Richard J Hillman
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Patricia Guzman
- Douglass Hanly Moir Pathology, Sydney, New South Wales, Australia
| | - Fengyi Jin
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
| | - David J Templeton
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
- Department of Sexual Health Medicine, Sydney Local Health District, Camperdown, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | | | - Carmella Law
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Suzanne M Garland
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, Melbourne, Victoria, Australia
- Molecular Microbiology, Murdoch Children's Research Institute, Parkville, Melbourne, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Andrew E Grulich
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
| | - Alyssa M Cornall
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, Melbourne, Victoria, Australia
- Molecular Microbiology, Murdoch Children's Research Institute, Parkville, Melbourne, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
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