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Zupancic M, Kostopoulou ON, Holzhauser S, Lukoseviciute M, Jylhä C, Marklund L, Näsman A, Sivars L, Dalianis T. Human papillomavirus (HPV) load is higher in HPVDNA/p16 positive than in HPVDNA positive/p16 negative oropharyngeal squamous cell carcinoma but does not differ significantly between various subsites or correlate to survival. Oral Oncol 2024; 151:106749. [PMID: 38461771 DOI: 10.1016/j.oraloncology.2024.106749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
OBJECTIVE Patients with human papillomavirus DNA positive (HPVDNA+) and p16ink4a overexpressing (p16+) oropharyngeal squamous cell carcinoma (OPSCC), especially those with cancer in the tonsillar and base of tongue subsites as compared to other OPSCC subsites have a better outcome than those with only HPVDNA+ or only p16+ cancer. Likewise having a high viral load has been suggested to be a positive prognostic factor. We therefore hypothesized, that HPV viral load could vary depending on OPSCC subsite, as well as with regard to whether the cancer was HPVDNA+ and p16+, or only HPVDNA+, or only p16+ and that this affected outcome. MATERIAL AND METHODS To address these issues HPV viral load was determined by HPV digital droplet (dd) PCR in tumor biopsies with previously known HPVDNA/p16 status from 270 OPSCC patients diagnosed 2000-2016 in Stockholm, Sweden. More specifically, of these patients 235 had HPVDNA+/p16+, 10 had HPVDNA+/p16-, 13 had HPVDNA-/p16+ and 12 had HPVDNA-/p16- cancer. RESULTS We found that HPVDNA+/p16+ OPSCC had a significantly higher viral load than HPVDNA+/p16- OPSCC. Moreover, there was a tendency for a higher viral load in the tonsillar and base of tongue OPSCC subsites compared to the other subsites and for a low viral load to correlate to a better clinical outcome but none of these tendencies reached statistical significance. CONCLUSION To conclude, the mean viral load in HPVDNA+/p16+ OPSCC was higher than in HPVDNA+/p16- OPSCC, but there was no statistically significant difference in viral load depending on OPSCC subsite or on clinical outcome.
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Affiliation(s)
- Mark Zupancic
- Dept. of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Medical Unit Head, Neck, Lung, and Skin Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | | | - Stefan Holzhauser
- Dept. of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Dept of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Linda Marklund
- Medical Unit Head, Neck, Lung, and Skin Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden; Department of Clinical Sciences, Intervention and Technology, Division of ENT Diseases, Karolinska Institutet, Sweden; Department of Surgical Sciences, Section of Otolaryngology and Head and Neck Surgery, Uppsala University, Uppsala, Sweden
| | - Anders Näsman
- Dept. of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Dept of Clinical Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Sivars
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| | - Tina Dalianis
- Dept. of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Medical Unit Head, Neck, Lung, and Skin Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden.
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Jarych D, Mikulski D, Wilczyński M, Wilczyński JR, Kania KD, Haręża D, Malinowski A, Perdas E, Nowak M, Paradowska E. Differential microRNA Expression Analysis in Patients with HPV-Infected Ovarian Neoplasms. Int J Mol Sci 2024; 25:762. [PMID: 38255835 PMCID: PMC10815566 DOI: 10.3390/ijms25020762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
This study aimed to identify microRNAs (miRNAs) whose expression levels are altered by high-risk human papillomavirus (HR-HPV) infection in women with epithelial ovarian neoplasms. MiRNA expression was quantified by real-time polymerase chain reaction, while HR-HPV DNA was quantified using digital-droplet PCR. Analysis of 11 miRNAs demonstrated significantly lower hsa-miR-25-5p expression in HPV-infected compared to uninfected ovarian tissues (p = 0.0405), while differences in miRNA expression in corresponding serum were statistically insignificant. The expression of hsa-miR-218-5p in ovarian tumors was significantly higher in high-grade serous ovarian carcinoma (HGSOC) cases than in other neoplasms (p = 0.0166). In addition, hsa-miR-218-5p was significantly upregulated, whereas hsa-miR-191-5p was significantly downregulated in tissues with stage III/IV FIGO (p = 0.0009 and p = 0.0305, respectively). Using unsupervised clustering, we identified three unique patient groups with significantly varied frequencies of HPV16/18-positive samples and varied miRNA expression profiles. In multivariate analysis, high expression of hsa-miR-16-5p was an independent prognostic factor for poor overall survival (p = 0.0068). This preliminary analysis showed the changes in miRNA expression in ovarian neoplasms during HPV infection and those collected from HGSOCs or patients with advanced disease. This prospective study can provide new insights into the pathogenesis of ovarian neoplasms and host-virus interactions.
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Affiliation(s)
- Dariusz Jarych
- Laboratory of Virology, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (D.J.); (K.D.K.); (D.H.)
| | - Damian Mikulski
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland; (D.M.); (E.P.)
| | - Miłosz Wilczyński
- Department of Surgical, Endoscopic and Oncological Gynecology, Institute of the Polish Mother’s Health Center, 93-338 Lodz, Poland; (M.W.); (A.M.)
| | - Jacek R. Wilczyński
- Department of Surgical and Oncological Gynecology, Medical University of Lodz, 90-419 Lodz, Poland;
- Department of Gynecology and Obstetrics, Tomaszow Health Center, 97-200 Tomaszow Mazowiecki, Poland;
| | - Katarzyna D. Kania
- Laboratory of Virology, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (D.J.); (K.D.K.); (D.H.)
| | - Daria Haręża
- Laboratory of Virology, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (D.J.); (K.D.K.); (D.H.)
- Bio-Med-Chem Doctoral School of University of Lodz and Lodz Institutes of the Polish Academy of Sciences, 90-136 Lodz, Poland
| | - Andrzej Malinowski
- Department of Surgical, Endoscopic and Oncological Gynecology, Institute of the Polish Mother’s Health Center, 93-338 Lodz, Poland; (M.W.); (A.M.)
| | - Ewelina Perdas
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland; (D.M.); (E.P.)
| | - Mateusz Nowak
- Department of Gynecology and Obstetrics, Tomaszow Health Center, 97-200 Tomaszow Mazowiecki, Poland;
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (D.J.); (K.D.K.); (D.H.)
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Chihu-Amparan L, Pedroza-Saavedra A, Gutierrez-Xicotencatl L. The Immune Response Generated against HPV Infection in Men and Its Implications in the Diagnosis of Cancer. Microorganisms 2023; 11:1609. [PMID: 37375112 DOI: 10.3390/microorganisms11061609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Human papillomavirus (HPV) infection is associated with precancerous lesions and cancer of the genital tract both in women and men. The high incidence of cervical cancer worldwide focused the research on this infection mainly in women and to a lesser extent in men. In this review, we summarized epidemiological, immunological, and diagnostic data associated with HPV and cancer in men. We presented an overview of the main characteristics of HPV and infection in men that are associated with different types of cancer but also associated with male infertility. Men are considered important vectors of HPV transmission to women; therefore, identifying the sexual and social behavioral risk factors associated with HPV infection in men is critical to understand the etiology of the disease. It is also essential to describe how the immune response develops in men during HPV infection or when vaccinated, since this knowledge could help to control the viral transmission to women, decreasing the incidence of cervical cancer, but also could reduce other HPV-associated cancers among men who have sex with men (MSM). Finally, we summarized the methods used over time to detect and genotype HPV genomes, as well as some diagnostic tests that use cellular and viral biomarkers that were identified in HPV-related cancers.
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Affiliation(s)
- Lilia Chihu-Amparan
- Center of Research for Infection Diseases, National Institute of Public Health, Cuernavaca 62100, Morelos, Mexico
| | - Adolfo Pedroza-Saavedra
- Center of Research for Infection Diseases, National Institute of Public Health, Cuernavaca 62100, Morelos, Mexico
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Abstract
The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.
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Affiliation(s)
- Danfeng Xu
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Weifei Zhang
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Hongmei Li
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Nan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), China.
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), China.
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Guerendiain D, Grigorescu R, Kirk A, Stevenson A, Holden MTG, Pan J, Kavanagh K, Graham SV, Cuschieri K. HPV status and HPV16 viral load in anal cancer and its association with clinical outcome. Cancer Med 2022; 11:4193-4203. [PMID: 35785486 PMCID: PMC9678095 DOI: 10.1002/cam4.4771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/22/2022] [Accepted: 04/06/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The incidence of anal cancer is increasing globally. Evidence-based improvement in early detection and management of this morbid cancer is thus required. In other cancers associated with Human Papillomavirus (HPV), viral status and dynamics, including viral load (VL) has been shown to influence clinical outcome. Our aim was to determine the influence of HPV status and HPV16 VL on the clinical outcomes of anal cancer patients. METHODS A total of 185 anal cancer lesions were genotyped for HPV. Of the HPV16 positive component, VL was determined using a digital droplet PCR assay. The association of qualitative HPV status and VL (low (<12.3), medium (12.3-57) and high (>57 copies/cell)) on overall survival and hazard of death was assessed. RESULTS Of the 185 cases, 164 (88.6%) samples were HPV positive. HPV16 was detected in 154/185 samples (83.2%). HPV positive status was associated with improved overall survival in the univariate analysis [hazard ratio (HR) of 0.44, 0.23-0.82, p = 0.01]. When adjusted by age, sex, stage and response to treatment, the association of positive HPV status with improved survival remained (HR 0.24 [0.11-0.55] p < 0.001). High VL was associated with improved overall survival in the univariate analysis with a HR of 0.28 (0.11-0.71, p = 0.007). When adjusted only by age and sex, high VL was associated with better overall survival (HR 0.27, 0.11-0.68 p = 0.006). CONCLUSIONS HPV status appears to be independently associated with improved outcomes in anal cancer patients. Moreover, HPV viral load quantification may be informative for further risk stratification and warrants further investigation.
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Affiliation(s)
- Daniel Guerendiain
- Scottish HPV Reference Laboratory, NHS Lothian, Edinburgh, UK.,School of Medicine, University of St Andrews, St Andrews, UK
| | | | - Anna Kirk
- Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andrew Stevenson
- Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Jiafeng Pan
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Kim Kavanagh
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Sheila V Graham
- Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Kate Cuschieri
- Scottish HPV Reference Laboratory, NHS Lothian, Edinburgh, UK
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Mainguené J, Vacher S, Kamal M, Hamza A, Masliah‐Planchon J, Baulande S, Ibadioune S, Borcoman E, Cacheux W, Calugaru V, Courtois L, Crozes C, Deloger M, Girard E, Delord J, Dubray‐Vautrin A, Larbi Chérif L, Dupain C, Jeannot E, Klijanienko J, Lameiras S, Lecerf C, Modesto A, Nicolas A, Rouzier R, Saada‐Bouzid E, Saintigny P, Sudaka A, Servant N, Le Tourneau C, Bièche I. Human papilloma virus integration sites and genomic signatures in head and neck squamous cell carcinoma. Mol Oncol 2022; 16:3001-3016. [PMID: 35398964 PMCID: PMC9394244 DOI: 10.1002/1878-0261.13219] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
A prevalence of around 26% of human papillomavirus (HPV) in head and neck squamous cell carcinoma (HNSCC) has been previously reported. HPV induced oncogenesis mainly involving E6 and E7 viral oncoproteins. In some cases, HPV viral DNA has been detected to integrate with the host genome and possibly contributes to carcinogenesis by affecting the gene expression. We retrospectively assessed HPV integration sites and signatures in 80 HPV positive patients with HNSCC, by using a double capture‐HPV method followed by next‐generation Sequencing. We detected HPV16 in 90% of the analyzed cohort and confirmed five previously described mechanistic signatures of HPV integration [episomal (EPI), integrated in a truncated form revealing two HPV‐chromosomal junctions colinear (2J‐COL) or nonlinear (2J‐NL), multiple hybrid junctions clustering in a single chromosomal region (MJ‐CL) or scattered over different chromosomal regions (MJ‐SC) of the human genome]. Our results suggested that HPV remained episomal in 38.8% of the cases or was integrated/mixed in the remaining 61.2% of patients with HNSCC. We showed a lack of association of HPV genomic signatures to tumour and patient characteristics, as well as patient survival. Similar to other HPV associated cancers, low HPV copy number was associated with worse prognosis. We identified 267 HPV‐human junctions scattered on most chromosomes. Remarkably, we observed four recurrent integration regions: PDL1/PDL2/PLGRKT (8.2%), MYC/PVT1 (6.1%), MACROD2 (4.1%) and KLF5/KLF12 regions (4.1%). We detected the overexpression of PDL1 and MYC upon integration by gene expression analysis. In conclusion, we identified recurrent targeting of several cancer genes such as PDL1 and MYC upon HPV integration, suggesting a role of altered gene expression by HPV integration during HNSCC carcinogenesis.
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Hashida Y, Higuchi T, Matsumoto S, Iguchi M, Murakami I, Hyodo M, Daibata M. Prognostic significance of human papillomavirus 16 viral load level in patients with oropharyngeal cancer. Cancer Sci 2021; 112:4404-4417. [PMID: 34382311 PMCID: PMC8486212 DOI: 10.1111/cas.15105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 12/16/2022] Open
Abstract
Human papillomavirus (HPV) infection in patients with oropharyngeal squamous cell carcinoma (OPSCC) is a major determinant for better prognosis. However, there remain HPV‐positive patients who have poor outcomes. The stratification strategy for detecting high‐risk patients among those with HPV‐positive OPSCC has not been well delineated, especially for Asian patients. We undertook a retrospective cohort study on the survival rate of 89 Japanese patients diagnosed with primary OPSCC. The tumors were concurrently analyzed for the presence of HPV E6 DNA/mRNA, viral DNA load, p16 expression, viral physical status, and viral variant lineage. Human papillomavirus 16 viral DNA was found in 45 (51%) OPSCCs. Human papillomavirus 16 DNA‐positive OPSCCs with higher viral load (classified as HPV16 DNA‐medium/high OPSCCs) showed significantly favorable overall survival and progression‐free survival compared with HPV16 DNA‐positive OPSCCs with lower viral load (<10 copies/cell; HPV16 DNA‐low OPSCCs) and HPV16 DNA‐negative OPSCCs. E6 mRNA expression was observed in all HPV16 DNA‐medium/high OPSCCs but not in HPV16 DNA‐low OPSCCs. Notably, p16‐positive and HPV16 DNA‐negative/low OPSCCs showed significantly worse survival than p16‐positive and HPV16 DNA‐medium/high OPSCCs and resembled HPV‐unrelated OPSCCs with regard to survival and risk factor profile. Although not significant, a trend toward shorter survival was observed for HPV16‐integrated OPSCCs. Phylogenetic analysis revealed two major types of HPV16 variants termed Asian (A4) and European (A1/A2/A3) variants, but no difference in survival between these variants was observed. Altogether, these findings suggest that HPV viral load is a potentially informative factor for more accurate risk stratification of patients with OPSCC.
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Affiliation(s)
- Yumiko Hashida
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Tomonori Higuchi
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Shuichi Matsumoto
- Department of Otolaryngology, Head and Neck Surgery, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Mitsuko Iguchi
- Department of Pathology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Ichiro Murakami
- Department of Pathology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Masamitsu Hyodo
- Department of Otolaryngology, Head and Neck Surgery, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Masanori Daibata
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Japan
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Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
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Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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Kinloch NN, Ritchie G, Dong W, Cobarrubias KD, Sudderuddin H, Lawson T, Matic N, Montaner JSG, Leung V, Romney MG, Lowe CF, Brumme CJ, Brumme ZL. SARS-CoV-2 RNA Quantification Using Droplet Digital RT-PCR. J Mol Diagn 2021; 23:907-19. [PMID: 34062285 DOI: 10.1016/j.jmoldx.2021.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 12/23/2022] Open
Abstract
Quantitative viral load assays have transformed our understanding of viral diseases. They hold similar potential to advance COVID-19 control and prevention, but SARS-CoV-2 viral load tests are not yet widely available. SARS-CoV-2 molecular diagnostic tests, which typically employ real-time RT-PCR, yield semiquantitative results only. Droplet digital RT-PCR (RT-ddPCR) offers an attractive platform for SARS-CoV-2 RNA quantification. Eight primer/probe sets originally developed for real-time RT-PCR–based SARS-CoV-2 diagnostic tests were evaluated for use in RT-ddPCR; three were identified as the most efficient, precise, and sensitive for RT-ddPCR–based SARS-CoV-2 RNA quantification. For example, the analytical efficiency for the E-Sarbeco primer/probe set was approximately 83%, whereas assay precision, measured as the coefficient of variation, was approximately 2% at 1000 input copies/reaction. Lower limits of quantification and detection for this primer/probe set were 18.6 and 4.4 input SARS-CoV-2 RNA copies/reaction, respectively. SARS-CoV-2 RNA viral loads in a convenience panel of 48 COVID-19–positive diagnostic specimens spanned a 6.2log10 range, confirming substantial viral load variation in vivo. RT-ddPCR–derived SARS-CoV-2 E gene copy numbers were further calibrated against cycle threshold values from a commercial real-time RT-PCR diagnostic platform. This log-linear relationship can be used to mathematically derive SARS-CoV-2 RNA copy numbers from cycle threshold values, allowing the wealth of available diagnostic test data to be harnessed to address foundational questions in SARS-CoV-2 biology.
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Abstract
Worldwide there has been a significant increase in the incidence of oropharyngeal squamous cell carcinoma (OPSCC) etiologically attributed to oncogenic human papillomavirus (HPV). Reliable and accurate identification and detection tools are important as the incidence of HPV-related cancer is on the rise. Several HPV detection methods for OPSCC have been developed and each has its own advantages and disadvantages in regard to sensitivity, specificity, and technical difficulty. This review summarizes our current knowledge of molecular methods for detecting HPV in OPSCC, including HPV DNA/RNA polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), p16 immunohistochemistry (IHC), and DNA/RNA in situ hybridization (ISH) assays. This summary may facilitate the selection of a suitable method for detecting HPV infection, and therefore may help in the early diagnosis of HPV-related carcinoma to reduce its mortality, incidence, and morbidity.
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Affiliation(s)
- Fatin Hazwani Fauzi
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nurul Izzati Hamzan
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nurhayu Ab Rahman
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Siti Suraiya
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Suharni Mohamad
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
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Rotondo JC, Oton-Gonzalez L, Mazziotta C, Lanzillotti C, Iaquinta MR, Tognon M, Martini F. Simultaneous Detection and Viral DNA Load Quantification of Different Human Papillomavirus Types in Clinical Specimens by the High Analytical Droplet Digital PCR Method. Front Microbiol 2020; 11:591452. [PMID: 33329471 PMCID: PMC7710522 DOI: 10.3389/fmicb.2020.591452] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Human papillomaviruses (HPVs) are small DNA tumor viruses that mainly infect mucosal epithelia of anogenital and upper respiratory tracts. There has been progressive demand for more analytical assays for HPV DNA quantification. A novel droplet digital PCR (ddPCR) method was developed to simultaneously detect and quantify HPV DNA from different HPV types. DdPCR was initially tested for assay sensitivity, accuracy, specificity as well as intra- and inter-run assay variation employing four recombinant plasmids containing HPV16, HPV18, HPV11, and HPV45 DNAs. The assay was extended to investigate/quantify HPV DNA in Cervical Intraepithelial Neoplasia (CIN, n = 45) specimens and human cell lines (n = 4). DdPCR and qPCR data from clinical samples were compared. The assay showed high accuracy, sensitivity and specificity, with low intra-/inter- run variations, in detecting/quantifying HPV16/18/11/45 DNAs. HPV DNA was detected in 51.1% (23/45) CIN DNA samples by ddPCR, whereas 40% (18/45) CIN tested HPV-positive by qPCR. Five CIN, tested positive by ddPCR, were found to be negative by qPCR. In CIN specimens, the mean HPV DNA loads determined by ddPCR were 3.81 copy/cell (range 0.002–51.02 copy/cell), whereas 8.04 copy/cell (range 0.003–78.73 copy/cell) by qPCR. DdPCR and qPCR concordantly detected HPV DNA in SiHa, CaSki and Hela cells, whereas HaCaT tested HPV-negative. The correlation between HPV DNA loads simultaneously detected by ddPCR/qPCR in CINs/cell lines was good (R2 = 0.9706, p < 0.0001). Our data indicate that ddPCR is a valuable technique in quantifying HPV DNA load in CIN specimens and human cell lines, thereby improving clinical applications, such as patient management after primary diagnosis of HPV-related lesions with HPV-type specific assays.
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Affiliation(s)
- John Charles Rotondo
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Lucia Oton-Gonzalez
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Mazziotta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Carmen Lanzillotti
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria Rosa Iaquinta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Mauro Tognon
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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