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Zhao Y, Chen D, Xu Z, Li T, Zhu J, Hu R, Xu G, Li Y, Yang Y, Liu M. Integrating CRISPR-Cas12a into a Microfluidic Dual-Droplet Device Enables Simultaneous Detection of HPV16 and HPV18. Anal Chem 2023; 95:3476-3485. [PMID: 36724385 DOI: 10.1021/acs.analchem.2c05320] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fast, simplified, and multiplexed detection of human papillomaviruses (HPVs) is of great importance for both clinical management and population screening. However, current HPV detection methods often require sophisticated instruments and laborious procedures to detect multiple targets. In this work, we developed a simple microfluidic dual-droplet device (M-D3) for the simultaneous detection of HPV16 and HPV18 by combining the CRISPR-Cas12a system and multiplexed recombinase polymerase amplification (RPA) assay. A new approach of combining pressure/vacuum was proposed for efficient droplet generation with minimal sample consumption. Two groups of droplets that separately encapsulate the relevant Cas12a/crRNA and the fluorescent green or red reporters are parallelly generated, followed by automatic imaging to discriminate the HPV subtypes based on the specific fluorescence of the droplets. The M-D3 platform performs with high sensitivity (∼0.02 nM for unamplified plasmids) and specificity in detecting HPV16 and HPV18 DNA. By combining the RPA and Cas12a assay, M-D3 allows on-chip detection of HPV16 and HPV18 DNA simultaneously within 30 min, reaching a detection limit of 10-18 M (∼1 copy/reaction). Moreover, the outstanding performance of M-D3 was validated in testing 20 clinical patient samples with HPV infection risk, showing a sensitivity of 92.3% and a specificity of 100%. By integrating the dual-droplet generator, CRISPR-Cas12a, and multiplexed RPA, the M-D3 platform provides an efficient way to discriminate the two most harmful HPV subtypes and holds great potential in the applications of multiplexed nucleic acid testing.
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Affiliation(s)
- Yin Zhao
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan 430072, China.,State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Dongjuan Chen
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
| | - Zhichen Xu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan 430072, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Optics Valley Laboratory, Wuhan 430074, Hubei, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Optics Valley Laboratory, Wuhan 430074, Hubei, China
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2
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Soheili M, Keyvani H, Soheili M, Nasseri S. Human papilloma virus: A review study of epidemiology, carcinogenesis, diagnostic methods, and treatment of all HPV-related cancers. Med J Islam Repub Iran 2021; 35:65. [PMID: 34277502 PMCID: PMC8278030 DOI: 10.47176/mjiri.35.65] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Human papillomavirus (HPV) infection is considered as the most common viral sexually transmitted infection worldwide. This poses an increasingly interdisciplinary medical challenge. Since there is vast scattered information in databases about HPV and the correlated diseases, we decided to collect useful data so that the experts can get a more comprehensive view of HPV. Methods: In this article, HPV-associated diseases, prevalence, prevention, and new treatments are discussed. The retrieved articles reporting the latest data about the required information for our review were selected through searching in Web of Science, Scopus, Medline (PubMed), EMBASE, Cochrane Library, Ovid, and CINHAL with language limitations of English and German. Results: There are 2 groups of HPVs: (1) low-risk HPV types that can lead to genital warts, and (2) high-risk HPV types that are involved in HPV-associated oncogenesis. About 70% of all sexually active women are infected and most of these infections heal within many weeks or months. In the case of HPV-persistence, a risk of preneoplasia or carcinoma exists. These types of viruses are responsible for the existence of genitoanal, gastrointestinal, urinary tract, and head and neck tumors. There is still no definite successful treatment. The detection of HPV-related condylomata occurs macroscopically in women and men, and the diagnosis of the precursors of cervical carcinoma in women is possible by Pap smear. Conclusion: For extragenital manifestations, there is no structured early detection program. Meanwhile, studies on HPV vaccines confirm that they should be used for the primary prevention of HPV-dependent diseases. However, we need more research to find out the real advantages and disadvantages of vaccines.
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Affiliation(s)
- Maryam Soheili
- School of Kinesiology and Health Science, York University, Toronto, Canada
| | - Hossein Keyvani
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Gastrointestinal and Liver Disease Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Soheili
- Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Human Revivification Society of Congress 60, Tehran, Iran
| | - Sherko Nasseri
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Department of Molecular Medicine and Medical Genetics, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
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3
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Gautam A, Gedda MR, Rai M, Sundar S, Chakravarty J. Human Papillomavirus Genome based Detection and Typing: A Holistic Molecular Approach. Curr Mol Med 2020; 19:237-246. [PMID: 30950352 DOI: 10.2174/1566524019666190405120441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022]
Abstract
Human Papillomavirus (HPV) is a species specific double-stranded DNA virus infecting human cutaneous or mucosal tissues. The genome structure of HPV is extremely polymorphic hence making it difficult to discriminate between them. HPV exhibits numerous dissimilar types that can be subdivided into high-risk (HR), probably high-risk and low-risk (LR), causing numerous types of cancers and warts around the genital organs in humans. Several screening methods are performed in order to detect cytological abnormalities and presence or absence of HPV genome. Currently available commercial kits and methods are designed to detect only a few HR/LR-HPV types, which are expensive adding to the economic burden of the affected individual and are not freely available. These gaps could be minimized through Polymerase Chain reaction (PCR) method, which is a gold standard and a cost-effective technique for the detection of most HPV (both known and unknown) types by using specific consensus primers in minimal lab setup. In this context, numerous studies have validated the effectiveness of different sets of consensus primers in the screening of HPVs. Numerous consensus primers, such as E6, E6/E7, GP-E6/E7, MY09/11, GP5+/GP6+, SPF10, and PGMY09/11 have been developed to detect the presence of HPV DNA. In addition, HPV detection sensitivity could be achieved through consensus primer sets targeting specific ORF regions like L1 and E6, which may finally assist in better diagnosis of several unknown HR-HPVs. The present review, provides a summary of the available methods, kits and consensus primer sets for HPV genome based detection, their advantages and limitations along with future goals to be set for HPV detection.
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Affiliation(s)
- Abhilasha Gautam
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Mallikarjuna R Gedda
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Madhukar Rai
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Jaya Chakravarty
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
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4
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Kano M, Kondo S, Wakisaka N, Wakae K, Aga M, Moriyama-Kita M, Ishikawa K, Ueno T, Nakanishi Y, Hatano M, Endo K, Sugimoto H, Kitamura K, Muramatsu M, Yoshizaki T. Expression of estrogen receptor alpha is associated with pathogenesis and prognosis of human papillomavirus-positive oropharyngeal cancer. Int J Cancer 2019; 145:1547-1557. [PMID: 31228270 DOI: 10.1002/ijc.32500] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
Abstract
Human papillomavirus (HPV) has been identified as a causative agent of cervical cancer and oropharyngeal cancer (OPC). Intriguingly, estrogen and HPV were shown to play synergistic roles in cervical carcinogenesis. We recently demonstrated that the apolipoprotein B mRNA-editing catalytic polypeptide 3 (APOBEC3, A3) family, which is inducible by estrogen, could lead to HPV DNA hypermutation and cause viral DNA integration. In the present study, we examined the relationships between estrogen-estrogen receptor α (ERα) and A3s in HPV-positive OPC. ERα expression was associated with HPV positivity in OPC biopsy samples using immunohistochemical analysis and reverse-transcription quantitative polymerase chain reaction. In addition, ERα was significantly associated with improved overall survival in HPV-positive OPC (hazard ratio, 0.26; p = 0.029). APOBEC3A (A3A) mRNA was induced by estrogen in HPV and ERα-positive OPC cells. Furthermore, A3A mRNA and protein expression were significantly higher in ERα-positive cases than in ERα-negative ones, among HPV-positive biopsy samples (p = 0.037 and 0.047). These findings suggest that A3A is associated with a good prognosis in ERα-positive OPC, and indicate the prognostic significance of ERα in HPV-positive OPC. This is the first study to demonstrate the prognostic role of ERα in HPV-positive OPC.
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Affiliation(s)
- Makoto Kano
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Otolaryngology, National Hospital Organization Kanazawa Medical Center, Kanazawa, Ishikawa, Japan
| | - Satoru Kondo
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Naohiro Wakisaka
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kosho Wakae
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mituharu Aga
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Makiko Moriyama-Kita
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuya Ishikawa
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takayoshi Ueno
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yosuke Nakanishi
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Miyako Hatano
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuhira Endo
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hisashi Sugimoto
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kouichi Kitamura
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masamichi Muramatsu
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomokazu Yoshizaki
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
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5
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Mahantshetty U, Teni T, Naga P, Hotwani C, Umesh S, Kannan S, Hande V, Pawar S, Engineer R, Chopra S, Deodhar K, Maheshwari A, Gurram L, Gupta S, Shrivastava SK. Impact of HPV 16/18 infection on clinical outcomes in locally advanced cervical cancers treated with radical radio (chemo) therapy - A prospective observational study. Gynecol Oncol 2018; 148:299-304. [DOI: 10.1016/j.ygyno.2017.11.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 10/18/2022]
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6
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Togtema M, Jackson R, Grochowski J, Villa PL, Mellerup M, Chattopadhyaya J, Zehbe I. Synthetic siRNA targeting human papillomavirus 16 E6: a perspective on in vitro nanotherapeutic approaches. Nanomedicine (Lond) 2018; 13:455-474. [PMID: 29382252 DOI: 10.2217/nnm-2017-0242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
High-risk human papillomaviruses infect skin and mucosa, causing approximately 5% of cancers worldwide. In the search for targeted nanotherapeutic approaches, siRNAs against the viral E6 transcript have been molecules of interest but have not yet seen successful translation into the clinic. By reviewing the past approximately 15 years of in vitro literature, we identify the need for siRNA validation protocols which concurrently evaluate ranges of key treatment parameters as well as characterize downstream process restoration in a methodical, quantitative manner and demonstrate their implementation using our own data. We also reflect on the future need for more appropriate cell culture models to represent patient lesions as well as the application of personalized approaches to identify optimal treatment strategies.
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Affiliation(s)
- Melissa Togtema
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Biotechnology Program, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
| | - Robert Jackson
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Biotechnology Program, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
| | - Jessica Grochowski
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada
| | - Peter L Villa
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Department of Biology, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
| | - Miranda Mellerup
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada
| | - Jyoti Chattopadhyaya
- Program of Chemical Biology, Institute of Cell & Molecular Biology, Uppsala University, Uppsala, SE-75123, Sweden
| | - Ingeborg Zehbe
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Department of Biology, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
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7
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Zaravinos A, Mammas IN, Sourvinos G, Spandidos DA. Molecular detection methods of human papillomavirus (HPV). Int J Biol Markers 2018; 24:215-22. [DOI: 10.1177/172460080902400401] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human papillomavirus (HPV) testing can identify women at risk of cervical cancer. Currently, molecular detection methods are the gold standard for identification of HPV. The three categories of molecular assays that are available are based on the detection of HPV DNA and include (1) non-amplified hybridization assays, such as Southern transfer hybridization (STH), dot blot hybridization (DB) and in situ hybridization (ISH); (2) signal amplified hybridization assays, such as hybrid capture assays (HC2); (3) target amplification assays, such as polymerase chain reaction (PCR) and in situ PCR. STH requires large amounts of DNA, is laborious and not reproducible, while ISH has only moderate sensitivity for HPV. The sensitivity of the HC2 assay is similar to that of PCR-based assays, with high sensitivity being achieved by signal rather than target amplification. PCR-based detection is both highly sensitive and specific. Since PCR can be performed on very small amounts of DNA, it is ideal for use on specimens with low DNA content. In the future, with the advance of technology, viral DNA extraction and amplification systems will become more rapid, more sensitive, and more automated.
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Affiliation(s)
- Apostolos Zaravinos
- Department of Clinical Virology, School of Medicine, University of Crete, Heraklion, Crete - Greece
| | - Ioannis N. Mammas
- Department of Clinical Virology, School of Medicine, University of Crete, Heraklion, Crete - Greece
| | - George Sourvinos
- Department of Clinical Virology, School of Medicine, University of Crete, Heraklion, Crete - Greece
| | - Demetrios A. Spandidos
- Department of Clinical Virology, School of Medicine, University of Crete, Heraklion, Crete - Greece
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8
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Biesaga B, Mucha-Małecka A, Janecka-Widła A, Kołodziej-Rzepa M, Szostek S, Słonina D, Kowalczyk A, Halaszka K, Przewoźnik M. Differences in the prognosis of HPV16-positive patients with squamous cell carcinoma of head and neck according to viral load and expression of P16. J Cancer Res Clin Oncol 2017; 144:63-73. [PMID: 29043437 PMCID: PMC5756549 DOI: 10.1007/s00432-017-2531-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/05/2017] [Indexed: 12/11/2022]
Abstract
Purpose To evaluate the impact of HPV16 load (VL—the number of virus genome copies per cell) and P16 expression on prognosis of patients with squamous cell carcinomas (SCCs) of head and neck (HN). Materials and methods HPV16 presence was assessed in the group of 109 patients with HNSCCs by quantitative polymerase chain reaction (qPCR). VL (assessed by qPCR) and P16 expression (evaluated by immunohistochemistry) were analysed only in the subgroup of HPV16-positive tumours. These features were correlated with 5-year overall survival (OS) and disease-free survival (DFS). Results HPV16 infection was found in 36 tumours (33.0%). Virus-positive patients had better OS and DFS than those without infection (P = 0.041 and 0.005). Among HPV16-positive HNSCCs, 18 (50.0%) had higher VL (median value > 6764.3 copies/cell) and 25 (73.5%) P16 over expression. The significant differences in OS and DFS (P = 0.008 and 0.004) were noticed according to VL, wherein 100% DFS was found for patients with higher VL. According to P16 expression, significant difference was found only for OS (P = 0.020). In multivariate analysis, VL (P = 0.045; HR = 2.795; CI 0.121–1.060) and the level of smoking (P = 0.023, HR = 2.253; CI 1.124–4.514) were independent factors affecting DFS of HPV16-positive patients. Conclusion On the basis of viral load, it is possible to differentiate prognosis of patients with HPV16-positive HNSCCs. In this subgroup, viral load has stronger prognostic potential than P16 expression.
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Affiliation(s)
- Beata Biesaga
- Department of Applied Radiobiology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland.
| | - Anna Mucha-Małecka
- Department of Radiation Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland
| | - Anna Janecka-Widła
- Department of Applied Radiobiology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland
| | - Marta Kołodziej-Rzepa
- Department of Surgical Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland
| | - Sława Szostek
- Department of Virology, Chair of Microbiology, Jagiellonian University Medical College, 18 Czysta Street, 31-121, Cracow, Poland
| | - Dorota Słonina
- Department of Applied Radiobiology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland
| | - Aleksandra Kowalczyk
- Department of Applied Radiobiology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland
| | - Krzysztof Halaszka
- Department of Tumour Pathology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland
| | - Marcin Przewoźnik
- Department of Tumour Pathology, Maria Sklodowska-Curie Institute-Oncology Center, Cracow Branch, 11 Garncarska Street, 31-115, Cracow, Poland
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9
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Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Towle RM, Haynes C, Poh CF. Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR. Sci Rep 2017; 7:11855. [PMID: 28928368 PMCID: PMC5605662 DOI: 10.1038/s41598-017-11201-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays. Furthermore, we demonstrate that the ability to target specific locations of the genome permits detection of clinically relevant oncogenic events such as small, submicroscopic homozygous deletions. Additional capabilities of the multiplexed ddPCR assay include the ability to infer ploidy level, quantify the change in copy number of target loci with high-level gains, and simultaneously assess the status and viral load for high-risk human papillomavirus types 16 and 18. This novel multiplexed ddPCR assay therefore may have clinical value in differentiating between benign oral lesions from those that are at risk of progressing to oral cancer.
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Affiliation(s)
- Curtis B Hughesman
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - X J David Lu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Kelly Y P Liu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Yuqi Zhu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca M Towle
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Catherine F Poh
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada.
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10
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Combined SYBR Green real-time polymerase chain reaction and microarray method for the simultaneous determination of human papillomavirus loads and genotypes. Obstet Gynecol Sci 2016; 59:489-497. [PMID: 27896251 PMCID: PMC5120068 DOI: 10.5468/ogs.2016.59.6.489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/04/2016] [Accepted: 07/31/2016] [Indexed: 11/16/2022] Open
Abstract
Objective The aim of this study was to describe the principle of the Cheil HPV DNA Chip assay and evaluate its accuracy. In order to quantify the human papillomavirus (HPV) load and identify HPV genotypes simultaneously, this assay combined the two methods: SYBR Green quantitative real-time polymerase chain reaction (PCR) and DNA microarray. Methods We designed novel consensus primer sets that target the conserved region of the HPV L1 gene for quantifying and detecting a broad range of HPV types by quantitative real-time PCR. Subsequently, using the PCR products, DNA microarray was performed with 36 HPV type-specific probes. To validate this method, direct sequencing and correlation analysis among HPV genotype, viral load, and cytological abnormality was performed by Cohen’s kappa values, two-sided McNemar chi-square test, Kruskal-Wallis test, and odds ratios. Results The kappa value of the Cheil HPV DNA Chip was 0.963 (95% confidence interval, 0.919 to 0.98), which was significantly higher than the value of 0.527 (95% confidence interval, 0.447 to 0.59) obtained using a conventional HPV DNA Chip. HPV16 (χ2=62.28, P<0.01), HPV33 (χ2=7.18, P<0.01), and HPV58 (χ2=9.52, P<0.01), which are classified as high-risk HPVs, were detected at significant levels in samples with high-grade lesions. And viral loads tended to be higher in groups with high odds ratios. Conclusion The Cheil HPV DNA Chip is an effective diagnostic assay for simultaneously detecting HPV genotypes and loads in cervical samples.
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11
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APOBEC3A associates with human papillomavirus genome integration in oropharyngeal cancers. Oncogene 2016; 36:1687-1697. [PMID: 27694899 DOI: 10.1038/onc.2016.335] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 07/27/2016] [Accepted: 08/02/2016] [Indexed: 12/27/2022]
Abstract
The prevalence of human papillomavirus (HPV)-related oropharyngeal cancers has been increasing in developed countries. We recently demonstrated that members of the apolipoprotein B mRNA-editing catalytic polypeptide 3 (APOBEC3, A3) family, which are antiviral factors, can induce hypermutation of HPV DNA in vitro. In the present study, we found numerous C-to-T and G-to-A hypermutations in the HPV16 genome in oropharyngeal cancer (OPC) biopsy samples using differential DNA denaturation PCR and next-generation sequencing. A3s were more abundantly expressed in HPV16-positive OPCs than in HPV-negative, as assessed using immunohistochemistry and reverse transcription quantitative PCR. In addition, interferons upregulated A3s in an HPV16-positive OPC cell line. Furthermore, quantitative PCR analysis of HPV DNA suggests that APOBEC3A (A3A) expression is strongly correlated with the integration of HPV DNA. These results suggest that HPV16 infection may upregulate A3A expression, thereby increasing the chance of viral DNA integration. The role of A3A in HPV-induced carcinogenesis is discussed.
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12
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Sannigrahi MK, Singh V, Sharma R, Panda NK, Radotra BD, Khullar M. Detection of active human papilloma virus-16 in head and neck cancers of Asian North Indian patients. Oral Dis 2015; 22:62-8. [DOI: 10.1111/odi.12382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/01/2015] [Accepted: 10/06/2015] [Indexed: 12/17/2022]
Affiliation(s)
- MK Sannigrahi
- Department of Otolaryngology; Post Graduate Institute of Medical Education and Research (PGIMER); Chandigarh India
| | - V Singh
- Department of Otolaryngology; Post Graduate Institute of Medical Education and Research (PGIMER); Chandigarh India
| | - R Sharma
- Department of Experimental Medicine and Biotechnology; PGIMER; Chandigarh India
| | - NK Panda
- Department of Otolaryngology; Post Graduate Institute of Medical Education and Research (PGIMER); Chandigarh India
| | - BD Radotra
- Department of Histopathology; PGIMER; Chandigarh India
| | - M Khullar
- Department of Experimental Medicine and Biotechnology; PGIMER; Chandigarh India
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13
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Jackson R, Togtema M, Lambert PF, Zehbe I. Tumourigenesis driven by the human papillomavirus type 16 Asian-American e6 variant in a three-dimensional keratinocyte model. PLoS One 2014; 9:e101540. [PMID: 24983759 PMCID: PMC4077794 DOI: 10.1371/journal.pone.0101540] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/30/2014] [Indexed: 12/22/2022] Open
Abstract
Infection with a transforming human papillomavirus (HPV) such as type 16 (of species Alphapapillomavirus 9) causes ano-genital and oral tumours via viral persistence in human squamous cell epithelia. Epidemiological studies showed that the naturally occurring HPV16 Asian-American (AA) variant (sublineage D2/D3) is found more often than the European Prototype (EP) (sublineage A1) in high-grade cervical neoplasia and tumours compared to non-cancer controls. Just three amino acid changes within the early gene, E6, of HPV16 AA have been linked to this augmented tumourigenicity. The AAE6 variant's greater immortalizing and transforming potential over EPE6 has recently been confirmed in retrovirally-transduced keratinocytes expressing the E6 gene only. However, the tumourigenic role of the full-length viral genome of HPV16 has not yet been addressed with regard to these E6 variants. To investigate this process in the context of these two HPV16 E6 genotypes, an organotypic tissue culture model was used to simulate the HPV infectious life cycle. The AAE6 variant demonstrated an enhanced ability over EPE6 to drive the viral life cycle toward tumourigenesis, as evidenced phenotypically—by a more severe grade of epithelial dysplasia with higher proliferation and deregulated differentiation, and molecularly—by high viral oncogene E6 and E7 expression, but lack of productive viral life cycle markers. In contrast, EPE6 had low E6 and E7 but high E1∧E4 expression, indicative of a productive life cycle. We suggest increased viral integration into the host genome for AAE6 as one possible mechanism for these observed differences from EPE6. Additionally, we found downstream effects on immortalization and host innate immune evasion. This study highlights how minor genomic variations in transforming viruses can have a significant affect on their tumourigenic ability.
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Affiliation(s)
- Robert Jackson
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Melissa Togtema
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Ingeborg Zehbe
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
- * E-mail:
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Bryant D, Onions T, Raybould R, Flynn Á, Tristram A, Meyrick S, Giles P, Ashelford K, Hibbitts S, Fiander A, Powell N. mRNA sequencing of novel cell lines from human papillomavirus type-16 related vulval intraepithelial neoplasia: consequences of expression of HPV16 E4 and E5. J Med Virol 2014; 86:1534-41. [PMID: 24898764 DOI: 10.1002/jmv.23994] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2014] [Indexed: 11/11/2022]
Abstract
Vulval intraepithelial neoplasia is a precursor of vulval cancer and is commonly caused by infection with Human Papillomavirus (HPV). Development of topical treatments for vulval intraepithelial neoplasia requires appropriate in vitro models. This study evaluated the feasibility of primary culture of vulval intraepithelial neoplasia biopsy tissue to produce cell lines for use as in vitro models. A potentially immortal cell line was produced which gave rise to three monoclonal lines. These lines were characterized for HPV genomic integration and for viral gene expression using ligation-mediated PCR and quantitative PCR. Distinct patterns of viral integration and gene expression were observed among the three lines. Integration and expression data were validated using deep sequencing of mRNA. Gene ontology analyses of these data also demonstrated that expression of the HPV16 E4 and E5 proteins resulted in substantial changes in the composition of the cell membrane and extracellular space, associated with alterations in cell adhesion and differentiation. These data illustrate the diverse patterns of HPV gene expression potentially present within a single lesion. The derived cell lines provide useful models to investigate the biology of vulval intraepithelial neoplasia and the interactions between different HPV gene products and potential therapeutic agents.
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Affiliation(s)
- Dean Bryant
- HPV Research Group, School of Medicine, Cardiff University, Wales, United Kingdom
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15
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Jackson R, Togtema M, Zehbe I. Subcellular localization and quantitation of the human papillomavirus type 16 E6 oncoprotein through immunocytochemistry detection. Virology 2013; 435:425-32. [DOI: 10.1016/j.virol.2012.09.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/11/2012] [Accepted: 09/26/2012] [Indexed: 11/28/2022]
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16
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Abreu ALP, Souza RP, Gimenes F, Consolaro MEL. A review of methods for detect human Papillomavirus infection. Virol J 2012; 9:262. [PMID: 23131123 PMCID: PMC3507852 DOI: 10.1186/1743-422x-9-262] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 11/02/2012] [Indexed: 02/07/2023] Open
Abstract
Human Papillomavirus (HPV) is the most common sexually transmitted virus. Worldwide, the most common high-risk (HR)-HPV are -16/18, and approximately 70% of cervical cancers (CC) are due to infection by these genotypes. Persistent infection by HR-HPV is a necessary but not sufficient cause of this cancer, which develops over a long period through precursor lesions, which can be detected by cytological screening. Although this screening has decreased the incidence of CC, HPV-related cervical disease, including premalignant and malignant lesions, continues to be a major burden on health-care systems. Although not completely elucidated, the HPV-driven molecular mechanisms underlying the development of cervical lesions have provided a number of potential biomarkers for both diagnostic and prognostic use in the clinical management of women with HPV-related cervical disease, and these biomarkers can also be used to increase the positive predictive value of current screening methods. In addition, they can provide insights into the biology of HPV-induced cancer and thus lead to the development of nonsurgical therapies. Considering the importance of detecting HPV and related biomarkers, a variety of methods are being developed for these purposes. This review summarizes current knowledge of detection methods for HPV, and related biomarkers that can be used to discriminate lesions with a high risk of progression to CC.
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Affiliation(s)
- André L P Abreu
- Division of Clinical Cytology, Department of Clinical Analysis and Biomedicine, State University of Maringá, Av, Colombo 5790, 87020-900, Paraná, Brazil
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De Marco F, Bucaj E, Foppoli C, Fiorini A, Blarzino C, Filipi K, Giorgi A, Schininà ME, Di Domenico F, Coccia R, Butterfield DA, Perluigi M. Oxidative stress in HPV-driven viral carcinogenesis: redox proteomics analysis of HPV-16 dysplastic and neoplastic tissues. PLoS One 2012; 7:e34366. [PMID: 22470562 PMCID: PMC3314612 DOI: 10.1371/journal.pone.0034366] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 02/27/2012] [Indexed: 11/18/2022] Open
Abstract
Genital infection by high risk Human Papillomavirus (HR-HPV), although recognized as the main etio-pathogenetic factor of cervical cancer, is not per se sufficient to induce tumour development. Oxidative stress (OS) represents an interesting and under-explored candidate as a promoting factor in HPV-initiated carcinogenesis. To gain insight into the role of OS in cervical cancer, HPV-16 positive tissues were collected from patients with invasive squamous cervical carcinoma, from patients with High Grade dysplastic HPV lesions and from patients with no clinical evidence of HPV lesions. After virological characterization, modulation of proteins involved in the redox status regulation was investigated. ERp57 and GST were sharply elevated in dysplastic and neoplastic tissues. TrxR2 peaked in dysplastic samples while iNOS was progressively reduced in dysplastic and neoplastic samples. By redox proteomic approach, five proteins were found to have increased levels of carbonyls in dysplastic samples respect to controls namely: cytokeratin 6, actin, cornulin, retinal dehydrogenase and GAPDH. In carcinoma samples the peptidyl-prolyl cis-trans isomerase A, ERp57, serpin B3, Annexin 2 and GAPDH were found less oxidized than in dysplastic tissues. HPV16 neoplastic progression seems associated with increased oxidant environment. In dysplastic tissues the oxidative modification of DNA and proteins involved in cell morphogenesis and terminal differentiation may provide the conditions for the neoplastic progression. Conversely cancer tissues seem to attain an improved control on oxidative damage as shown by the selective reduction of carbonyl adducts on key detoxifying/pro-survival proteins.
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Affiliation(s)
- Federico De Marco
- Laboratory of Virology. The Regina Elena Cancer Institute, Rome, Italy
| | - Elona Bucaj
- Laboratory of Virology. The Regina Elena Cancer Institute, Rome, Italy
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Cesira Foppoli
- CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | - Ada Fiorini
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Carla Blarzino
- Laboratory of Virology. The Regina Elena Cancer Institute, Rome, Italy
| | - Kozeta Filipi
- Cancer Unit - Department of Epidemiology, Institute of Public Health, Tirana, Albania
| | - Alessandra Giorgi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Fabio Di Domenico
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Raffaella Coccia
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - D. Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marzia Perluigi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- * E-mail:
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Schache AG, Liloglou T, Risk JM, Filia A, Jones TM, Sheard J, Woolgar JA, Helliwell TR, Triantafyllou A, Robinson M, Sloan P, Harvey-Woodworth C, Sisson D, Shaw RJ. Evaluation of human papilloma virus diagnostic testing in oropharyngeal squamous cell carcinoma: sensitivity, specificity, and prognostic discrimination. Clin Cancer Res 2011; 17:6262-71. [PMID: 21969383 PMCID: PMC3188400 DOI: 10.1158/1078-0432.ccr-11-0388] [Citation(s) in RCA: 266] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
PURPOSE Human papillomavirus-16 (HPV16) is the causative agent in a biologically distinct subset of oropharyngeal squamous cell carcinoma (OPSCC) with highly favorable prognosis. In clinical trials, HPV16 status is an essential inclusion or stratification parameter, highlighting the importance of accurate testing. EXPERIMENTAL DESIGN Fixed and fresh-frozen tissue from 108 OPSCC cases were subject to eight possible assay/assay combinations: p16 immunohistochemistry (p16 IHC); in situ hybridization for high-risk HPV (HR HPV ISH); quantitative PCR (qPCR) for both viral E6 RNA (RNA qPCR) and DNA (DNA qPCR); and combinations of the above. RESULTS HPV16-positive OPSCC presented in younger patients (mean 7.5 years younger, P = 0.003) who smoked less than HPV-negative patients (P = 0.007). The proportion of HPV16-positive cases increased from 15% to 57% (P = 0.001) between 1988 and 2009. A combination of p16 IHC/DNA qPCR showed acceptable sensitivity (97%) and specificity (94%) compared with the RNA qPCR "gold standard", as well as being the best discriminator of favorable outcome (overall survival P = 0.002). p16 IHC/HR HPV ISH also had acceptable specificity (90%) but the substantial reduction in its sensitivity (88%) impacted upon its prognostic value (P = 0.02). p16 IHC, HR HPV ISH, or DNA qPCR was not sufficiently specific to recommend in clinical trials when used in isolation. CONCLUSIONS Caution must be exercised in applying HPV16 diagnostic tests because of significant disparities in accuracy and prognostic value in previously published techniques.
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Affiliation(s)
- Andrew G Schache
- Department of Molecular & Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
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Specific magnetic isolation for direct detection of HPV16. Eur J Clin Microbiol Infect Dis 2011; 31:539-46. [DOI: 10.1007/s10096-011-1345-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022]
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20
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Détection et quantification des infections génitales à papillomavirus humains : conséquences virologiques, épidémiologiques et cliniques. Med Mal Infect 2011; 41:68-79. [DOI: 10.1016/j.medmal.2010.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 05/16/2010] [Accepted: 07/26/2010] [Indexed: 12/24/2022]
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21
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Vidal RO, Mondego JMC, Pot D, Ambrósio AB, Andrade AC, Pereira LFP, Colombo CA, Vieira LGE, Carazzolle MF, Pereira GAG. A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica. PLANT PHYSIOLOGY 2010; 154:1053-66. [PMID: 20864545 PMCID: PMC2971587 DOI: 10.1104/pp.110.162438] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed.
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Theelen W, Speel EJM, Herfs M, Reijans M, Simons G, Meulemans EV, Baldewijns MM, Ramaekers FCS, Somja J, Delvenne P, Hopman AHN. Increase in viral load, viral integration, and gain of telomerase genes during uterine cervical carcinogenesis can be simultaneously assessed by the HPV 16/18 MLPA-assay. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 177:2022-33. [PMID: 20813962 DOI: 10.2353/ajpath.2010.090901] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Oncogenic human papillomavirus (HPV) infection is the most important risk factor in cervical carcinogenesis cases; high viral loads, viral integration into the host genome, and gain of the telomerase-related genes, TERT and TERC, are all factors associated with progression to cancer. A recently developed multiparameter HPV 16/18 multiplex ligation-dependent probe amplification (MLPA) assay, which allows the simultaneous assessment of these factors, was applied to a series of 67 normal and (pre)malignant frozen uterine cervical samples, as well as to 91 cytological preparations, to test the ability of the MLPA assay to identify high-risk lesions on the basis of these factors. Validation was performed using quantitative PCR, the PapilloCheck and fluorescence in situ hybridization. Only 5 out of 37 normal tissue samples or low-grade cervical lesions (ie, CIN1 and condyloma) showed either an HPV16 viral load higher than 25 copies per cell, viral integration, and/or gain of one of the telomerase-related genes, whereas for the high-grade cervical lesions, one or more of these risk factors was found in 25 of 30 cases. The HPV MLPA assay showed a sensitivity of 83% and a specificity of 86% in frozen cervical specimens. Furthermore, the feasibility of the MLPA assay was shown for cytological samples, where in 57% of high-grade squamous intraepithelial lesion cases, the high-risk factors were detected using this assay.
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Affiliation(s)
- Wendy Theelen
- Departments of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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Das D, Bhattacharjee B, Sen S, Mukhopadhyay I, Sengupta S. Association of viral load with HPV16 positive cervical cancer pathogenesis: causal relevance in isolates harboring intact viral E2 gene. Virology 2010; 402:197-202. [PMID: 20394955 DOI: 10.1016/j.virol.2010.03.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 02/03/2010] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
Abstract
We tested the hypothesis that cervical cancers (CaCx) harbor high HPV16 viral load compared to controls and this is influenced by E2 status and age of subjects. Viral load (natural log transformed values) per 100ng genomic DNA was estimated (152 cases and 87 controls) by Taqman assay. Median viral load was significantly higher (Mann-Whitney U test) among cases (17.21) compared to controls (9.86), irrespective of E2 status or upon considering E2 status as a covariate in logistic regression model (p<0.001). Viral load of E2 intact cases (17.80) was significantly higher (p<0.001) compared to those with disrupted E2 (9.78). At equivalent probability of being a case, viral load was higher among individuals (i) of lower age, irrespective of E2 status, and (ii) with intact E2 but of similar age as those with disrupted E2. Thus viral load in association with E2 status and/or age might be of causal relevance in CaCx pathogenesis.
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Affiliation(s)
- Damayanti Das
- Human Genetics Unit, Indian Statistical Institute, 203, B.T. Road, Kolkata 700108, India
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Theelen W, Reijans M, Simons G, Ramaekers FCS, Speel EJM, Hopman AHN. A new multiparameter assay to assess HPV 16/18, viral load and physical status together with gain of telomerase genes in HPV-related cancers. Int J Cancer 2010; 126:959-75. [PMID: 19711394 DOI: 10.1002/ijc.24844] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oncogenic human papillomavirus (HPV) is the most important risk factor for cancer of the uterine cervix and a subgroup of head and neck cancers. Viral load has been associated with persistence of infection, whereas integration of HPV into the host cell genome is associated with transition to invasive disease. Viral integration is frequently correlated with loss of viral E2 and gain of the telomerase-related genes TERC and TERT. The objective of this study was to develop a rapid and sensitive multiplex ligation-dependent probe amplification (MLPA) assay for the simultaneous analysis of viral load, integration and copy number gain of TERC and TERT in HPV16/18-associated lesions. The performance of the assay was tested for HPV vs. human gene copy number ratios ranging from 0.1 to 100 and for percentages of integration ranging from 0 to 100%. The model systems used include plasmid mixtures and the HPV-positive cell lines SiHa, HeLa and CaSki described to contain a range of 2-600 viral copies per cell. In samples with low-viral load, viral integration can be reliably determined when more than 30% of the virus is integrated. Gain of the telomerase-related genes in the cell lines as determined by our MLPA assay was in accordance with data reported in the literature. Our study demonstrates that within a single MLPA-reaction viral type, load, integration and gain of TERC and TERT can be reliably determined, which will improve risk assessment for patients suspected for HPV infection.
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Affiliation(s)
- Wendy Theelen
- Department of Molecular Cell Biology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, The Netherlands.
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