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Molina MA, Leenders WPJ, Huynen MA, Melchers WJG, Andralojc KM. Temporal composition of the cervicovaginal microbiome associates with hrHPV infection outcomes in a longitudinal study. BMC Infect Dis 2024; 24:552. [PMID: 38831406 PMCID: PMC11145797 DOI: 10.1186/s12879-024-09455-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Persistent infections with high-risk human papillomavirus (hrHPV) can cause cervical squamous intraepithelial lesions (SIL) that may progress to cancer. The cervicovaginal microbiome (CVM) correlates with SIL, but the temporal composition of the CVM after hrHPV infections has not been fully clarified. METHODS To determine the association between the CVM composition and infection outcome, we applied high-resolution microbiome profiling using the circular probe-based RNA sequencing technology on a longitudinal cohort of cervical smears obtained from 141 hrHPV DNA-positive women with normal cytology at first visit, of whom 51 were diagnosed by cytology with SIL six months later. RESULTS Here we show that women with a microbial community characterized by low diversity and high Lactobacillus crispatus abundance at both visits exhibit low risk to SIL development, while women with a microbial community characterized by high diversity and Lactobacillus depletion at first visit have a higher risk of developing SIL. At the level of individual species, we observed that a high abundance for Gardnerella vaginalis and Atopobium vaginae at both visits associate with SIL outcomes. These species together with Dialister micraerophilus showed a moderate discriminatory power for hrHPV infection progression. CONCLUSIONS Our results suggest that the CVM can potentially be used as a biomarker for cervical disease and SIL development after hrHPV infection diagnosis with implications on cervical cancer prevention strategies and treatment of SIL.
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Affiliation(s)
- Mariano A Molina
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.
| | - Karolina M Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
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Molina MA, Melchers WJ, Andralojc KM, Leenders WP, Huynen MA. Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection. Comput Struct Biotechnol J 2023; 21:4424-4431. [PMID: 37731597 PMCID: PMC10507478 DOI: 10.1016/j.csbj.2023.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease.
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Affiliation(s)
- Mariano A. Molina
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Willem J.G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands
| | - Karolina M. Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands
| | | | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, the Netherlands
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E6/E7 mRNA Expression of the Most Prevalent High-Risk HPV Genotypes in Cervical Samples from Serbian Women. Diagnostics (Basel) 2023; 13:diagnostics13050917. [PMID: 36900061 PMCID: PMC10000477 DOI: 10.3390/diagnostics13050917] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Cervical cancer caused by persistent infection with HR HPV genotypes is the second leading cause of death in women aged 15 to 44 in Serbia. The expression of the E6 and E7 HPV oncogenes is considered as a promising biomarker in diagnosing high-grade squamous intraepithelial lesions (HSIL). This study aimed to evaluate HPV mRNA and DNA tests, compare the results according to the severity of the lesions, and assess the predictive potential for the diagnosis of HSIL. Cervical specimens were obtained at the Department of Gynecology, Community Health Centre Novi Sad, Serbia, and the Oncology Institute of Vojvodina, Serbia, during 2017-2021. The 365 samples were collected using the ThinPrep Pap test. The cytology slides were evaluated according to the Bethesda 2014 System. Using a real-time PCR test, HPV DNA was detected and genotyped, while the RT-PCR proved the presence of E6 and E7 mRNA. The most common genotypes in Serbian women are HPV 16, 31, 33, and 51. Oncogenic activity was demonstrated in 67% of HPV-positive women. A comparison of the HPV DNA and mRNA tests to assess the progression of cervical intraepithelial lesions indicated that higher specificity (89.1%) and positive predictive value (69.8-78.7%) were expressed by the E6/E7 mRNA test, while higher sensitivity was recorded when using the HPV DNA test (67.6-88%). The results determine the higher probability of detecting HPV infection by 7% provided by the mRNA test. The detected E6/E7 mRNA HR HPVs have a predictive potential in assessing the diagnosis of HSIL. The oncogenic activity of HPV 16 and age were the risk factors with the strongest predictive values for the development of HSIL.
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Molina MA, Andralojc KM, Huynen MA, Leenders WPJ, Melchers WJG. In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling. NPJ Biofilms Microbiomes 2022; 8:75. [PMID: 36171433 PMCID: PMC9519886 DOI: 10.1038/s41522-022-00336-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022] Open
Abstract
The cervicovaginal microbiome (CVM) correlates with women's cervical health, and variations in its composition are associated with high-risk human papillomavirus (hrHPV) infection outcomes. Cervicovaginal microbes have been grouped into five community state types (CSTs) based on microbial community composition and abundance. However, studying the impact of CSTs in health and disease is challenging because the current sequencing technologies have limited confident discrimination between closely related and yet functionally different bacterial species. Circular probe-based RNA sequencing (ciRNAseq) achieves high-resolution microbiome profiling and therefore provides in-depth and unambiguous knowledge about the composition of the CVM. Based on ciRNAseq profiling of a large cohort of cervical smears (n = 541), we here define subgroups of CSTs I, III, and IV based on intra-CST differences with respect to abundances of Lactobacillus acidophilus (CSTs I-A vs. I-B and CSTs III-A vs. III-B), Lactobacillus iners (CSTs I-A vs. I-B and CSTs III-A vs. III-B), and Megasphaera genomosp type 1 (CSTs IV-A vs. IV-B). Our results further support the existence of subgroups of CST IV-C that are dominant for non-Lactobacillus species and have intermediate microbial diversity. We also show that CST V is associated with uninfected conditions, and CST IV-A associates with hrHPV-induced cervical disease. In conclusion, we characterized new subdivisions of cervicovaginal CSTs, which may further advance our understanding of women's cervical health and hrHPV-related progression to disease.
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Affiliation(s)
- Mariano A Molina
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Karolina M Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, The Netherlands
| | - William P J Leenders
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, The Netherlands
- Predica Diagnostics, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.
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Prevalence, Diversity, and Risk Factors for Cervical HPV Infection in Women Screened for Cervical Cancer in Belém, Pará, Northern Brazil. Pathogens 2022; 11:pathogens11090960. [PMID: 36145392 PMCID: PMC9506000 DOI: 10.3390/pathogens11090960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Human papillomavirus (HPV) is the most common viral sexually transmitted infection of the reproductive tract, and cervical cancer is the most common HPV-related disease. This study estimated the prevalence, diversity of HPV genotypes, and associated risk factors in women screened for cervical cancer in northern Brazil. Methods: The cross-sectional study was conducted in Belém, Pará, in the Amazon region of Brazil, and it included 162 women who were spontaneously undergoing a Pap-smear routine. Epidemiological, sexual, and health-related information was collected by interviews, and cervical samples were collected for cytological examination and HPV-DNA detection. HPV genotypes were classified as low risk (LR) and high risk (HR) by nucleotide sequencing. Results: In total, 17.3% (28/162) of the participants had HPV-DNA, and LR-HPV was the most prevalent (71.4%). Among the 13 different types of HPV detected, HPV-11 was found most frequently (12/28; 42.9%), followed by HPV-31 (3/28; 10.7%). Of the participants with cytological alterations, HPV infection was detected in only four: two were diagnosed with low-grade squamous intraepithelial lesions (15.4%), one with atypical squamous cells of undetermined significance (7.7%), and one with atypical squamous cells, cannot exclude high-grade squamous intraepithelial lesions (7.7%). Of the 61 women who presented a normal cytology, 13 (21.3%) had positive tests for HPV infection, 4 (8.2%) of which were positive for a high-risk genotype. Conclusion: The prevalence of HPV was high in Belém, Pará, and especially in women who had normal cytology results, which suggests the need for greater screening for HPV infection in women’s primary health care.
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Yang Y, Qing Y, Hao X, Fang C, Ouyang P, Li H, Wang Z, Liao Y, Fang H, Du J. APTES-Modified Remote Self-Assembled DNA-Based Electrochemical Biosensor for Human Papillomavirus DNA Detection. BIOSENSORS 2022; 12:bios12070449. [PMID: 35884252 PMCID: PMC9312881 DOI: 10.3390/bios12070449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022]
Abstract
High-risk human papillomavirus (HPV) infection is an important cause of cervical cancer formation; therefore, being able to detect high-risk HPV (e.g., HPV-16) is important for the early treatment and prevention of cervical cancer. In this study, a combination of a 3-aminopropyltriethoxysilane (APTES) modified gold electrode and a super sandwich structure was creatively developed, resulting in the development of a biosensor that is both sensitive and stable for the detection of HPV-16. The electrochemical biosensor possesses a lower detection limit compared with previous studies with an LOD of 5.475 × 10−16 mol/L and it possesses a wide linear range from 1.0 × 10−13 mol/L to 1.0 × 10−6 mol/L (R2 = 0.9923) for the target DNA. The experimental data show that the sensor has good stability, and there is no significant decrease in the current response value after 7 days in the low-temperature environment. In addition, the sensor proved to be a powerful clinical tool for disease diagnosis because it showed good interference resistance in complex human serum samples.
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Andralojc KM, Elmelik D, Rasing M, Pater B, Siebers AG, Bekkers R, Huynen MA, Bulten J, Loopik D, Melchers WJG, Leenders WPJ. Targeted RNA next generation sequencing analysis of cervical smears can predict the presence of hrHPV-induced cervical lesions. BMC Med 2022; 20:206. [PMID: 35676700 PMCID: PMC9178797 DOI: 10.1186/s12916-022-02386-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Because most cervical cancers are caused by high-risk human papillomaviruses (hrHPVs), cervical cancer prevention programs increasingly employ hrHPV testing as a primary test. The high sensitivity of HPV tests is accompanied by low specificity, resulting in high rates of overdiagnosis and overtreatment. Targeted circular probe-based RNA next generation sequencing (ciRNAseq) allows for the quantitative detection of RNAs of interest with high sequencing depth. Here, we examined the potential of ciRNAseq-testing on cervical scrapes to identify hrHPV-positive women at risk of having or developing high-grade cervical intraepithelial neoplasia (CIN). METHODS We performed ciRNAseq on 610 cervical scrapes from the Dutch cervical cancer screening program to detect gene expression from 15 hrHPV genotypes and from 429 human genes. Differentially expressed hrHPV- and host genes in scrapes from women with outcome "no CIN" or "CIN2+" were identified and a model was built to distinguish these groups. RESULTS Apart from increasing percentages of hrHPV oncogene expression from "no CIN" to high-grade cytology/histology, we identified genes involved in cell cycle regulation, tyrosine kinase signaling pathways, immune suppression, and DNA repair being expressed at significantly higher levels in scrapes with high-grade cytology and histology. Machine learning using random forest on all the expression data resulted in a model that detected 'no CIN' versus CIN2+ in an independent data set with sensitivity and specificity of respectively 85 ± 8% and 72 ± 13%. CONCLUSIONS CiRNAseq on exfoliated cells in cervical scrapes measures hrHPV-(onco)gene expression and host gene expression in one single assay and in the process identifies HPV genotype. By combining these data and applying machine learning protocols, the risk of CIN can be calculated. Because ciRNAseq can be performed in high-throughput, making it cost-effective, it can be a promising screening technology to stratify women at risk of CIN2+. Further increasing specificity by model improvement in larger cohorts is warranted.
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Affiliation(s)
- Karolina M Andralojc
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands.,Department of Medical Microbiology, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Duaa Elmelik
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands
| | - Menno Rasing
- Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands
| | - Bernard Pater
- Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands
| | - Albert G Siebers
- Department of Pathology, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.,PALGA, De Bouw 123, Houten, 3991 SZ, The Netherlands
| | - Ruud Bekkers
- Department of Obstetrics and Gynecology, Catharina Hospital Eindhoven, Michelangelolaan 2, Eindhoven, 5623 EJ, The Netherlands.,GROW, School for Oncology and Reproductive Biology, Maastricht University, Maastricht, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute of Molecular Life Sciences, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Johan Bulten
- Department of Pathology, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Diede Loopik
- Department of Gynecology and Obstetrics, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - William P J Leenders
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands. .,Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands.
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Andralojc KM, Molina MA, Qiu M, Spruijtenburg B, Rasing M, Pater B, Huynen MA, Dutilh BE, Ederveen THA, Elmelik D, Siebers AG, Loopik D, Bekkers RLM, Leenders WPJ, Melchers WJG. Novel high-resolution targeted sequencing of the cervicovaginal microbiome. BMC Biol 2021; 19:267. [PMID: 34915863 PMCID: PMC8680041 DOI: 10.1186/s12915-021-01204-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The cervicovaginal microbiome (CVM) plays a significant role in women's cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. RESULTS We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes' abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. CONCLUSIONS CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions.
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Affiliation(s)
- Karolina M. Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Mariano A. Molina
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mengjie Qiu
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bram Spruijtenburg
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Menno Rasing
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bernard Pater
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bas E. Dutilh
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Duaa Elmelik
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Albert G. Siebers
- Department of Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Diede Loopik
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Ruud L. M. Bekkers
- Department of Obstetrics and Gynecology, Catharina Hospital, 5602 ZA Eindhoven, The Netherlands
- GROW, School for Oncology & Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - William P. J. Leenders
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
- Predica Diagnostics, Toernooiveld 1, 6525 GA Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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Gao J, Wu L, Yang D, Gong W, Wang J. A One-Pot CRISPR/Cas9-Typing PCR for DNA Detection and Genotyping. J Mol Diagn 2021; 23:46-60. [PMID: 33127524 DOI: 10.1016/j.jmoldx.2020.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/05/2020] [Accepted: 10/06/2020] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonuclease Cas9 (Cas9) has high specificity to its target DNA as a gene editing tool. This characteristic makes it useful for DNA detection. Combining the advantages of CRISPR/Cas9 and PCR, this study establishes a novel CRISPR/Cas9-based DNA detection method, named CRISPR/Cas9-typing PCR version 4.0 (ctPCR4.0). This method can detect target DNA in one pot with high specificity and sensitivity. In a homogenous reaction, the target DNA is first cleaved by a pair of Cas9- single-guide RNA complexes and thus releases two single strands with free 3' ends, allowing a pair of oligonucleotides to anneal with the strands. The annealed oligonucleotides provide templates for DNA polymerization from the free 3' ends. A universal primer annealing site is thus produced at the end of two single strands. The target DNA is then amplified by PCR using a universal primer. This method was first verified by accurately detecting the cloned L1 fragments of 10 genotypes of high-risk human papilloma viruses (HPVs). This method was then validated by detecting the L1 fragments of two highest-risk HPVs, HPV 16 and HPV 18, in the genomic DNA of two HPV-positive cervical carcinoma cells, HeLa and SiHa. Finally, this method was further validated by accurately detecting 10 high-risk HPVs in 30 clinical samples.
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Affiliation(s)
- Jinliang Gao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing
| | - Lin Wu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing
| | - Daidi Yang
- Clinical Laboratory, Yixing Tumor Hospital, Yixing, China
| | - Weida Gong
- Clinical Laboratory, Yixing Tumor Hospital, Yixing, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing.
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Molina MA, Carosi Diatricch L, Castany Quintana M, Melchers WJ, Andralojc KM. Cervical cancer risk profiling: molecular biomarkers predicting the outcome of hrHPV infection. Expert Rev Mol Diagn 2020; 20:1099-1120. [PMID: 33044104 DOI: 10.1080/14737159.2020.1835472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Cervical cancer affects half a million women worldwide annually. Given the association between high-risk human papillomavirus (hrHPV) infection and carcinogenesis, hrHPV DNA testing became an essential diagnostic tool. However, hrHPV alone does not cause the disease, and, most importantly, many cervical lesions regress to normal in a year because of the host immune system. Hence, the low specificity of hrHPV DNA tests and their inability to predict the outcome of infections have triggered a further search for biomarkers. AREAS COVERED We evaluated the latest viral and cellular biomarkers validated for clinical use as primary screening or triage for cervical cancer and assessed their promise for prevention as well as potential use in the future. The literature search focused on effective biomarkers for different stages of the disease, aiming to determine their significance in predicting the outcome of hrHPV infections. EXPERT OPINION Biomarkers such as p16/Ki-67, hrHPV genotyping, hrHPV transcriptional status, and methylation patterns have demonstrated promising results. Their eventual implementation in the screening programs may support the prompt diagnosis of hrHPV infection and its progression to cancer. These biomarkers will help in making clinical management decisions on time, thus, saving the lives of hrHPV-infected women, particularly in developing countries.
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Affiliation(s)
- Mariano A Molina
- Department of Microbiology, Faculty of Science, Radboud University , Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | | | - Marina Castany Quintana
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | - Willem Jg Melchers
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | - Karolina M Andralojc
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands.,Department of Biochemistry, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands
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