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Fackler MJ, Pleas M, Li Y, Soni A, Xing D, Cope L, Ali S, Van Le Q, Van Nguyen C, Pham HT, Duong LM, Vanden Berg E, Wadee R, Michelow P, Chen WC, Joffe M, Fjeldbo CS, Lyng H, Sukumar S. Discovery and technical validation of high-performance methylated DNA markers for the detection of cervical lesions at risk of malignant progression in low- and middle-income countries. Clin Epigenetics 2024; 16:56. [PMID: 38643219 PMCID: PMC11032610 DOI: 10.1186/s13148-024-01669-z] [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: 12/08/2023] [Accepted: 04/04/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Cervical cancer remains a leading cause of death, particularly in developing countries. WHO screening guidelines recommend human papilloma virus (HPV) detection as a means to identify women at risk of developing cervical cancer. While HPV testing identifies those at risk, it does not specifically distinguish individuals with neoplasia. We investigated whether a quantitative molecular test that measures methylated DNA markers could identify high-risk lesions in the cervix with accuracy. RESULTS Marker discovery was performed in TCGA-CESC Infinium Methylation 450 K Array database and verified in three other public datasets. The panel was technically validated using Quantitative Multiplex-Methylation-Specific PCR in tissue sections (N = 252) and cervical smears (N = 244) from the USA, South Africa, and Vietnam. The gene panel consisted of FMN2, EDNRB, ZNF671, TBXT, and MOS. Cervical tissue samples from all three countries showed highly significant differential methylation in squamous cell carcinoma (SCC) with a sensitivity of 100% [95% CI 74.12-100.00], and specificity of 91% [95% CI 62.26-99.53] to 96% [95% CI 79.01-99.78], and receiver operating characteristic area under the curve (ROC AUC) = 1.000 [95% CI 1.00-1.00] compared to benign cervical tissue, and cervical intraepithelial neoplasia 2/3 with sensitivity of 55% [95% CI 37.77-70.84] to 89% [95% CI 67.20-98.03], specificity of 93% [95% CI 84.07-97.38] to 96% [95% CI 79.01-99.78], and a ROC AUC ranging from 0.793 [95% CI 0.68-0.89] to 0.99 [95% CI 0.97-1.00] compared to CIN1. In cervical smears, the marker panel detected SCC with a sensitivity of 87% [95% CI 77.45-92.69], specificity 95% [95% CI 88.64-98.18], and ROC AUC = 0.925 [95% CI 0.878-0.974] compared to normal, and high-grade squamous intraepithelial lesion (HSIL) at a sensitivity of 70% (95% CI 58.11-80.44), specificity of 94% (95% CI 88.30-97.40), and ROC AUC = 0.884 (95% CI 0.822-0.945) compared to low-grade intraepithelial lesion (LSIL)/normal in an analysis of pooled data from the three countries. Similar to HPV-positive, HPV-negative cervical carcinomas were frequently hypermethylated for these markers. CONCLUSIONS This 5-marker panel detected SCC and HSIL in cervical smears with a high level of sensitivity and specificity. Molecular tests with the ability to rapidly detect high-risk HSIL will lead to timely treatment for those in need and prevent unnecessary procedures in women with low-risk lesions throughout the world. Validation of these markers in prospectively collected cervical smear cells followed by the development of a hypermethylated marker-based cervical cancer detection test is warranted.
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Affiliation(s)
- Mary Jo Fackler
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Madison Pleas
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Youran Li
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Anushri Soni
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Deyin Xing
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Leslie Cope
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA
| | - Syed Ali
- Division of Cytopathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Quang Van Le
- Hanoi Medical University, National Cancer Hospital, Hanoi, Vietnam
| | - Chu Van Nguyen
- Department of Quansu Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Han Thi Pham
- Department of Quansu Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Long Minh Duong
- Department of Quansu Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Eunice Vanden Berg
- Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand/National Health Laboratory Service, Johannesburg, South Africa
| | - Reubina Wadee
- Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand/National Health Laboratory Service, Johannesburg, South Africa
| | - Pamela Michelow
- Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand/National Health Laboratory Service, Johannesburg, South Africa
| | - Wenlong Carl Chen
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maureen Joffe
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christina Saetan Fjeldbo
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Heidi Lyng
- Department of Radiation Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Physics, University of Oslo, Oslo, Norway
| | - Saraswati Sukumar
- Women's Malignancies Program, Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, Rm 144, CRB1, Baltimore, MD, 21231, USA.
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Loomans-Kropp HA. The utility of liquid biopsy-based methylation biomarkers for colorectal cancer detection. Front Oncol 2024; 14:1351514. [PMID: 38595823 PMCID: PMC11002156 DOI: 10.3389/fonc.2024.1351514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers and the second leading cause of cancer-related deaths in the United States. It is also one of the few cancers with established screening guidelines, however these methods have significant patient burden (e.g., time, invasive). In recent years, the development of liquid biopsy-based screening methods for biomarker detection have emerged as alternatives to traditional screening. Methylation biomarkers are of particular interest, and these markers can be identified and measured on circulating tumor and cell-free DNA. This perspective summarizes the current state of CRC screening and the potential integration of DNA methylation markers into liquid biopsy-based techniques. Finally, I discuss limitations to these methods and strategies for improvement. The continued development and implementation of liquid biopsy-based cancer screening approaches may provide an acceptable alternative to individuals unwilling to be screened by traditional methods.
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Affiliation(s)
- Holli A. Loomans-Kropp
- Cancer Control Program, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
- Division of Cancer Prevention and Control, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, United States
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Botezatu IV, Kondratova VN, Stroganova AM, Dranko SL, Lichtenstein AV. Aberrant methylation scanning by quantitative DNA melting analysis with hybridization probes as exemplified by liquid biopsy of SEPT9 and HIST1H4F in colorectal cancer. Clin Chim Acta 2023; 551:117591. [PMID: 37832390 DOI: 10.1016/j.cca.2023.117591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/05/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
OBJECTIVE The generally accepted method of quantifying hypermethylated DNA by qPCR using methylation-specific primers has the risk of underestimating DNA methylation and requires data normalization. This makes the analysis complicated and less reliable. METHODS The end-point PCR method, called qDMA-HP (for quantitative DNA Melting Analysis with hybridization probes), which excludes the normalization procedure, is multiplexed and quantitative, has been proposed. qDMA-HP is characterized by the following features: (i) asymmetric PCR with methylation-independent primers; (ii) fluorescent dual-labeled, self-quenched probes (commonly known as TaqMan probes) covering several interrogated CpGs; (iii) post-PCR melting analysis of amplicon/probe hybrids; (iv) quantitation of unmethylated and methylated DNA alleles by measuring the areas under the corresponding melt peaks. RESULTS qDMA-HP was tested in liquid biopsy of colorectal cancer by evaluating SEPT9 and HIST1H4F methylations simultaneously in the single-tube reaction. Differences in the methylation levels in healthy donors versus cancer patients were statistically significant (p < 0.0001), AUCROC values were 0.795-0.921 for various marker combinations. CONCLUSIONS This proof-of-concept study shows that qDMA-HP is a simple, normalization-independent, quantitative, multiplex and "closed tube" method easily adapted to clinical settings. It is demonstrated, for the first time, that HIST1H4F is a perspective marker for liquid biopsy of colorectal cancer.
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Affiliation(s)
- Irina V Botezatu
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Valentina N Kondratova
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Anna M Stroganova
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Svetlana L Dranko
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Anatoly V Lichtenstein
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia.
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Dare AJ, Olatoke SA, Okereke CE, Abdulkareem FB, Adeyeye A, Badejo O, Du M, Fayenuwo OJ, Gali BM, Kahn R, Knapp G, Ntiamoah P, Olcese C, Oludara MA, Omisore A, Omoyiola OZ, Owoade IA, Brennan MF, Kingham TP, Alatise OI. The African Research Group for Oncology: A decade fostering colorectal cancer research in Nigeria. J Surg Oncol 2023; 128:1011-1020. [PMID: 37818907 DOI: 10.1002/jso.27444] [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: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 10/13/2023]
Abstract
The African Research Group for Oncology (ARGO) was formed in 2013 to undertake methodologically rigorous cancer research in Nigeria, and to strengthen cancer research capacity in the country through training and mentorship of physicians, scientists, and other healthcare workers. Here, we describe how ARGO's work in colorectal cancer (CRC) has evolved over the past decade. This includes the consortium's scientific contributions to the understanding of CRC in Nigeria and globally and its research capacity-building program.
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Affiliation(s)
- Anna J Dare
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Samuel A Olatoke
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
| | | | - Fatimah B Abdulkareem
- Department of Anatomic and Molecular Pathology, Faculty of Basic Medical Sciences, University of Lagos, Lagos, Nigeria
| | - Ademola Adeyeye
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
| | - Olawale Badejo
- Department of Surgery, National Hospital Abuja, Abuja, Nigeria
| | - Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | | - Bata M Gali
- Department of Surgery, University of Maiduguri, Maiduguri, Nigeria
| | - Rivka Kahn
- Global Cancer Disparities Initiative, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Gregory Knapp
- Department of Surgery, Division of General Surgery, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Peter Ntiamoah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Cristina Olcese
- Global Cancer Disparities Initiative, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Mobolaji A Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos State, Nigeria
| | - Adeleye Omisore
- Department of Radiology, College of Health Sciences, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Oluwatosin Z Omoyiola
- Department of Morbid Anatomy, College of Health Sciences, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Israel A Owoade
- African Research Group for Oncology, Ile Ife, Osun State, Nigeria
| | - Murray F Brennan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - T Peter Kingham
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Olusegun I Alatise
- Department of Surgery, College of Health Sciences, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
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Ye Z, Song G, Liang J, Yi S, Gao Y, Jiang H. Optimized screening of DNA methylation sites combined with gene expression analysis to identify diagnostic markers of colorectal cancer. BMC Cancer 2023; 23:617. [PMID: 37400791 DOI: 10.1186/s12885-023-10922-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/05/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The prognosis of patients with colorectal cancer is related to early detection. However, commonly used screening markers lack sensitivity and specificity. In this study, we identified diagnostic methylation sites for colorectal cancer. METHODS After screening the colorectal cancer methylation dataset, diagnostic sites were identified via survival analysis, difference analysis, and ridge regression dimensionality reduction. The correlation between the selected methylation sites and the estimation of immune cell infiltration was analyzed. The accuracy of the diagnosis was verified using different datasets and the 10-fold crossover method. RESULTS According to Gene Ontology, the main enrichment pathways of genes with hypermethylation sites are axon development, axonogenesis, and pattern specification processes. However, the Kyoto Encyclopedia of Genes and Genomes (KEGG) suggests the following main enrichment pathways: neuroactive ligand-receptor interaction, calcium signaling, and cAMP signaling. In The Cancer Genome Atlas (TCGA) and GSE131013 datasets, the area under the curve of cg07628404 was > 0.95. For the NaiveBayes machine model of cg02604524, cg07628404, and cg27364741, the accuracies of 10-fold cross-validation in the GSE131013 and TCGA datasets were 95% and 99.4%, respectively. The survival prognosis of the hypomethylated group (cg02604524, cg07628404, and cg27364741) was better than that of the hypermethylated group. The mutation risk did not differ between the hypermethylated and hypomethylated groups. The correlation coefficient between the three loci and CD4 central memory T cells, hematological stem cells, and other immune cells was not high (p < 0.05). CONCLUSION In cases of colorectal cancer, the main enrichment pathway of genes with hypermethylated sites was axon and nerve development. In the biopsy tissues, the hypermethylation sites were diagnostic for colorectal cancer, and the NaiveBayes machine model of the three loci showed good diagnostic performance. Site (cg02604524, cg07628404, and cg27364741) hypermethylation predicts poor survival for colorectal cancer. Three methylation sites were weakly correlated with individual immune cell infiltration. Hypermethylation sites may be a useful repository for diagnosing colorectal cancer.
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Affiliation(s)
- Zhen Ye
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China
| | - Guangle Song
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China
| | - Jianwei Liang
- Department of General Surgery, Tai'an City Center Hospital, Taian, 271000, Shandong, China
| | - Shuying Yi
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China
| | - Yuqi Gao
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China.
| | - Hanming Jiang
- Department of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China.
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Fatemi N, Tierling S, Es HA, Varkiani M, Nazemalhosseini Mojarad E, Asadzadeh Aghdaei H, Walter J, Totonchi M. DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine. Int J Cancer 2022; 151:2068-2081. [PMID: 35730647 DOI: 10.1002/ijc.34186] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death worldwide that is attributed to gradual long-term accumulation of both genetic and epigenetic changes. To reduce the mortality rate of CRC and to improve treatment efficacy, it will be important to develop accurate noninvasive diagnostic tests for screening, acute, and personalized diagnosis. Epigenetic changes such as DNA methylation play an important role in the development and progression of CRC. Over the last decade, a panel of DNA methylation markers has been reported showing a high accuracy and reproducibility in various semi-invasive or noninvasive biosamples. Research to obtain comprehensive panels of markers allowing a highly sensitive and differentiating diagnosis of CRC is ongoing. Moreover, the epigenetic alterations for cancer therapy, as a precision medicine strategy will increase their therapeutic potential over time. Here, we discuss the current state of DNA methylation-based biomarkers and their impact on CRC diagnosis. We emphasize the need to further identify and stratify methylation-biomarkers and to develop robust and effective detection methods that are applicable for a routine clinical setting of CRC diagnostics particularly at the early stage of the disease.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sascha Tierling
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | | | - Maryam Varkiani
- Department of Molecular Genetics, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jörn Walter
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | - Mehdi Totonchi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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