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Gallardo-Gómez M, Rodríguez-Girondo M, Planell N, Moran S, Bujanda L, Etxart A, Castells A, Balaguer F, Jover R, Esteller M, Cubiella J, Gómez-Cabrero D, De Chiara L. Serum methylation of GALNT9, UPF3A, WARS, and LDB2 as noninvasive biomarkers for the early detection of colorectal cancer and advanced adenomas. Clin Epigenetics 2023; 15:157. [PMID: 37794510 PMCID: PMC10552320 DOI: 10.1186/s13148-023-01570-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Early detection has proven to be the most effective strategy to reduce the incidence and mortality of colorectal cancer (CRC). Nevertheless, most current screening programs suffer from low participation rates. A blood test may improve both the adherence to screening and the selection to colonoscopy. In this study, we conducted a serum-based discovery and validation of cfDNA methylation biomarkers for CRC screening in a multicenter cohort of 433 serum samples including healthy controls, benign pathologies, advanced adenomas (AA), and CRC. RESULTS First, we performed an epigenome-wide methylation analysis with the MethylationEPIC array using a sample pooling approach, followed by a robust prioritization of candidate biomarkers for the detection of advanced neoplasia (AN: AA and CRC). Then, candidate biomarkers were validated by pyrosequencing in independent individual cfDNA samples. We report GALNT9, UPF3A, WARS, and LDB2 as new noninvasive biomarkers for the early detection of AN. The combination of GALNT9/UPF3A by logistic regression discriminated AN with 78.8% sensitivity and 100% specificity, outperforming the commonly used fecal immunochemical test and the methylated SEPT9 blood test. CONCLUSIONS Overall, this study highlights the utility of cfDNA methylation for CRC screening. Our results suggest that the combination methylated GALNT9/UPF3A has the potential to serve as a highly specific and sensitive blood-based test for screening and early detection of CRC.
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Affiliation(s)
- María Gallardo-Gómez
- CINBIO, Universidade de Vigo, Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, CINBIO, Universidade de Vigo, Campus As Lagoas-Marcosende s/n. 36310, Vigo, Spain
- Translational Oncology Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Mar Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Núria Planell
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de La Granvia, 199. 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Ane Etxart
- Department of Surgery, Hospital Universitario Donostia, San Sebastián, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Rodrigo Jover
- Department of Gastroenterology, Hospital General Universitario de Alicante, Alicante, Spain
- Servicio de Medicina Digestiva. ISABIAL. Universidad Miguel Hernández, Hospital General Universitario Dr. Balmis, Alicante, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Joaquín Cubiella
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Biomédica Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - David Gómez-Cabrero
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
- Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
- Mucosal & Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK
| | - Loretta De Chiara
- CINBIO, Universidade de Vigo, Vigo, Spain.
- Department of Biochemistry, Genetics and Immunology, CINBIO, Universidade de Vigo, Campus As Lagoas-Marcosende s/n. 36310, Vigo, Spain.
- Translational Oncology Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
- Cancer Genomics Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
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Goyal R, Wassie MM, Winter JM, Lathlean TJ, Young GP, Symonds EL. Progress in the field of noninvasive diagnostics for colorectal cancer: a systematic review for the accuracy of blood-based biomarkers for detection of advanced pre-cancerous lesions. Expert Rev Mol Diagn 2023; 23:1233-1250. [PMID: 38044883 DOI: 10.1080/14737159.2023.2290646] [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: 05/23/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND Early detection of pre-cancerous adenomas through screening can reduce colorectal cancer (CRC) incidence. Fecal immunochemical tests are commonly used, but have limited sensitivity for pre-cancerous lesions. Blood-based screening may improve test sensitivity. This systematic review and meta-analysis was conducted to evaluate the accuracy of blood-based biomarkers for detection of advanced pre-cancerous lesions. RESEARCH DESIGN AND METHODS We present the accuracy of blood-based biomarkers for the detection of advanced pre-cancerous lesions. EMBASE, Web of Science and PubMed databases were searched, with study populations limited to adults diagnosed with advanced pre-cancerous lesions at colonoscopy, who had a blood-based biomarker test analyzed with reports of sensitivity and specificity. RESULTS 69 studies were identified, which assessed 133 unique biomarkers sets. The best performing test was a panel of 6 miRNAs, with a sensitivity of 95% and specificity of 90% for advanced pre-cancerous lesions. Only 6 biomarkers demonstrated sensitivity ≥ 50% and specificity ≥ 90% for the detection of advanced pre-cancerous lesions. CONCLUSION Many different blood-based biomarkers have been assessed for detection of advanced pre-cancerous lesions, but few have progressed beyond the discovery stage. While some biomarkers have reported high sensitivity and specificity, larger prospective studies in unbiased intended-use screening populations are required for validation.
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Affiliation(s)
- Rishabh Goyal
- Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Molla M Wassie
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - Jean M Winter
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - Timothy Jh Lathlean
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- ROSA Research Centre, South Australian Health and Medical Research Institue, Adelaide, Australia
| | - Graeme P Young
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - Erin L Symonds
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- Gastroenterology Department, Flinders Medical Centre, Bedford Park, Australia
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Using Circulating Tumor DNA as a Novel Biomarker to Screen and Diagnose Colorectal Cancer: A Meta-Analysis. J Clin Med 2023; 12:jcm12020408. [PMID: 36675337 PMCID: PMC9860998 DOI: 10.3390/jcm12020408] [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: 11/21/2022] [Revised: 12/27/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
(1) Background: Circulating tumor DNA (ctDNA) has emerged as a promising biomarker for many kinds of tumors. However, whether ctDNA could be an accurate diagnostic biomarker in colorectal cancer (CRC) remains to be clarified. The aim of this study was to evaluate the diagnostic accuracy of ctDNA in CRC. (2) Methods: PubMed, Web of Science, and Cochrane databases were searched to identify studies reporting the use of ctDNA to screen and diagnose CRC, and all relevant studies published until October 2022 were enrolled for our analysis. These studies were divided into three primer subgroups: the subgroup of quantitative or qualitative analysis of ctDNA and the subgroup of septin9 (SEPT9) methylation assay. (3) Results: A total of 79 qualified articles with 25,240 subjects were incorporated into our meta-analysis. For quantitative studies, the combined sensitivity (SEN), specificity (SPE), and diagnostic odds ratio (DOR) were 0.723 (95% CI: 0.623-0.803), 0.920 (95% CI: 0.827-0.966), and 23.305 (95% CI: 9.378-57.906), respectively, yielding an AUC of 0.860. The corresponding values for qualitative studies were 0.610 (95% CI: 0.566-0.651), 0.891 (95% CI: 0.878-0.909), 12.569 (95% CI: 9.969-15.848), and 0.823, respectively. Detection of SEPT9 methylation depicted an AUC of 0.879, with an SEN of 0.679 (95% CI: 0.622-0.732), an SPE of 0.903 (95% CI: 0.878-0.923), and a DOR of 20.121 (95% CI:14.404-28.106), respectively. (4) Conclusion: Blood-based ctDNA assay would be a potential novel biomarker for CRC screening and diagnosis. Specifically, quantitative analysis of ctDNA or qualitative analysis of SEPT9 methylation exhibited satisfying diagnostic efficiency. Larger sample studies are needed to further confirm our conclusions and to make the ctDNA approach more sensitive and specific.
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Li J, Li H, Run ZC, Wang ZL, Jiang T, An Y, Li Z. RASSF1A methylation as a biomarker for detection of colorectal cancer and hepatocellular carcinoma. World J Gastrointest Oncol 2022; 14:1574-1584. [PMID: 36160746 PMCID: PMC9412931 DOI: 10.4251/wjgo.v14.i8.1574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/02/2022] [Accepted: 07/22/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Studies have validated the potential of methylated cell-free DNA as a biomarker in various tumors, and methylated DNA in plasma may be a potential biomarker for cancer.
AIM To evaluate the diagnostic value of RASSF1A methylation in plasma for colorectal cancer (CRC) and hepatocellular carcinoma (HCC).
METHODS A total of 92 CRC patients, 67 colorectal polyp (CRP) patients, 63 HCC patients, and 66 liver cirrhosis (LC) patients were enrolled. The plasma DNA was subjected to DNA extraction, double-strand DNA concentration determination, bisulfite conversion, purification, single-strand DNA concentration determination, and digital polymerase chain reaction (PCR) detection. The methylation rate was calculated. The diagnostic value was evaluated by the area under the curve (AUC).
RESULTS The age and sex in the CRC and CRP groups and the HCC and LC groups were also matched. The DNA methylation rate of RASSF1A in plasma in the CRC group was 2.87 ± 1.80, and that in the CRP group was 1.50 ± 0.64. DNA methylation of RASSF1A in plasma showed a significant difference between the CRC and CRP groups. The AUC of RASSF1A methylation for discriminating the CRC and CRP groups was 0.82 (0.76-0.88). The AUCs of T1, T2, T3 and T4 CRC and CRP were 0.83 (0.72-0.95), 0.87 (0.78-0.95), 0.86 (0.77-0.95), and 0.75 (0.64-0.85), respectively. The DNA methylation rate of RASSF1A in plasma in the HCC group was 4.45 ± 2.93, and that in the LC group was 2.46 ± 2.07. DNA methylation of RASSF1A in plasma for the HCC and LC groups showed a significant difference. The AUC of RASSF1A methylation for discriminating the HCC and LC groups was 0.70 (0.60-0.79). The AUCs of T1, T2, T3 and T4 HCC and LC were 0.80 (0.61, 1.00), 0.74 (0.59-0.88), 0.60 (0.42-0.79), and 0.68 (0.53-0.82), respectively.
CONCLUSION RASSF1A methylation in plasma detected by digital PCR may be a potential biomarker for CRC and HCC.
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Affiliation(s)
- Jian Li
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Huan Li
- Department of Gastroenterology, Sixth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Zeng-Ci Run
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Zhen-Lei Wang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Tao Jiang
- Medicine Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Yang An
- Faculty of Hepato-Pancreato-Biliary Surgery, Sixth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Zhi Li
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
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Anghel SA, Ioniță-Mîndrican CB, Luca I, Pop AL. Promising Epigenetic Biomarkers for the Early Detection of Colorectal Cancer: A Systematic Review. Cancers (Basel) 2021; 13:4965. [PMID: 34638449 PMCID: PMC8508438 DOI: 10.3390/cancers13194965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
In CRC, screening compliance is decreased due to the experienced discomfort associated with colonoscopy, although this method is the gold standard in terms of sensitivity and specificity. Promoter DNA methylation (hypomethylation or hypermethylation) has been linked to all CRC stages. Study objectives: to systematically review the current knowledge on approved biomarkers, reveal new potential ones, and inspect tactics that can improve performance. This research was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines; the risk of bias was evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies criteria (QUADAS-2). The Web of Science® Core Collection, MEDLINE® and Scopus® databases were searched for original articles published in peer-reviewed journals with the specific keywords "colorectal cancer", "early detection", "early-stage colorectal cancer", "epigenetics", "biomarkers", "DNA methylation biomarkers", "stool or blood or tissue or biopsy", "NDRG4", "BMP3", "SEPT9", and "SDC2". Based on eligibility criteria, 74 articles were accepted for analysis. mSDC2 and mSEPT9 were frequently assessed in studies, alone or together as part of the ColoDefense panel test-the latter with the greatest performance. mBMP3 may not be an appropriate marker for detecting CRC. A panel of five methylated binding sites of the CTCF gene holds the promise for early-stage specific detection of CRC. CRC screening compliance and accuracy can be enhanced by employing a stool mt-DNA methylation test.
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Affiliation(s)
- Sorina Andreea Anghel
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Corina-Bianca Ioniță-Mîndrican
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
- Department of Toxicology, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020945 Bucharest, Romania
| | - Ioana Luca
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
| | - Anca Lucia Pop
- Department of Clinical Laboratory, Food Safety, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia Street, 020945 Bucharest, Romania
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Lepore Signorile M, Disciglio V, Di Carlo G, Pisani A, Simone C, Ingravallo G. From Genetics to Histomolecular Characterization: An Insight into Colorectal Carcinogenesis in Lynch Syndrome. Int J Mol Sci 2021; 22:ijms22136767. [PMID: 34201893 PMCID: PMC8268977 DOI: 10.3390/ijms22136767] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Lynch syndrome is a hereditary cancer-predisposing syndrome caused by germline defects in DNA mismatch repair (MMR) genes such as MLH1, MSH2, MSH6, and PMS2. Carriers of pathogenic mutations in these genes have an increased lifetime risk of developing colorectal cancer (CRC) and other malignancies. Despite intensive surveillance, Lynch patients typically develop CRC after 10 years of follow-up, regardless of the screening interval. Recently, three different molecular models of colorectal carcinogenesis were identified in Lynch patients based on when MMR deficiency is acquired. In the first pathway, adenoma formation occurs in an MMR-proficient background, and carcinogenesis is characterized by APC and/or KRAS mutation and IGF2, NEUROG1, CDK2A, and/or CRABP1 hypermethylation. In the second pathway, deficiency in the MMR pathway is an early event arising in macroscopically normal gut surface before adenoma formation. In the third pathway, which is associated with mutations in CTNNB1 and/or TP53, the adenoma step is skipped, with fast and invasive tumor growth occurring in an MMR-deficient context. Here, we describe the association between molecular and histological features in these three routes of colorectal carcinogenesis in Lynch patients. The findings summarized in this review may guide the use of individualized surveillance guidelines based on a patient’s carcinogenesis subtype.
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Affiliation(s)
- Martina Lepore Signorile
- Medical Genetics, National Institute for Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (M.L.S.); (V.D.)
| | - Vittoria Disciglio
- Medical Genetics, National Institute for Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (M.L.S.); (V.D.)
| | - Gabriella Di Carlo
- Department of Emergency and Organ Transplantation, Section of Pathology, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Antonio Pisani
- Gastroenterology and Digestive Endoscopy Unit, National Institute for Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy;
| | - Cristiano Simone
- Medical Genetics, National Institute for Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (M.L.S.); (V.D.)
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari Aldo Moro, 70124 Bari, Italy
- Correspondence: (C.S.); (G.I.)
| | - Giuseppe Ingravallo
- Department of Emergency and Organ Transplantation, Section of Pathology, University of Bari Aldo Moro, 70124 Bari, Italy;
- Correspondence: (C.S.); (G.I.)
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Gallardo-Gómez M, De Chiara L, Álvarez-Chaver P, Cubiella J. Colorectal cancer screening and diagnosis: omics-based technologies for development of a non-invasive blood-based method. Expert Rev Anticancer Ther 2021; 21:723-738. [PMID: 33507120 DOI: 10.1080/14737140.2021.1882858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Colorectal cancer (CRC) is one of the most important health problems in the Western world. In order to reduce the burden of the disease, two strategies are proposed: screening and prompt detection in symptomatic patients. Although diagnosis and prevention are mainly based on colonoscopy, fecal hemoglobin detection has been widely implemented as a noninvasive strategy. Various studies aiming to discover blood-based biomarkers have recently emerged.Areas covered: The burgeoning omics field provides diverse high-throughput approaches for CRC blood-based biomarker discovery. In this review, we appraise the most robust and commonly used technologies within the fields of genomics, transcriptomics, epigenomics, proteomics, and metabolomics, together with their targeted validation approaches. We summarize the transference process from the discovery phase until clinical translation. Finally, we review the best candidate biomarkers and their potential clinical applicability.Expert opinion: Some available biomarkers are promising, especially in the field of epigenomics: DNA methylation and microRNA. Transference requires the joint collaboration of basic researchers, intellectual property experts, technology transfer officers and clinicians. Blood-based biomarkers will be selected not only based on their diagnostic accuracy and cost but also on their reliability, applicability to clinical analysis laboratories and their acceptance by the population.
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Affiliation(s)
- María Gallardo-Gómez
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Loretta De Chiara
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Paula Álvarez-Chaver
- Proteomics Unit, Service of Structural Determination, Proteomics and Genomics, Center for Scientific and Technological Research Support (CACTI), University of Vigo, Vigo, Spain
| | - Joaquin Cubiella
- Department of Gastroenterology, Hospital Universitario De Ourense, Ourense, Spain.,Instituto De Investigación Sanitaria Galicia Sur, Ourense, Spain.,Centro De Investigación Biomédica En Red Enfermedades Hepáticas Y Digestivas, Ourense, Spain
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