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Shirley M. Epi proColon ® for Colorectal Cancer Screening: A Profile of Its Use in the USA. Mol Diagn Ther 2021; 24:497-503. [PMID: 32557236 DOI: 10.1007/s40291-020-00473-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epi proColon® is a blood-based colorectal cancer (CRC) screening test that presents a convenient, non-invasive option for CRC screening in average-risk adults aged ≥ 50 years who are otherwise non-compliant to guideline-recommended screening programs. The Epi proColon test involves the use of a real-time PCR assay to detect methylated Sept9 DNA (a biomarker for CRC) in plasma derived from a whole blood sample. Epi proColon generally performed well in prospective clinical trials, having non-inferior sensitivity for detecting CRC compared with a fecal immunochemical test (FIT). Microsimulation modeling supports annual Epi proColon testing, as for FIT. Although the Epi proColon test specificity is lower than that of a FIT, the Epi proColon test may be useful for improving participation and compliance in CRC screening, as evidenced in a small randomized controlled clinical trial which showed that uptake of an offer of an Epi proColon blood test was significantly higher than that for a FIT in subjects who were overdue for CRC screening.
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Affiliation(s)
- Matt Shirley
- Springer Nature, Mairangi Bay, Private Bag 65901, Auckland, 0754, New Zealand.
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Wang X, Zhou S, Chu C, Yang M, Huo D, Hou C. Dual Methylation-Sensitive Restriction Endonucleases Coupling with an RPA-Assisted CRISPR/Cas13a System (DESCS) for Highly Sensitive Analysis of DNA Methylation and Its Application for Point-of-Care Detection. ACS Sens 2021; 6:2419-2428. [PMID: 34019391 DOI: 10.1021/acssensors.1c00674] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-performance detection of DNA methylation possesses great significance for the diagnosis and therapy of cancer. Herein, for the first time, we present a digestion strategy based on dual methylation-sensitive restriction endonucleases coupling with a recombinase polymerase amplification (RPA)-assisted CRISPR/Cas13a system (DESCS) for accurate and sensitive determination of site-specific DNA methylation. This dual methylation-sensitive restriction endonuclease system selectively digests the unmethylated target but exhibits no response to methylated DNA. Therefore, the intact methylated DNA target triggers the RPA reaction for rapid signal amplification. In contrast, the digested unmethylated target initiates no RPA reaction. RPA products with a T7 promoter can execute the T7 transcription in the presence of T7 RNA polymerase to generate a large number of single-stranded RNA (ssRNA). This ssRNA can be recognized by CRISPR/Cas13a to induce the ssRNase activity of Cas13a, showing the indiscriminate cleavage of the collateral FQ reporter to release the fluorescence signal. With such a design, by combining the unique features of dual methylation-sensitive restriction endonucleases with RPA-assisted CRISPR/Cas13a, the DESCS system not only presents the rapid and powerful signal amplification for the determination of methylated DNA with ultrahigh sensitivity but also effectively eliminates the false positive influences from incomplete digestion of the unmethylated target. More importantly, 0.01% methylation level can be effectively distinguished with the existence of excess unmethylated DNA. In addition, the DESCS assay is integrated into the lateral flow biosensor (LFB) for the point-of-care determination of DNA methylation. In view of the superiorities in high sensitivity, outstanding selectivity, and ease of operation, the DESCS system will provide a reliable assay for site-specific analysis of methylation.
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Affiliation(s)
- Xianfeng Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Chengxiang Chu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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Circulating Biomarkers of Colorectal Cancer (CRC)-Their Utility in Diagnosis and Prognosis. J Clin Med 2021; 10:jcm10112391. [PMID: 34071492 PMCID: PMC8199026 DOI: 10.3390/jcm10112391] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
The global burden of colorectal cancer (CRC) is expected to increase, with 2.2 million new cases and 1.1 million annual deaths by 2030. Therefore, the establishment of novel biomarkers useful in the early diagnosis of CRC is of utmost importance. A number of publications have documented the significance of the overexpression of several specific proteins, such as inflammatory mediators, in CRC progression. However, little is known about the potential utility of these proteins as circulating blood tumor biomarkers of CRC. Therefore, in the present review we report the results of our previous original studies as well as the findings of other authors who investigated whether inflammatory mediators might be used as novel biomarkers in the diagnosis and prognosis of CRC. Our study revealed that among all of the tested proteins, serum M-CSF, CXCL-8, IL-6 and TIMP-1 have the greatest value in the diagnosis and progression of CRC. Serum TIMP-1 is useful in differentiating between CRC and colorectal adenomas, whereas M-CSF and CRP are independent prognostic factors for the survival of patients with CRC. This review confirms the promising significance of these proteins as circulating biomarkers for CRC. However, due to their non-specific nature, further validation of their sensitivity and specificity is required.
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Sun J, Xu J, Sun C, Zheng M, Li Y, Zhu S, Zhang S. Screening and Prognostic Value of Methylated Septin9 and its Association With Clinicopathological and Molecular Characteristics in Colorectal Cancer. Front Mol Biosci 2021; 8:568818. [PMID: 34095214 PMCID: PMC8173126 DOI: 10.3389/fmolb.2021.568818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 04/22/2021] [Indexed: 12/24/2022] Open
Abstract
Screening of CRC continues to show poor compliance of endoscopy examination. The detection of mSEPT9 in peripheral blood is among the safe and simple early screening methods for CRC. The issue of how to elucidate whether detection of mSEPT9 in peripheral blood can effectively improve compliance of endoscopy and increase the early diagnosis rate of CRC and the relationship between levels of mSEPT9 in the peripheral blood and clinical stage, pathological classification, and expression of characteristic molecules in CRC remains unsolved. A total of 7759 individuals participated in the study that was performed using a questionnaire for screening of high-risk CRC. The endoscopic detection compliance of individuals with high-risk CRC who underwent the fecal occult blood test (FOBT) or mSEPT9 test was compared based on the results of the questionnaire. Additionally, correlation of mSEPT9 levels in the peripheral blood with clinicopathological features, mutation status of TP53, mismatch repair deficiency (dMMR), and KRAS/NRAS/BRAF/PIK3CA genotype was analyzed, and association of biomarkers with cancer-specific survival (CSS) and time to recurrence (TTR) was compared. We also detected levels of mSEPT9 in the peripheral blood of patients with CRC 7 days after surgery and compared the prognostic value of mSEPT9 with CEA. Results of our study showed that the mSEPT9 test could improve compliance of endoscopy and indicated a higher percentage of patients with positive mSEPT9 willing to undergo endoscopy detection than in those with positive FOBT. The specificity and sensitivity of mSEPT9 were better than that of FOBT for the detection of CRC. mSEPT9 was associated with the TNM stage, dMMR, and mutations in TP53, BRAF, and PIK3CA. A Ct value of mSEPT9 ≤ 37.5 was significantly related to poor CSS. mSEPT9 could affect association of dMMR and BRAF and PIK3CA mutations with CSS in a specific stage of CRC. The positive rate of mSEPT9 after surgery was found to correlate with poor TTR, and sensitivity was higher than CEA. The combination of mSEPT9 with CEA had a better prognostic value than that of mSEPT9 alone. The level of mSEPT9 was related to dMMR, mutations in TP53, BRAF, and PIK3CA, and was an effective biomarker for the prognosis of patients with CRC.
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Affiliation(s)
- Jie Sun
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Jinling Xu
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Chao Sun
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Minying Zheng
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Yuwei Li
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Siwei Zhu
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
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Nassar FJ, Msheik ZS, Nasr RR, Temraz SN. Methylated circulating tumor DNA as a biomarker for colorectal cancer diagnosis, prognosis, and prediction. Clin Epigenetics 2021; 13:111. [PMID: 34001239 PMCID: PMC8130320 DOI: 10.1186/s13148-021-01095-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022] Open
Abstract
Worldwide, colorectal cancer (CRC) is a deadly disease whose death rate ranks second among cancers though its incidence ranks third. Early CRC detection is key and is associated with improved survival outcomes. However, existing tests for CRC diagnosis have several weaknesses thus rendering them inefficient. Moreover, reliable prognostic tests that can predict the overall cancer outcome and recurrence of the disease as well as predictive markers that can assess effectiveness of therapy are still lacking. Thus, shifting to noninvasive liquid biopsy or blood-based biomarkers is vital to improving CRC diagnosis, prognosis, and prediction. Methylated circulating tumor DNA (ctDNA) has gained increased attention as a type of liquid biopsy that is tumor-derived fragmented DNA with epigenetic alterations. Methylated ctDNA are more consistently present in blood of cancer patients as compared to mutated ctDNA. Hence, methylated ctDNA serves as a potential biomarker for CRC that is worth investigating. In this review, we explore what has been reported about methylated ctDNA as a biomarker for CRC diagnosis that can distinguish between CRC patients or those having adenoma and healthy controls as validated specifically through ROC curves. We also examine methylated ctDNA as a biomarker for CRC prognosis and prediction as confirmed through robust statistical analyses. Finally, we discuss the major technical challenges that limits the use of methylated ctDNA for clinical application and suggest possible recommendations to enhance its usage.
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Affiliation(s)
- Farah J Nassar
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon
| | - Zahraa S Msheik
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon
| | - Rihab R Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon.
| | - Sally N Temraz
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon.
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Shafiei M, Alemrajabi M, Najafi A, Keihan AH, Sohrabi MR. Candidate Molecular Biomarkers for the Non- Invasive Detection of Colorectal Cancer using Gene Expression Profiling. IRANIAN JOURNAL OF PATHOLOGY 2021; 16:205-214. [PMID: 33936232 PMCID: PMC8085285 DOI: 10.30699/ijp.2021.132385.2475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/17/2021] [Indexed: 11/07/2022]
Abstract
Background & Objective: olorectal Cancer (CRC) is the third most common cancer after prostate (breast in women) and lung cancer; it is also the third cause of cancer deaths reported in both men and women in 2020. Currently, the most commonly used diagnostic tools for CRC are colonoscopy, serological methods, and other imaging techniques. Despite the benefits and abilities of these methods, each of them has disadvantages that reduce its functionality and acceptance. The aim of this study was identifying specific and non-invasive genetic biomarkers to diagnose colorectal cancer. Methods: In this study, changes in the expression of HLTF and SEPT9 genes were evaluated by Real Time PCR in blood and tissue samples of CRC patients. A total of 100 samples (50 Blood and 50 Tissue samples) were evaluated with a definite diagnosis of CRC in Firoozgar Hspital, Tehran, Iran, in 2018. The QPCR method was used to compare the expression of candidate genes between the patients group and control group in both samples. Sensitivity and specificity of the test were examined using ROC curve analysis. Results: The results showed a significant down-regulation in the expression of both selected genes in tissue and peripheral blood in the various stages of the CRC. The sensitivity and specifity of both genes was about 80%. Conclusion: The findings showed that the two candidate genes can be suggested as specific biomarkers for diagnosis of CRC using the peripheral blood as a non-invasive method. For a definite conclusion, more research is needed.
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Affiliation(s)
- Mohammad Shafiei
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahdi Alemrajabi
- Gastrointestinal and Liver Disease Research Center (GILDRC), Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Amir Homayoun Keihan
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Masoud Reza Sohrabi
- Gastrointestinal and Liver Disease Research Center (GILDRC), Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
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Yi JM. DNA Methylation Change Profiling of Colorectal Disease: Screening towards Clinical Use. Life (Basel) 2021; 11:life11050412. [PMID: 33946400 PMCID: PMC8147151 DOI: 10.3390/life11050412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Colon cancer remains one of the leading causes of cancer-related deaths worldwide. Transformation of colon epithelial cells into invasive adenocarcinomas has been well known to be due to the accumulation of multiple genetic and epigenetic changes. In the past decade, the etiology of inflammatory bowel disease (IBD) which is characterized by chronic inflammation of the intestinal mucosa, was only partially explained by genetic studies providing susceptibility loci, but recently epigenetic studies have provided critical evidences affecting IBD pathogenesis. Over the past decade, A deep understanding of epigenetics along with technological advances have led to identifying numerous genes that are regulated by promoter DNA hypermethylation in colorectal diseases. Recent advances in our understanding of the role of DNA methylation in colorectal diseases could improve a multitude of powerful DNA methylation-based biomarkers, particularly for use as diagnosis, prognosis, and prediction for therapeutic approaches. This review focuses on the emerging potential for translational research of epigenetic alterations into clinical utility as molecular biomarkers. Moreover, this review discusses recent progress regarding the identification of unknown hypermethylated genes in colon cancers and IBD, as well as their possible role in clinical practice, which will have important clinical significance, particularly in the era of the personalized medicine.
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Affiliation(s)
- Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea;
- Innovative Therapeutics Research Institute, College of Medicine, Inje University, Busan 47392, Korea
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Combining Serum DNA Methylation Biomarkers and Protein Tumor Markers Improved Clinical Sensitivity for Early Detection of Colorectal Cancer. Int J Genomics 2021; 2021:6613987. [PMID: 33977101 PMCID: PMC8084680 DOI: 10.1155/2021/6613987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/13/2021] [Indexed: 12/14/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the leading causes of cancer deaths worldwide and in China. Early CRC screening is the best approach to reduce its incidence and mortality rates. The ColoDefense test, a multiplex qPCR assay simultaneously detecting both methylated SEPT9 and SDC2 genes, has demonstrated improved clinical performance on either methylation biomarker alone for CRC screening with both blood and stool samples. Method Leftover blood chemistry test samples from 125 CRC, 35 advanced adenoma, and 35 small polyp patients and 92 healthy control subjects were examined by the ColoDefense test. Among these samples, the levels of three circulating tumor markers, CEA, AFP, and CA19-9, were also measured for 106 CRC, 28 advanced adenoma, and 20 small polyp patients and all control subjects. Results Due to the smaller volume and extended storage in nonfrozen state, the ColoDefense test with these samples exhibited reduced performance for all stages of CRC and advanced adenomas. The performance of CEA, AFP, and CA19-9 and their various combinations was also evaluated for CRC screening to identify the tumor marker combinations with the best performance. When combined with the ColoDefense test, the identified combinations did improve the clinical performance. Conclusion These results suggested a rational path towards developing a CRC screening method that takes advantage of leftover blood chemistry test samples. The successful development of such a method will undoubtedly help promote early CRC screening by increasing its accessibility for the general public.
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Kalyta A, De Vera MA, Peacock S, Telford JJ, Brown CJ, Donnellan F, Gill S, Loree JM. Canadian Colorectal Cancer Screening Guidelines: Do They Need an Update Given Changing Incidence and Global Practice Patterns? Curr Oncol 2021; 28:1558-1570. [PMID: 33919428 PMCID: PMC8161738 DOI: 10.3390/curroncol28030147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/07/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer and second leading cause of cancer death in Canada. Organized screening programs targeting Canadians aged 50 to 74 at average risk of developing the disease have contributed to decreased rates of CRC, improved patient outcomes and reduced healthcare costs. However, data shows that recent incidence reductions are unique to the screening-age population, while rates in people under-50 are on the rise. Similar incidence patterns in the United States prompted the American Cancer Society and U.S. Preventive Services Task Force to recommend screening begin at age 45 rather than 50. We conducted a review of screening practices in Canada, framing them in the context of similar global health systems as well as the evidence supporting the recent U.S. recommendations. Epidemiologic changes in Canada suggest earlier screening initiation in average-risk individuals may be reasonable, but the balance of costs to benefits remains unclear.
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Affiliation(s)
- Anastasia Kalyta
- Division of Medical Oncology, BC Cancer/University of British Columbia, Vancouver, BC V5Z 4E6, Canada; (A.K.); (S.G.)
| | - Mary A. De Vera
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
| | - Stuart Peacock
- Cancer Control Research, BC Cancer, Vancouver, BC V5Z 4E6, Canada;
| | - Jennifer J. Telford
- Division of Gastroenterology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (J.J.T.); (F.D.)
| | - Carl J. Brown
- Division of General Surgery, St. Paul’s Hospital, Vancouver, BC V6Z 1Y6, Canada;
| | - Fergal Donnellan
- Division of Gastroenterology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (J.J.T.); (F.D.)
| | - Sharlene Gill
- Division of Medical Oncology, BC Cancer/University of British Columbia, Vancouver, BC V5Z 4E6, Canada; (A.K.); (S.G.)
| | - Jonathan M. Loree
- Division of Medical Oncology, BC Cancer/University of British Columbia, Vancouver, BC V5Z 4E6, Canada; (A.K.); (S.G.)
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Diagnostic DNA Methylation Biomarkers for Renal Cell Carcinoma: A Systematic Review. Eur Urol Oncol 2021; 4:215-226. [DOI: 10.1016/j.euo.2019.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/23/2019] [Accepted: 07/16/2019] [Indexed: 01/22/2023]
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Jensen SØ, Øgaard N, Nielsen HJ, Bramsen JB, Andersen CL. Enhanced Performance of DNA Methylation Markers by Simultaneous Measurement of Sense and Antisense DNA Strands after Cytosine Conversion. Clin Chem 2021; 66:925-933. [PMID: 32460325 DOI: 10.1093/clinchem/hvaa100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/03/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Most existing DNA methylation-based methods for detection of circulating tumor DNA (ctDNA) are based on conversion of unmethylated cytosines to uracil. After conversion, the 2 DNA strands are no longer complementary; therefore, targeting only 1 DNA strand merely utilizes half of the available input DNA. We investigated whether the sensitivity of methylation-based ctDNA detection strategies could be increased by targeting both DNA strands after bisulfite conversion. METHODS Dual-strand digital PCR assays were designed for the 3 colorectal cancer (CRC)-specific methylation markers KCNQ5, C9orf50, and CLIP4 and compared with previously reported single-strand assays. Performance was tested in tumor and leukocyte DNA, and the ability to detect ctDNA was investigated in plasma from 43 patients with CRC stages I to IV and 42 colonoscopy-confirmed healthy controls. RESULTS Dual-strand assays quantified close to 100% of methylated control DNA input, whereas single-strand assays quantified approximately 50%. Furthermore, dual-strand assays showed a 2-fold increase in the number of methylated DNA copies detected when applied to DNA purified from tumor tissue and plasma from CRC patients. When the results of the 3 DNA methylation markers were combined into a ctDNA detection test and applied to plasma, the dual-strand assay format detected 86% of the cancers compared with 74% for the single-strand assay format. The specificity was 100% for both the dual- and single-strand test formats. CONCLUSION Dual-strand assays enabled more sensitive detection of methylated ctDNA than single-strand assays.
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Affiliation(s)
- Sarah Ø Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology, Center for Surgical Research, Hvidovre Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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Grady WM. Epigenetic alterations in the gastrointestinal tract: Current and emerging use for biomarkers of cancer. Adv Cancer Res 2021; 151:425-468. [PMID: 34148620 DOI: 10.1016/bs.acr.2021.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is a leading cause of cancer related deaths worldwide. One of the hallmarks of cancer and a fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological process of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the initiation and progression of cancers, including colorectal cancer. Epigenetic alterations, which include changes affecting DNA methylation, histone modifications, chromatin structure, and noncoding RNA expression, have emerged as a major class of molecular alteration in colon polyps and colorectal cancer. The classes of epigenetic alterations, their status in colorectal polyps and cancer, their effects on neoplasm biology, and their application to clinical care will be discussed.
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Affiliation(s)
- William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, United States.
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Rodriguez-Casanova A, Costa-Fraga N, Bao-Caamano A, López-López R, Muinelo-Romay L, Diaz-Lagares A. Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer. Front Cell Dev Biol 2021; 9:622459. [PMID: 33614651 PMCID: PMC7892964 DOI: 10.3389/fcell.2021.622459] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and is a major cause of cancer-related deaths worldwide. Thus, there is a clinical need to improve early detection of CRC and personalize therapy for patients with this disease. In the era of precision oncology, liquid biopsy has emerged as a major approach to characterize the circulating tumor elements present in body fluids, including cell-free DNA and RNA, circulating tumor cells, and extracellular vesicles. This non-invasive tool has allowed the identification of relevant molecular alterations in CRC patients, including some indicating the disruption of epigenetic mechanisms. Epigenetic alterations found in solid and liquid biopsies have shown great utility as biomarkers for early detection, prognosis, monitoring, and evaluation of therapeutic response in CRC patients. Here, we summarize current knowledge of the most relevant epigenetic mechanisms associated with cancer development and progression, and the implications of their deregulation in cancer cells and liquid biopsy of CRC patients. In particular, we describe the methodologies used to analyze these epigenetic alterations in circulating tumor material, and we focus on the clinical utility of epigenetic marks in liquid biopsy as tumor biomarkers for CRC patients. We also discuss the great challenges and emerging opportunities of this field for the diagnosis and personalized management of CRC patients.
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Affiliation(s)
- Aitor Rodriguez-Casanova
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Laura Muinelo-Romay
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
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Sui J, Wu X, Wang C, Wang G, Li C, Zhao J, Zhang Y, Xiang J, Xu Y, Nian W, Cao F, Yu G, Lou Z, Hao L, Liu L, Li B, Zhang Z, Cai S, Liu H, Lan P, Zhang W. Discovery and validation of methylation signatures in blood-based circulating tumor cell-free DNA in early detection of colorectal carcinoma: a case-control study. Clin Epigenetics 2021; 13:26. [PMID: 33536049 PMCID: PMC7856810 DOI: 10.1186/s13148-020-00985-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Early detection of colorectal carcinoma (CRC) would help to identify tumors when curative treatments are available and beneficial. However, current screening methods for CRC, e.g., colonoscopy, may affect patients' compliance due to the uncomfortable, invasive and time-consuming process. In recent decades, methylation profiles of blood-based circulating tumor DNA (ctDNA) have shown promising results in the early detection of multiple tumors. Here we conducted a study to investigate the performance of ctDNA methylation markers in early detection of CRC. RESULTS In total, 742 participants were enrolled in the study including CRC (n = 332), healthy control (n = 333), benign colorectal disease (n = 65) and advanced adenoma (n = 12). After age-matched and randomization, 298 participants (149 cancer and 149 healthy control) were included in training set and 141 (67 cancer and 74 healthy control) were in test set. In the training set, the specificity was 89.3% (83.2-93.7%) and the sensitivity was 88.6% (82.4-93.2%). In terms of different stages, the sensitivities were 79.4% (62.1-91.2%) in patients with stage I, 88.9% (77.3-95.8%) in patients with stage II, 91.4% (76.9-98.2%) in patients with stage III and 96.2% (80.3-99.9%) in patients with stage IV. Similar results were validated in the test set with the specificity of 91.9% (83.1-97.0%) and sensitivity of 83.6% (72.5-91.6%). Sensitivities for stage I-III were 87.0% (79.7-92.4%) in the training set and 82.5% (70.2-91.3%) in the test set, respectively. In the unmatched total population, the positive ratios were 7.8% (5.2-11.2%) in healthy control, 30.8% (19.9-43.5%) in benign colorectal disease and 58.3% (27.5-84.7%) in advanced adenoma, while the sensitivities of stage I-IV were similar with training and test sets. Compared with methylated SEPT9 model, the present model had higher sensitivity (87.0% [81.8-91.2%] versus 41.2% [34.6-48.1%], P < 0.001) under comparable specificity (90.1% [85.4-93.7%] versus 90.6% [86.0-94.1%]). CONCLUSIONS Together our findings showed that ctDNA methylation markers were promising in the early detection of CRC. Further validation of this model is warranted in prospective studies.
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Affiliation(s)
- Jinke Sui
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Changhai Road No.168, Yangpu District, Shanghai, 200433, China
| | - Xianrui Wu
- Colorectal Surgery Department, The Sixth Affiliated Hospital of Sun Yat-Sen University, Yuancun Erheng Road No. 26, Guangzhou, 510655, China
| | | | | | | | - Jing Zhao
- Burning Rock Biotech, Guangzhou, China
| | | | | | - Yu Xu
- Burning Rock Biotech, Guangzhou, China
| | - Weiqi Nian
- Phase I Ward, Chongqing University Cancer Hospital, Chongqing, China
| | - Fuao Cao
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Changhai Road No.168, Yangpu District, Shanghai, 200433, China
| | - Guanyu Yu
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Changhai Road No.168, Yangpu District, Shanghai, 200433, China
| | - Zheng Lou
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Changhai Road No.168, Yangpu District, Shanghai, 200433, China
| | - Liqiang Hao
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Changhai Road No.168, Yangpu District, Shanghai, 200433, China
| | - Lianjie Liu
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Changhai Road No.168, Yangpu District, Shanghai, 200433, China
| | - Bingsi Li
- Burning Rock Biotech, Guangzhou, China
| | | | | | - Hao Liu
- Burning Rock Biotech, Guangzhou, China
| | - Ping Lan
- Colorectal Surgery Department, The Sixth Affiliated Hospital of Sun Yat-Sen University, Yuancun Erheng Road No. 26, Guangzhou, 510655, China.
| | - Wei Zhang
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Changhai Road No.168, Yangpu District, Shanghai, 200433, China.
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Grady WM, Yu M, Markowitz SD. Epigenetic Alterations in the Gastrointestinal Tract: Current and Emerging Use for Biomarkers of Cancer. Gastroenterology 2021; 160:690-709. [PMID: 33279516 PMCID: PMC7878343 DOI: 10.1053/j.gastro.2020.09.058] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer, liver cancer, stomach cancer, pancreatic cancer, and esophageal cancer are leading causes of cancer-related deaths worldwide. A fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological processes of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the clinical behavior of the precancers and cancers and can be used as biomarkers for cancer risk determination, early detection of cancer and precancer, determination of the prognosis of cancer and prediction of the response to therapy. Epigenetic alterations have emerged as one of most robust classes of biomarkers and are the basis for a growing number of clinical tests for cancer screening and surveillance.
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Affiliation(s)
- William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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67
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Shiu BH, Lu WY, Tantoh DM, Chou MC, Nfor ON, Huang CC, Liaw YP. Interactive association between dietary fat and sex on CDH13 cg02263260 methylation. BMC Med Genomics 2021; 14:13. [PMID: 33407434 PMCID: PMC7788866 DOI: 10.1186/s12920-020-00858-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation of Cadherin 13 (CDH13), a tumor suppressor gene is associated with gene repression and carcinogenesis. We determined the relation of dietary fat and sex with CDH13 cg02263260 methylation in Taiwanese adults. METHODS Data of 870 eligible participants (430 men and 440 women) between 30 and 70 years were obtained from the Taiwan Biobank (TWB) database. The association of dietary fat and sex with CDH13 cg02263260 methylation was determined using multiple linear regression. RESULTS The association between sex and cg02263260 methylation was significant: beta-coefficient (β) = 0.00532; 95% confidence interval (CI) = 0.00195-0.00868. Moreover, the interaction between sex and dietary fat on cg02263260 methylation was significant (P-value = 0.0145). After stratification by sex, the association of dietary fat with cg02263260 methylation was significant only in women. Specifically, high dietary fat was positively associated with cg02263260 methylation in women (β = 0.00597; 95% CI = 0.00061-0.01133) and the test for trend was significant (P-value = 0.0283). CONCLUSION High fat intake was significantly associated with higher cg02263260 methylation in women and the test for trend was significant. These findings suggest that the association of fat intake and CDH13 cg02263260 might vary by sex and CDH13 cg02263260 methylation levels in women might increase as fat intake increases.
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Affiliation(s)
- Bei-Hao Shiu
- Institute of Medicine, Chung Shan Medical University, Taichung City, 40201, Taiwan
- Division of Colon-Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung City, 40201, Taiwan
| | - Wen-Yu Lu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Disline Manli Tantoh
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, 40201, Taiwan
| | - Ming-Chih Chou
- Institute of Medicine, Chung Shan Medical University, Taichung City, 40201, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Chi-Chou Huang
- Division of Colon-Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung City, 40201, Taiwan.
- School of Medicine, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan.
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan.
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, 40201, Taiwan.
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Jamialahmadi K, Azghandi M, Javadmanesh A, Zardadi M, Shams Davodly E, Kerachian MA. A DNA methylation panel for high performance detection of colorectal cancer. Cancer Genet 2020; 252-253:64-72. [PMID: 33387936 DOI: 10.1016/j.cancergen.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/25/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
One of the most promising ways to diagnose cancer especially colorectal cancer (CRC) is to trace its epigenetic events. In this article, a discovery step for detection of methylated DNA markers (MDMs) was performed using SureSelectXT Methyl-Seq in CRC case and control groups in addition to several methylation profiling datasets (GSE48684, GSE53051, GSE77718, GSE101764, and GSE42752). In silico validation of MDMs in colorectal and other cancers was conducted by Lnc2met. MethyLight assay was run on 40 and 47 case and control formalin-fixed paraffin-embedded tissues, respectively and the performance of selected genes were classified by support vector machine (SVM). As a result, 180 regions were identified among all common genes. In addition to SEPT9 and SFRP2, the best three MDM regions were selected from SLC30A10, AKR1B1 and GALNT14. Based on all assays, the best performance was accomplished by SEPT9/AKR1B1 with 98% sensitivity, 99% specificity, 125 positive likelihood ratio, 0.02 negative likelihood ratio and 5074 diagnostic odds ratio. Our results indicate that the AKR1B1/SEPT9 methylation panel detects CRC with a higher performance than SEPT9 methylation, which is a commercial diagnostic test for CRC. However, the creation of a clinically valuable test derived from this study requires performance evaluation in liquid biopsies.
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Affiliation(s)
- Khadijeh Jamialahmadi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran; Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Javadmanesh
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran; Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Zardadi
- Surgical Oncology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Shams Davodly
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Mohammad Amin Kerachian
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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69
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Alves G, Chantre M, Delmonico L. The contribution of the 20th century discoveries on the circulating DNA as biomarkers for cancer screening. AN ACAD BRAS CIENC 2020; 92:e20200919. [PMID: 33206793 DOI: 10.1590/0001-3765202020200919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023] Open
Abstract
Circulating DNA can be released in the biological fluids by a physiological process and by different pathological conditions. The first reports detecting circulating DNA in human plasma date from the late 40s. Even when specific pathological conditions were analyzed, the clinical importance of circulating DNA remained unclear. After PCR introduction, genetic and epigenetic alterations in circulating DNA gained more prominence for understanding the mechanisms of cancer development and progression. Nowadays, the circulating DNA assays are highlighted for their clinical relevance for cancer screening in liquid biopsy. In this review, we described the landscape of studies on circulating DNA isolated from human plasma or serum and the molecular tools used to obtain these findings throughout the 20th century and the current application in cancer.
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Affiliation(s)
- Gilda Alves
- Universidade do Estado do Rio de Janeiro/UERJ, Faculdade de Ciências Médicas, Departamento de Patologia e Laboratórios, Laboratório de Marcadores Circulantes, Avenida Prof. Manuel de Abreu, 444, 4° andar, Vila Isabel, 20550-170 Rio de Janeiro, RJ, Brazil
| | - Mariana Chantre
- Universidade do Estado do Rio de Janeiro/UERJ, Faculdade de Ciências Médicas, Departamento de Patologia e Laboratórios, Laboratório de Marcadores Circulantes, Avenida Prof. Manuel de Abreu, 444, 4° andar, Vila Isabel, 20550-170 Rio de Janeiro, RJ, Brazil
| | - Lucas Delmonico
- Universidade Federal do Rio de Janeiro/UFRJ, Instituto de Biofísica Carlos Chagas Filho/IBCCF, Laboratório de Radiações em Biologia, Avenida Carlos Chagas Filho, 373, Bloco G, Sala G0-036, Cidade Universitária, 21941-902 Rio de Janeiro, RJ, Brazil
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70
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Zhou Z, Ge S, Li Y, Ma W, Liu Y, Hu S, Zhang R, Ma Y, Du K, Syed A, Chen P. Human Gut Microbiome-Based Knowledgebase as a Biomarker Screening Tool to Improve the Predicted Probability for Colorectal Cancer. Front Microbiol 2020; 11:596027. [PMID: 33329482 PMCID: PMC7717945 DOI: 10.3389/fmicb.2020.596027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is a common clinical malignancy globally ranked as the fourth leading cause of cancer mortality. Some microbes are known to contribute to adenoma-carcinoma transition and possess diagnostic potential. Advances in high-throughput sequencing technology and functional studies have provided significant insights into the landscape of the gut microbiome and the fundamental roles of its components in carcinogenesis. Integration of scattered knowledge is highly beneficial for future progress. In this study, literature review and information extraction were performed, with the aim of integrating the available data resources and facilitating comparative research. A knowledgebase of the human CRC microbiome was compiled to facilitate understanding of diagnosis, and the global signatures of CRC microbes, sample types, algorithms, differential microorganisms and various panels of markers plus their diagnostic performance were evaluated based on statistical and phylogenetic analyses. Additionally, prospects about current changelings and solution strategies were outlined for identifying future research directions. This type of data integration strategy presents an effective platform for inquiry and comparison of relevant information, providing a tool for further study about CRC-related microbes and exploration of factors promoting clinical transformation (available at: http://gsbios.com/index/experimental/dts_ mben?id=1).
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Affiliation(s)
- Zhongkun Zhou
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Shiqiang Ge
- Department of Electronic Information Engineering, Lanzhou Vocational Technical College, Lanzhou, China
| | - Yang Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Wantong Ma
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Yuheng Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Shujian Hu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Rentao Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Yunhao Ma
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Kangjia Du
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | | | - Peng Chen
- School of Pharmacy, Lanzhou University, Lanzhou, China
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71
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Song L, Chen Y, Gong Y, Wan J, Guo S, Liu H, Li Y, Zeng Z, Lu Y. Opportunistic screening and survival prediction of digestive cancers by the combination of blood mSEPT9 with protein markers. Ther Adv Med Oncol 2020; 12:1758835920962966. [PMID: 33403008 PMCID: PMC7745555 DOI: 10.1177/1758835920962966] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
Background: The early detection of digestive cancers and precancerous diseases remains a significant challenge. This study aimed to investigate the performance of the blood methylated SEPT9 (mSEPT9) assay, and the combination of this assay with serum protein markers, in hospital-based opportunistic screening strategies for digestive cancers. Methods: Opportunistic screening was performed in the participating hospitals on outpatients and inpatients who met specific inclusion criteria. We recruited a total of 2030 subjects, including 764 cancer patients [291 colorectal cancer (CRC), 239 gastric cancer (GC), 106 esophageal cancer (EC), and 128 hepatocellular carcinoma (HCC)], 423 subjects with precancerous diseases, and 843 normal subjects. All samples were transported to an authenticated clinical laboratory where the mSEPT9 tests were performed. Results: When used separately, the mSEPT9 detected CRC, GC, EC, and HCC, with a sensitivity of 76.6% [area under the receiver operating characteristic curve (AUC) = 0.86)], 47.7% (AUC = 0.76), 42.6% (AUC = 0.69), and 76.7% (AUC = 0.85) and a specificity of 94.6%, 92.3%, 92.5%, and 87.7%, respectively. The mSEPT9 assay also had potent ability to discriminate cancer from non-cancer subjects. The combination of mSEPT9 with CEA, CA724, SNCG, or AFP significantly enhanced the sensitivity for CRC, GC, EC, and HCC to 86.4% (AUC = 0.99, specificity = 92.8%), 63.6% (AUC = 0.86, specificity = 91.1%), 71.3% (AUC = 0.81, specificity = 82.1%), and 83.3% (AUC = 0.93, specificity = 85.1%), respectively. The performance of the mSEPT9 assay was influenced by cancer stage, patient age, pathological types, and the location of cancer. We also identified that mSEPT9 was an independent risk factor and was a valuable predictor for the long-term survival of digestive cancer patients, with a hazard ratio of 2.84, 2.07, 1.88, and 2.45, for CRC, GC, EC, and HCC, respectively. Conclusion: The blood mSEPT9 assay, whether used alone or in combination with serum protein markers, is effective for the opportunistic screening of digestive cancers. Furthermore, mSEPT9 is an independent risk factor and a predictive marker for the long-term survival of digestive cancer patients.
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Affiliation(s)
- Lele Song
- Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, No.17, Heishanhu Road, Beijing 100091, P.R. China
| | - Yan Chen
- Comprehensive Liver Cancer Department, The Fifth Medical Center of the Chinese PLA General Hospital, Beijing, P.R. China
| | - Yuan Gong
- Department of Gastroenterology, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Jun Wan
- Department of Gastroenterology, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Shaohua Guo
- Department of General Surgery, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Hongyi Liu
- Department of General Surgery, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Yuemin Li
- Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, P.R. China
| | - Zhen Zeng
- Comprehensive Liver Cancer Department, The Fifth Medical Center of the Chinese PLA General Hospital, Beijing, 100039 P.R. China
| | - Yinying Lu
- Comprehensive Liver Cancer Department, The Fifth Medical Center of the Chinese PLA General Hospital, Beijing, 100039 P.R. China
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72
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Musher BL, Melson JE, Amato G, Chan D, Hill M, Khan I, Kochuparambil ST, Lyons SE, Orsini J, Pedersen SK, Robb B, Saltzman J, Silinsky J, Gaur S, Tuck MK, LaPointe LC, Young GP. Evaluation of Circulating Tumor DNA for Methylated BCAT1 and IKZF1 to Detect Recurrence of Stage II/Stage III Colorectal Cancer (CRC). Cancer Epidemiol Biomarkers Prev 2020; 29:2702-2709. [DOI: 10.1158/1055-9965.epi-20-0574] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/27/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
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73
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Miller E, Schwartzberg L. Precision Medicine for Breast Cancer Utilizing Circulating Tumor DNA: It Is in the Blood. Curr Treat Options Oncol 2020; 21:89. [PMID: 32875404 DOI: 10.1007/s11864-020-00783-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OPINION STATEMENT Liquid biopsy using blood components to assess circulating tumor DNA (ctDNA) is rapidly becoming a new standard-of-care technology in many tumor types, including breast cancer, due to the potential to provide predictive and prognostic information. The minimally invasive and repeatable nature of plasma based mutational testing is appealing for patients and facilitates enhanced disease monitoring. It is important for the clinician to understand the benefits and limitations of this emerging assay and the potential applications in breast cancer. Multiple technologies have been employed to assess breast cancer ctDNA with high sensitivity and specificity leading to assays that have been useful in research trials and are entering widespread clinical application. ctDNA analysis of breast cancer is of clinical utility today in selecting targeted therapy for advanced breast cancer, most notably by assessing PIK3CA mutations in hormone receptor-positive, HER2-negative disease. It will be employed in the near future in a variety of clinical settings including early detection of primary breast cancer, minimal residual disease after initial therapy, and use in advanced breast cancer for prognosis, early identification of non-response, and monitoring genomic markers of resistance.
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Affiliation(s)
- Emily Miller
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lee Schwartzberg
- University of Tennessee Health Science Center, Memphis, TN, USA.
- West Cancer Center and Research Institute, 7945 Wolf River Blvd, Germantown, TN, 38138, USA.
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74
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Xie H, Kim RD. The Application of Circulating Tumor DNA in the Screening, Surveillance, and Treatment Monitoring of Colorectal Cancer. Ann Surg Oncol 2020; 28:1845-1858. [PMID: 32776184 DOI: 10.1245/s10434-020-09002-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
Precision medicine with genetic profiling of tumor tissue has become an essential part of routine clinical practice in colorectal cancer. However, tissue genetic profiling suffers from clonal evolution, tumor heterogeneity, and time needed to deliver critical information for prompt clinical decision making. In contrast, liquid biopsy with plasma circulating tumor DNA provides genetic and epigenetic information from both the primary and metastatic colorectal cancer, which can potentially capture tumor heterogeneity and evolution with time and treatment. In addition, liquid biopsy with circulating tumor DNA is minimally invasive, quicker, and easily repeatable with high patient compliance to provide both qualitative and quantitative molecular information in real-time. We provide an overview on the potential clinical applications of circulating tumor DNA in the screening, surveillance, and treatment monitoring of colorectal cancer.
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Affiliation(s)
- Hao Xie
- Division of Medical Oncology, Mayo Clinic, Rochester, USA
| | - Richard D Kim
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, USA.
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75
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Dong D, Zhang J, Zhang R, Li F, Li Y, Jia Y. Multiprobe Assay for Clinical SEPT9 Methylation Based on the Carbon Dot-Modified Liquid-Exfoliated Graphene Field Effect Transistor with a Potential to Present a Methylation Panorama. ACS OMEGA 2020; 5:16228-16237. [PMID: 32656445 PMCID: PMC7346271 DOI: 10.1021/acsomega.0c02022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/11/2020] [Indexed: 05/11/2023]
Abstract
The hypermethylation in the promoter region of the SEPT9 gene is associated with the development of colorectal cancer (CRC). Although its clinical significance for early diagnosis and screening of CRC has been demonstrated, the tedious operations in the conventional DNA methylation (DNAm) detection hinder its wide application. Herein, an electronic method for determining SEPT9 methylation in CRC patients is proposed by using the carbon dot-modified liquid exfoliated graphene field effect transistor (CDs-LEG-FET) as the DNAm sensor, the specifically designed probes to capture the SEPT9 gene and the immunologic recognition to recognize 5-methylcytosine (5mC) positions on the anchored sequences. The identification and nanomorphology of the as-prepared materials and devices are executed first by the characterizations of UV-vis, Raman, atomic force microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electronic measurements. Then, the role of CDs in enhancing DNAm sensitivity of CD-LEG-FET is manifested by comparing it with that of CD-free LEG-FET. Third, the captured SEPT9 genes on CD-LEG-FETs by different probes are evaluated, and the optimized temperature for hybridizing the target ssDNA sequences is determined to be 48 °C. Furthermore, the detection sensitivity for the low-quantity of DNA samples is demonstrated to be as low as 2 ng. Finally, the methylation degree of the tumor and corresponding noncancerous tissue DNA samples were examined by the proposed electric method and methylight assay in parallel. The diagnostic value of the electrical assay is confirmed by using the receiver operating characteristic curves; meanwhile, the superiority of the CD-LEG-FET platform is found to present a methylation panorama of the target gene.
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Affiliation(s)
- Dong Dong
- Department
of Laboratory, Tianjin’s Clinical Research Center for Cancer,
Key Laboratory of Cancer Prevention and Therapy, National Clinical
Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin 300060, China
| | - Jizhao Zhang
- College
of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Runshi Zhang
- Department
of Laboratory, Tianjin’s Clinical Research Center for Cancer,
Key Laboratory of Cancer Prevention and Therapy, National Clinical
Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin 300060, China
| | - Fang Li
- College
of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Yueguo Li
- Department
of Laboratory, Tianjin’s Clinical Research Center for Cancer,
Key Laboratory of Cancer Prevention and Therapy, National Clinical
Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yunfang Jia
- College
of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
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76
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Zhu Y, Yang T, Wu Q, Yang X, Hao J, Deng X, Yang S, Gu C, Wang Z. Diagnostic performance of various liquid biopsy methods in detecting colorectal cancer: A meta-analysis. Cancer Med 2020; 9:5699-5707. [PMID: 32628360 PMCID: PMC7433831 DOI: 10.1002/cam4.3276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/06/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is a promising method in detecting colorectal cancer (CRC). However, previous meta‐analyses only focused on the diagnostic performance of cell‐free DNA (cfDNA). Therefore, we firstly evaluated the overall performance of all liquid biopsy methods. The pooled sensitivities, specificities, diagnostic odds ratios, and area under curve (AUC) of summary receiver operating characteristic curve for all liquid biopsy methods, exosomes, circulating tumor cells (CTCs), and cfDNA were calculated, respectively. A total of 62 articles involving 18 739 individuals were included. Fifty‐one articles were about cfDNA, five articles were about CTCs, and six articles were about exosomes. The overall performance of all liquid biopsy methods had a pooled sensitivity, specificity, and AUC of 0.77 (95% confidence interval [CI] 0.76‐0.78), 0.89 (95% CI 0.88‐0.90), and 0.9004, respectively. The sensitivities were 0.82 (95% CI 0.79‐0.85), 0.76 (95% CI 0.72‐0.80), and 0.76 (95% CI 0.75‐0.77) for CTCs, exosomes, and cfDNA, respectively. The specificities were 0.97 (95% CI95% CI 0.95‐0.99), 0.92 (95% CI 0.89‐0.94), and 0.88 (95% CI 0.87‐0.89) for CTCs, exosomes, and cfDNA, respectively. The AUC were 0.9772, 0.9037, and 0.8963 for CTCs, exosomes, and cfDNA, respectively. The overall performance of all liquid biopsy methods had great diagnostic value in detecting CRC, regardless of subtypes. Among all liquid biopsy methods, CTCs showed the best diagnostic performance.
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Affiliation(s)
- Yuzhou Zhu
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Tinghan Yang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Qingbin Wu
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Xuyang Yang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Jianqi Hao
- West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Xiangbing Deng
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuo Yang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Chaoyang Gu
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ziqiang Wang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.,West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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77
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Cervena K, Siskova A, Buchler T, Vodicka P, Vymetalkova V. Methylation-Based Therapies for Colorectal Cancer. Cells 2020; 9:E1540. [PMID: 32599894 PMCID: PMC7349319 DOI: 10.3390/cells9061540] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
Colorectal carcinogenesis (CRC) is caused by the gradual long-term accumulation of both genetic and epigenetic changes. Recently, epigenetic alterations have been included in the classification of the CRC molecular subtype, and this points out their prognostic impact. As epigenetic modifications are reversible, they may represent relevant therapeutic targets. DNA methylation, catalyzed by DNA methyltransferases (DNMTs), regulates gene expression. For many years, the deregulation of DNA methylation has been considered to play a substantial part in CRC etiology and evolution. Despite considerable advances in CRC treatment, patient therapy response persists as limited, and their profit from systemic therapies are often hampered by the introduction of chemoresistance. In addition, inter-individual changes in therapy response in CRC patients can arise from their specific (epi)genetic compositions. In this review article, we summarize the options of CRC treatment based on DNA methylation status for their predictive value. This review also includes the therapy outcomes based on the patient's methylation status in CRC patients. In addition, the current challenge of research is to develop therapeutic inhibitors of DNMT. Based on the essential role of DNA methylation in CRC development, the application of DNMT inhibitors was recently proposed for the treatment of CRC patients, especially in patients with DNA hypermethylation.
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Affiliation(s)
- Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Anna Siskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59 Prague, Czech Republic;
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
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78
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Zhao G, Liu X, Liu Y, Li H, Ma Y, Li S, Zhu Y, Miao J, Xiong S, Fei S, Zheng M. Aberrant DNA Methylation of SEPT9 and SDC2 in Stool Specimens as an Integrated Biomarker for Colorectal Cancer Early Detection. Front Genet 2020; 11:643. [PMID: 32625237 PMCID: PMC7314930 DOI: 10.3389/fgene.2020.00643] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) has become the second leading cause of new cancer cases and the fifth of cancer deaths in China, and early detection is the most effective way to reduce the incidence and mortality of CRC. A number of methylated DNA biomarkers have been found to associate with CRC and precancerous lesions in stool samples, indicating stool methylated DNA biomarkers are potential tools for CRC early detection. In this study, approximately 5 g of stool specimen was collected from 230 subjects (124 in the training set and 106 in the validation set). Stool DNA was extracted and bisulfite-converted, followed by ColoDefense test, a multiplex qPCR assay, that simultaneously detects methylated SEPT9 (mSEPT9) and methylated SDC2 (mSDC2). Youden index was employed to determine the cut-off value of ColoDefense test for stool specimens. In the training set, the optimized cut-off value of stool ColoDefense test was: mSEPT9 analyzed with 3/3 algorithm and mean mSEPT9 Ct values of <38, or mSDC2 with 2/3 algorithm. Stool ColoDefense test achieved Youden indexes of 79.9 and 57.4% in detecting CRC and advanced adenomas (AA), respectively. Its sensitivities in the training set for AA and CRC were 66.7% (95% CI: 24.1-94.0%) and 89.1% (95% CI: 77.1-95.5%) with a 90.8% (95% CI: 80.3-96.2%) specificity, and AUC was 0.956 (95% CI: 0.924-0.988). In the validation set, its sensitivities for AA and CRC were 66.7% (95% CI: 24.1-94.0%) and 92.3% (95% CI: 78.0-98.0%) with a 93.2% (95% CI: 82.7-97.8%) specificity, and AUC was 0.977 (95% CI: 0.952-1.000). Positive detection rate of stool ColoDefense test has been found to be independent of age, gender, tumor location, and tumor size. In conclusion, stool ColoDefense test demonstrated high sensitivities and specificity for the detection of AA and CRC. Therefore, it has the potential to become a low-cost, convenient, and highly effective tool for CRC early detection.
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Affiliation(s)
- Guodong Zhao
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- Suzhou VersaBio Technologies Co., Ltd., Kunshan, China
| | - Xiaoyu Liu
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
| | - Yi Liu
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Hui Li
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Yong Ma
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Shiming Li
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
| | - Yun Zhu
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
| | - Jin Miao
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Shangmin Xiong
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
- Suzhou VersaBio Technologies Co., Ltd., Kunshan, China
| | - Sujuan Fei
- Department of Gastroenterology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Minxue Zheng
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
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79
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A First Step to a Biomarker of Curative Surgery in Colorectal Cancer by Liquid Biopsy of Methylated Septin 9 Gene. DISEASE MARKERS 2020; 2020:9761406. [PMID: 32566042 PMCID: PMC7293729 DOI: 10.1155/2020/9761406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 01/16/2020] [Indexed: 02/06/2023]
Abstract
Objectives To confirm that patients affected by colorectal cancer have the V2 region of Septin 9 (SEPT9) gene hypermethylated in the circulating free DNA from a peripheral blood sample before surgery and to determine if this hypermethylated DNA disappears from the patients after complete resection of the tumour. Methods Plasma from 10 patients with colorectal cancer was collected preoperative and three months after surgery. The analysis of the methylation status of the promoter region of the SEPT9 gene was performed using a 7500 Fast Real-Time PCR System. Results Hypermethylation of SEPT9 gene was detected in 8 out of 10 preoperative samples (one negative result was probed to be a Lynch syndrome) and in 4 out of 10 postoperative samples matching with the cases of recurrence or persistence of disease. This means that, in this sample, the preoperative sensitivity and specificity of the test were 88.9% and 100%, respectively, and there is 100% correlation between the positive results of the SEPT9 test and a recurrence/persistence of the disease in patients after surgical resection. Conclusions Our study shows that circulating hypermethylated SEPT9 is a specific colorectal cancer biomarker. This hypermethylated SEPT9 DNA disappears around three months after surgery and that circulating hypermethylated SEPT9 may be the first noninvasive marker for postsurgical diagnosis; this conclusion must be confirmed with a more significant number of patients.
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80
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Bacolod MD, Mirza AH, Huang J, Giardina SF, Feinberg PB, Soper SA, Barany F. Application of Multiplex Bisulfite PCR-Ligase Detection Reaction-Real-Time Quantitative PCR Assay in Interrogating Bioinformatically Identified, Blood-Based Methylation Markers for Colorectal Cancer. J Mol Diagn 2020; 22:885-900. [PMID: 32407802 DOI: 10.1016/j.jmoldx.2020.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
The analysis of CpG methylation in circulating tumor DNA fragments has emerged as a promising approach for the noninvasive early detection of solid tumors, including colorectal cancer (CRC). The most commonly employed assay involves bisulfite conversion of circulating tumor DNA, followed by targeted PCR, then real-time quantitative PCR (alias methylation-specific PCR). This report demonstrates the ability of a multiplex bisulfite PCR-ligase detection reaction-real-time quantitative PCR assay to detect seven methylated CpG markers (CRC or colon specific), in both simulated (approximately 30 copies of fragmented CRC cell line DNA mixed with approximately 3000 copies of fragmented peripheral blood DNA) and CRC patient-derived cell-free DNAs. This scalable assay is designed for multiplexing and incorporates steps for improved sensitivity and specificity, including the enrichment of methylated CpG fragments, ligase detection reaction, the incorporation of ribose bases in primers, and use of uracil DNA glycosylase. Six of the seven CpG markers (located in promoter regions of PPP1R16B, KCNA3, CLIP4, GDF6, SEPT9, and GSG1L) were identified through integrated analyses of genome-wide methylation data sets for 31 different types of cancer. These markers were mapped to CpG sites at the promoter region of VIM; VIM and SEPT9 are established epigenetic markers of CRC. Additional bioinformatics analyses show that the methylation at these CpG sites negatively correlates with the transcription of their corresponding genes.
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Affiliation(s)
- Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Aashiq H Mirza
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Jianmin Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Steven A Soper
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York.
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81
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Adir O, Poley M, Chen G, Froim S, Krinsky N, Shklover J, Shainsky-Roitman J, Lammers T, Schroeder A. Integrating Artificial Intelligence and Nanotechnology for Precision Cancer Medicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901989. [PMID: 31286573 PMCID: PMC7124889 DOI: 10.1002/adma.201901989] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/17/2019] [Indexed: 05/13/2023]
Abstract
Artificial intelligence (AI) and nanotechnology are two fields that are instrumental in realizing the goal of precision medicine-tailoring the best treatment for each cancer patient. Recent conversion between these two fields is enabling better patient data acquisition and improved design of nanomaterials for precision cancer medicine. Diagnostic nanomaterials are used to assemble a patient-specific disease profile, which is then leveraged, through a set of therapeutic nanotechnologies, to improve the treatment outcome. However, high intratumor and interpatient heterogeneities make the rational design of diagnostic and therapeutic platforms, and analysis of their output, extremely difficult. Integration of AI approaches can bridge this gap, using pattern analysis and classification algorithms for improved diagnostic and therapeutic accuracy. Nanomedicine design also benefits from the application of AI, by optimizing material properties according to predicted interactions with the target drug, biological fluids, immune system, vasculature, and cell membranes, all affecting therapeutic efficacy. Here, fundamental concepts in AI are described and the contributions and promise of nanotechnology coupled with AI to the future of precision cancer medicine are reviewed.
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Affiliation(s)
- Omer Adir
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Maria Poley
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gal Chen
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sahar Froim
- Department of Physical Electronics, School of Electrical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Nitzan Krinsky
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Jeny Shklover
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Janna Shainsky-Roitman
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Twan Lammers
- Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen, 52074, Germany
| | - Avi Schroeder
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
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82
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Lin K, Huang J, Luo H, Luo C, Zhu X, Bu F, Xiao H, Xiao L, Zhu Z. Development of a prognostic index and screening of potential biomarkers based on immunogenomic landscape analysis of colorectal cancer. Aging (Albany NY) 2020; 12:5832-5857. [PMID: 32235004 PMCID: PMC7185108 DOI: 10.18632/aging.102979] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/03/2020] [Indexed: 12/26/2022]
Abstract
Background: Colorectal cancer (CRC) accounts for the highest fatality rate among all malignant tumors. Immunotherapy has shown great promise in management of many malignant tumors, necessitating the need to explore its role in CRC. Results: Our analysis revealed a total of 71 differentially expressed IRGs, that were associated with prognosis of CRC patients. Ten IRGs (FABP4, IGKV1-33, IGKV2D-40, IGLV6-57, NGF, RETNLB, UCN, VIP, NGFR, and OXTR) showed high prognostic performance in predicting CRC outcomes, and were further associated with tumor burden, metastasis, tumor TNM stage, gender, age, and pathological stage. Interestingly, the IRG-based prognostic index (IRGPI) reflected infiltration of multiple immune cell types. Conclusions: This model provides an effective approach for stratification and characterization of patients using IRG-based immunolabeling tools to monitor prognosis of CRC. Methods: We performed a comprehensive analysis of expression profiles for immune-related genes (IRGs) and overall survival time in 437 CRC patients from the TCGA database. We employed computational algorithms and Cox regression analysis to estimate the relationship between differentially expressed IRGs and survival rates in CRC patients. Furthermore, we investigated the mechanisms of action of the IRGs involved in CRC, and established a novel prognostic index based on multivariate Cox models.
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Affiliation(s)
- Kang Lin
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Jun Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Chen Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Xiaojian Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Fanqin Bu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Han Xiao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Li Xiao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Zhengming Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
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Singh A, Gupta S, Badarukhiya JA, Sachan M. Detection of aberrant methylation of HOXA9 and HIC1 through multiplex MethyLight assay in serum DNA for the early detection of epithelial ovarian cancer. Int J Cancer 2020; 147:1740-1752. [PMID: 32191343 DOI: 10.1002/ijc.32984] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/22/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Accumulated evidence revealed that aberrant CpG island hypermethylation plays an important role in carcinogenesis which can serve as a promising target for molecular detection in body fluids. Despite a myriad of attempts to diagnose ovarian cancer (OC) at an early stage, this clinical aim remains a major challenge. To date, no single biomarker is able to accurately detect early OC in either tissue or body fluid. Aberrant DNA methylation patterns in circulating DNA provide highly specific cancer signals. In our study, we establish a novel panel of methylation-specific genes for the development of a TaqMan based qPCR assay to quantify methylation levels. We analyzed promoter methylation of homeobox A9 (HOXA9) and hypermethylated in cancer 1 (HIC1) quantitatively in 120 tissue samples and in 70 matched serum cell-free DNA (CFDNA) of cancerous and noncancerous samples by MethyLight assay. HOXA9 and HIC1 methylation occurred in 82.3 and 80.0% of OC tissue samples in singleplex assay, thereby confirming that methylation was highly cancer-specific. When either or both gene promoter showed methylation, the sensitivity was 88.2% with a specificity of 88.6% in tissue samples. The combined sensitivity for this novel marker panel in serum CFDNA was 88.9% (area under the curve [AUC] = 0.95). In contrast, no hypermethylation was observed in serum from matched cancer-free control women. Our results confirm the elevated performance of novel epigenetic marker panel (HOXA9 and HIC1) when analyzed in tissue and matched serum samples. Our findings reveal the potential of this biomarker panel as a suitable diagnostic serum biomarker for early screening of OC.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | | | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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84
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Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:E624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients' stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a "PanCancer" detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
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85
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Zhou Q, Perakis SO, Ulz P, Mohan S, Riedl JM, Talakic E, Lax S, Tötsch M, Hoefler G, Bauernhofer T, Pichler M, Gerger A, Geigl JB, Heitzer E, Speicher MR. Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer. Genome Med 2020; 12:20. [PMID: 32087735 PMCID: PMC7036260 DOI: 10.1186/s13073-020-0719-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/31/2020] [Indexed: 02/08/2023] Open
Abstract
Background Bevacizumab, a monoclonal antibody against soluble VEGFA, is an approved and commonly administered anti-angiogenic drug in patients with metastasized colorectal cancer (mCRC). The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months, and acquired resistance mechanisms are largely unknown. Here, we employed whole-genome sequencing of plasma DNA to evaluate the tumor genome of patients undergoing treatment with bevacizumab to determine novel aberrations associated with resistance. Methods Using longitudinal plasma analyses, we studied the evolution of tumor genomes in a mCRC cohort (n = 150) and conducted analyses of CRC cases from The Cancer Genome Atlas (TCGA) database (n = 619) to identify associations between genomic aberrations and clinical features. We employed whole-genome sequencing to identify the most frequently occurring focal somatic copy number alterations (SCNAs). Using the TCGA data as a comparative and supporting dataset, we defined the minimally amplified overlapping region and studied the mechanistic consequences of copy number gain of the involved genes in this segment. In addition, we established an in vitro cell model and conducted downstream gene expression and cell viability assays to confirm our findings from the patient dataset. Results We observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of CRC cases from the TCGA database suggested that this amplicon is associated with more advanced stages. We confirmed that this 13q12.2 amplicon frequently emerges later during the clinical course of disease. After defining the minimally amplified region, we observed that the amplification and expression of one gene, POLR1D, impacted cell proliferation and resulted in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab treatment. In fact, in several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with therapy resistance. Conclusions Non-invasive analyses of cell-free DNA from patients undergoing treatment with bevacizumab enabled the tracking of evolving tumor genomes and helped identify a recurrent focal SCNA of clinical relevance. Here, we describe a novel resistance mechanism against a widely applied treatment in patients with mCRC which will impact the clinical management of patients.
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Affiliation(s)
- Qing Zhou
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Samantha O Perakis
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria.,Present address: Freenome, South San Francisco, CA, USA
| | - Sumitra Mohan
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria.,Present address: Cancer Research UK-Manchester Institute, Manchester, UK
| | - Jakob M Riedl
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Emina Talakic
- Division of General Radiology, Medical University of Graz, Graz, Austria
| | - Sigurd Lax
- Department of Pathology, General Hospital Graz II, Graz, Austria.,Johannes Kepler University Linz, Linz, Austria
| | - Martin Tötsch
- Institute of Pathology, General Hospital Hochsteiermark, Leoben, Austria
| | - Gerald Hoefler
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Thomas Bauernhofer
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Jochen B Geigl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria.
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86
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Hariharan R, Jenkins M. Utility of the methylated SEPT9 test for the early detection of colorectal cancer: a systematic review and meta-analysis of diagnostic test accuracy. BMJ Open Gastroenterol 2020; 7:e000355. [PMID: 32128229 PMCID: PMC7039590 DOI: 10.1136/bmjgast-2019-000355] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Background Circulating tumour DNA from colorectal cancer (CRC) is a biomarker for early detection of the disease and therefore potentially useful for screening. One such biomarker is the methylated SEPT9 (mSEPT9) gene, which occurs during CRC tumourigenesis. This systematic review and meta-analysis aims to establish the sensitivity, specificity and accuracy of mSEPT9 tests for the early diagnosis of CRC. Methods A systematic search of the relevant literature was conducted using Medline and Embase databases. Data were extracted from the eligible studies and analysed to estimate pooled sensitivity, specificity and diagnostic test accuracy. Results Based on 19 studies, the pooled estimates (and 95% CIs) for mSEPT9 to detect CRC were: sensitivity 69% (62-75); specificity 92% (89-95); positive likelihood ratio 9.1 (6.1-13.8); negative likelihood ratio 0.34 (0.27-0.42); diagnostic OR 27 (15-48) and area under the curve 0.89 (0.86-0.91). The test has a positive predictive value of 2.6% and negative predictive value of 99.9% in an average risk population (0.3% CRC prevalence), and 9.5% (positive predictive value) and 99.6% (negative predictive value) in a high-risk population (1.2% CRC prevalence). Conclusion The mSEPT9 test has high specificity and moderate sensitivity for CRC and is therefore a potential alternative screening method for those declining faecal immunochemical test for occult blood (FIT) or other screening modalities. However, it is limited by its poor diagnostic performance for precancerous lesions (advanced adenomas and polyps) and its relatively high costs, and little is known about its acceptability to those declining to use the FIT.
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Affiliation(s)
- Rohit Hariharan
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
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87
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Binnie A, Walsh CJ, Hu P, Dwivedi DJ, Fox-Robichaud A, Liaw PC, Tsang JLY, Batt J, Carrasqueiro G, Gupta S, Marshall JC, Castelo-Branco P, Dos Santos CC. Epigenetic Profiling in Severe Sepsis: A Pilot Study of DNA Methylation Profiles in Critical Illness. Crit Care Med 2020; 48:142-150. [PMID: 31939781 DOI: 10.1097/ccm.0000000000004097] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Epigenetic alterations are an important regulator of gene expression in health and disease; however, epigenetic data in sepsis are lacking. To demonstrate proof of concept and estimate effect size, we performed the first epigenome-wide methylation analysis of whole blood DNA samples from a cohort of septic and nonseptic critically ill patients. DESIGN A nested case-control study using genomic DNA isolated from whole blood from septic (n = 66) and nonseptic (n = 68) critically ill patients on "Day 1" of ICU admission. Methylation patterns were identified using Illumina 450K arrays with percent methylation expressed as β values. After quality control, 134 participants and 414,818 autosomal cytosine-phosphate-guanine sites were used for epigenome-wide methylation analyses. SETTING Tertiary care hospitals. SUBJECTS Critically ill septic and nonseptic patients. INTERVENTIONS Observational study. MEASUREMENTS AND MAIN RESULTS A total of 668 differentially methylated regions corresponding to 443 genes were identified. Known sepsis-associated genes included complement component 3; angiopoietin 2; myeloperoxidase; lactoperoxidase; major histocompatibility complex, class I, A; major histocompatibility complex, class II, isotype DR β I; major histocompatibility complex, class I, C; and major histocompatibility complex, class II, isotype DQ β I. When compared with whole blood gene expression data from seven external datasets containing septic and nonseptic patients, 81% of the differentially methylated region-associated genes were differentially expressed in one or more datasets and 31% in three or more datasets. Functional analysis showed enrichment for antigen processing and presentation, methyltransferase activity, cell adhesion, and cell junctions. Analysis by weighted gene coexpression network analysis revealed DNA comethylation modules that were associated with clinical traits including severity of illness, need for vasopressors, and length of stay. CONCLUSIONS DNA methylation marks may provide important causal and potentially biomarker information in critically ill patients with sepsis.
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Affiliation(s)
- Alexandra Binnie
- Department of Critical Care, William Osler Health System, Brampton, ON, Canada
| | - Christopher J Walsh
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Dhruva J Dwivedi
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Alison Fox-Robichaud
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Patricia C Liaw
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jennifer L Y Tsang
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Niagara Health, St. Catharines, ON, Canada
| | - Jane Batt
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gabriela Carrasqueiro
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
- Algarve Biomedical Center, Faro, Portugal
| | - Sahil Gupta
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - John C Marshall
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pedro Castelo-Branco
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
- Algarve Biomedical Center, Faro, Portugal
- Regenerative Medicine Program, Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal
| | - Claudia C Dos Santos
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
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88
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Bacolod MD, Huang J, Giardina SF, Feinberg PB, Mirza AH, Swistel A, Soper SA, Barany F. Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection. BMC Cancer 2020; 20:85. [PMID: 32005108 PMCID: PMC6995062 DOI: 10.1186/s12885-020-6574-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/23/2020] [Indexed: 12/24/2022] Open
Abstract
Background Interrogation of site-specific CpG methylation in circulating tumor DNAs (ctDNAs) has been employed in a number of studies for early detection of breast cancer (BrCa). In many of these studies, the markers were identified based on known biology of BrCa progression, and interrogated using methyl-specific PCR (MSP), a technique involving bisulfite conversion, PCR, and qPCR. Methods In this report, we are demonstrating the development of a novel assay (Multiplex Bisulfite PCR-LDR-qPCR) which can potentially offer improvements to MSP, by integrating additional steps such as ligase detection reaction (LDR), methylated CpG target enrichment, carryover protection (use of uracil DNA glycosylase), and minimization of primer-dimer formation (use of ribose primers and RNAseH2). The assay is designed to for breast cancer-specific CpG markers identified through integrated analyses of publicly available genome-wide methylation datasets for 31 types of primary tumors (including BrCa), as well as matching normal tissues, and peripheral blood. Results Our results indicate that the PCR-LDR-qPCR assay is capable of detecting ~ 30 methylated copies of each of 3 BrCa-specific CpG markers, when mixed with excess amount unmethylated CpG markers (~ 3000 copies each), which is a reasonable approximation of BrCa ctDNA overwhelmed with peripheral blood cell-free DNA (cfDNA) when isolated from patient plasma. The bioinformatically-identified CpG markers are located in promoter regions of NR5A2 and PRKCB, and a non-coding region of chromosome 1 (upstream of EFNA3). Additional bioinformatic analyses would reveal that these methylation markers are independent of patient race and age, and positively associated with signaling pathways associated with BrCa progression (such as those related to retinoid nuclear receptor, PTEN, p53, pRB, and p27). Conclusion This report demonstrates the potential utilization of bisulfite PCR-LDR-qPCR assay, along with bioinformatically-driven biomarker discovery, in blood-based BrCa detection.
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Affiliation(s)
- Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Jianmin Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Aashiq H Mirza
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Alexander Swistel
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Steven A Soper
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS, 66047, USA
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA.
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89
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Haupts A, Roth W, Hartmann N. [Liquid biopsy in colorectal cancer : An overview of ctDNA analysis in tumour diagnostics]. DER PATHOLOGE 2020; 40:244-251. [PMID: 31797045 DOI: 10.1007/s00292-019-00698-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In current routine diagnostics, the gold standard to determine the genomic profile of colorectal cancers (CRCs) is using biopsy or surgically resected tissues. However, such a tissue sample cannot represent the entire tumour heterogeneity, because it only shows a local and temporal snapshot. As a complement to tumour tissue genotyping, liquid biopsies enable minimally invasive detection of all potential tumour-specific mutations and their dynamic changes for molecular profiling. Furthermore, they can be repeated in certain intervals for monitoring response to treatment, occurrence of drug resistance and detection of relapse. This review focusses on analyzing circulating cell-free tumour DNA (ctDNA), which is mostly released from apoptotic or necrotic tumour cells into the bloodstream or by active secretion of circulating tumour cells (CTCs). Nevertheless, there are some challenges in analyzing ctDNA. First, ctDNA represents only a small fraction of total circulating DNA, because there is an enormous wild-type background of cell-free DNA (cfDNA) released by healthy cells. Second, ctDNA is highly fragmented and the amount of ctDNA in the blood is very low. In this review, we discuss the potential, fields of application as well as challenges and limitations of liquid biopsy approaches. In more detail, we discuss the possibility of using liquid biopsies as a future application for molecular characterization of CRCs, particularly for monitoring CRC patients during anti-EGFR therapy to detect resistance mutations (e.g. KRAS mutations) or further therapy-relevant mutations. In addition, we investigate whether blood-based molecular profiling is a reliable addition to routine diagnostic approaches of tissue-based molecular characterization.
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Affiliation(s)
- A Haupts
- Institut für Pathologie, Universitätsmedizin Mainz, Langenbeckstr. 1, 55131, Mainz, Deutschland.
| | - W Roth
- Institut für Pathologie, Universitätsmedizin Mainz, Langenbeckstr. 1, 55131, Mainz, Deutschland
| | - N Hartmann
- Institut für Pathologie, Universitätsmedizin Mainz, Langenbeckstr. 1, 55131, Mainz, Deutschland
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90
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Kotoh Y, Suehiro Y, Saeki I, Hoshida T, Maeda M, Iwamoto T, Matsumoto T, Hidaka I, Ishikawa T, Takami T, Higaki S, Fujii I, Suzuki C, Shindo Y, Tokumitsu Y, Nagano H, Sakaida I, Yamasaki T. Novel Liquid Biopsy Test Based on a Sensitive Methylated SEPT9 Assay for Diagnosing Hepatocellular Carcinoma. Hepatol Commun 2020; 4:461-470. [PMID: 32140662 PMCID: PMC7049671 DOI: 10.1002/hep4.1469] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/07/2019] [Indexed: 12/15/2022] Open
Abstract
Liquid biopsies are not used in practice for hepatocellular carcinoma (HCC). Epi proColon is the first commercial blood-based test for colorectal cancer screening based on methylated DNA testing of the septin 9 gene (SEPT9). However, Epi proColon has some disadvantages, including the requirement of a large amount of blood and lack of quantitative performance. Therefore, we previously developed a novel liquid biopsy test that can quantitatively detect even a single copy of methylated SEPT9 in a small amount of DNA. In the current study, we evaluated the application potential of this assay for diagnosing HCC. Study subjects included 80 healthy volunteers, 45 patients with chronic liver disease (CLD) without HCC, and 136 patients with HCC (stage 0, 12; stage A, 50; stage B, 31; stage C, 41; and stage D, 2), according to the Barcelona Clinic Liver Cancer staging system. For the assay, DNA was treated with methylation-sensitive restriction enzymes in two steps, followed by multiplex droplet digital polymerase chain reaction. The median copy number of methylated SEPT9 was 0.0, 2.0, and 6.4 in the healthy control, CLD, and HCC groups, respectively, with significant differences among the groups (HCC vs. healthy control, P < 0.001; HCC vs. CLD, P = 0.002; CLD vs. healthy control, P = 0.008). Assay sensitivity and specificity were 63.2% and 90.0%, respectively (cutoff value, 4.6 copies), in detecting HCC when compared with healthy subjects. The positive rate of methylated SEPT9 increased with HCC progression (stage 0, 41.7%; stage A, 58.0%; stage B, 61.3%; stage C, 75.6%; and stage D, 100%). Conclusion: We developed a sensitive methylated SEPT9 assay that might serve as a liquid biopsy test for diagnosing HCC.
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Affiliation(s)
- Yurika Kotoh
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Yutaka Suehiro
- Department of Oncology and Laboratory Medicine Yamaguchi University Graduate School of Medicine Ube Japan
| | - Issei Saeki
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Tomomi Hoshida
- Department of Oncology and Laboratory Medicine Yamaguchi University Graduate School of Medicine Ube Japan
| | - Masaki Maeda
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Takuya Iwamoto
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Toshihiko Matsumoto
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan.,Department of Oncology and Laboratory Medicine Yamaguchi University Graduate School of Medicine Ube Japan
| | - Isao Hidaka
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Tsuyoshi Ishikawa
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Taro Takami
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Shingo Higaki
- Department of Gastroenterology Sentohiru Hospital Ube Japan
| | | | | | - Yoshitaro Shindo
- Department of Gastroenterological, Breast and Endocrine Surgery Yamaguchi University Graduate School of Medicine Ube Japan
| | - Yukio Tokumitsu
- Department of Gastroenterological, Breast and Endocrine Surgery Yamaguchi University Graduate School of Medicine Ube Japan
| | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery Yamaguchi University Graduate School of Medicine Ube Japan
| | - Isao Sakaida
- Department of Gastroenterology and Hepatology Yamaguchi University Graduate School of Medicine Ube Japan
| | - Takahiro Yamasaki
- Department of Oncology and Laboratory Medicine Yamaguchi University Graduate School of Medicine Ube Japan
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91
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Nguyen LH, Goel A, Chung DC. Pathways of Colorectal Carcinogenesis. Gastroenterology 2020; 158:291-302. [PMID: 31622622 PMCID: PMC6981255 DOI: 10.1053/j.gastro.2019.08.059] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 12/15/2022]
Abstract
Colorectal cancer is a heterogeneous disease that develops via stepwise accumulation of well-characterized genetic and epigenetic alterations. We review the genetic changes associated with the development of precancerous colorectal adenomas and their progression to tumors, as well as the effects of defective DNA repair, chromosome instability, microsatellite instability, and alterations in the serrated pathway and DNA methylation. We provide insights into the different molecular subgroups of colorectal tumors that develop via each of these different mechanisms and their associations with patient outcomes.
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Affiliation(s)
- Long H Nguyen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Dallas, Texas; Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas; Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California.
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Risk Assessment, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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Luo H, Zhao Q, Wei W, Zheng L, Yi S, Li G, Wang W, Sheng H, Pu H, Mo H, Zuo Z, Liu Z, Li C, Xie C, Zeng Z, Li W, Hao X, Liu Y, Cao S, Liu W, Gibson S, Zhang K, Xu G, Xu RH. Circulating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal cancer. Sci Transl Med 2020; 12:12/524/eaax7533. [PMID: 31894106 DOI: 10.1126/scitranslmed.aax7533] [Citation(s) in RCA: 234] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a useful diagnostic and prognostic biomarker in many cancers. Here, we conducted a study to investigate the potential use of ctDNA methylation markers for the diagnosis and prognostication of colorectal cancer (CRC) and used a prospective cohort to validate their effectiveness in screening patients at high risk of CRC. We first identified CRC-specific methylation signatures by comparing CRC tissues to normal blood leukocytes. Then, we applied a machine learning algorithm to develop a predictive diagnostic and a prognostic model using cell-free DNA (cfDNA) samples from a cohort of 801 patients with CRC and 1021 normal controls. The obtained diagnostic prediction model discriminated patients with CRC from normal controls with high accuracy (area under curve = 0.96). The prognostic prediction model also effectively predicted the prognosis and survival of patients with CRC (P < 0.001). In addition, we generated a ctDNA-based molecular classification of CRC using an unsupervised clustering method and obtained two subgroups of patients with CRC with significantly different overall survival (P = 0.011 in validation cohort). Last, we found that a single ctDNA methylation marker, cg10673833, could yield high sensitivity (89.7%) and specificity (86.8%) for detection of CRC and precancerous lesions in a high-risk population of 1493 participants in a prospective cohort study. Together, our findings showed the value of ctDNA methylation markers in the diagnosis, surveillance, and prognosis of CRC.
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Affiliation(s)
- Huiyan Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Qi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Wei Wei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Lianghong Zheng
- Guangzhou Youze Biological Pharmaceutical Technology Company Ltd., Guangzhou 510005, P.R. China
| | - Shaohua Yi
- Huazhong University of Science and Technology Tongji Medical College, Wuhan 430030, P. R. China
| | - Gen Li
- Guangzhou Women and Children’s Medical Center, Guangzhou 510623, P. R. China
| | - Wenqiu Wang
- Shanghai General Hospital, Shanghai 200080, P. R. China
| | - Hui Sheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Hengying Pu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Haiyu Mo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Zexian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Chaofeng Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Chuanbo Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Zhaolei Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Weimin Li
- Molecular Medicine Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Xiaoke Hao
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, P. R. China
| | - Yuying Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Sumei Cao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Wanli Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Sarah Gibson
- Guangzhou Women and Children’s Medical Center, Guangzhou 510623, P. R. China
| | - Kang Zhang
- Molecular Medicine Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
- Faculty of Medicine, Macau University of Science and Technology, Macau 999078, P. R. China
| | - Guoliang Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
| | - Rui-hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China
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93
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Nee J, Chippendale RZ, Feuerstein JD. Screening for Colon Cancer in Older Adults: Risks, Benefits, and When to Stop. Mayo Clin Proc 2020; 95:184-196. [PMID: 31902414 DOI: 10.1016/j.mayocp.2019.02.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 12/26/2022]
Abstract
Colorectal cancer (CRC) is the fourth leading cause of cancer and second leading cause of mortality from cancer in the United States. As the population ages, decisions regarding the initiation and cessation of screening and surveillance for CRC are of increasing importance. In elderly patients, the risks of CRC and the presenting signs and symptoms are similar to those in younger patients. Screening and ongoing surveillance should be considered in patients who have a life expectancy of 10 years or more. Life expectancy estimates can be calculated using online calculators. If screening is deemed appropriate, the choice of which test to use first is unclear. Currently, there are a number of modalities available to screen for CRC, including both invasive modalities (eg, colonoscopy, sigmoidoscopy, capsule colonoscopy, and computed tomographic colonography) and noninvasive modalities (fecal immunochemical test, stool DNA testing, and blood testing). Colonoscopy and other invasive testing options are considered safe, but the risks of complications of the bowel preparation, the procedure, and sedation medications are all increased in older patients. In contrast, noninvasive testing provides a safe initial test; however, it is important to consider the increased false-positive rates in the elderly, and a positive test result will usually necessitate colonoscopy to establish the diagnosis. Ongoing screening and surveillance should be a shared decision-making process with the patient based on multiple factors including the patient's morbidity and mortality risk from CRC and his or her underlying comorbidities, the patient's functional status, and the patient's preferences for screening. Ultimately, the decision to initiate or discontinue screening for CRC in older patients should be done based on a case-by-case individualized discussion.
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Affiliation(s)
- Judy Nee
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Ryan Z Chippendale
- Division of Geriatrics, Department of Medicine, Boston Medical Center, Boston MA
| | - Joseph D Feuerstein
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA.
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94
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Danese E, Montagnana M, Lippi G. Circulating molecular biomarkers for screening or early diagnosis of colorectal cancer: which is ready for prime time? ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:610. [PMID: 32047771 PMCID: PMC7011594 DOI: 10.21037/atm.2019.08.97] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
According to recent statistics, colorectal cancer (CRC) is a frequent disease, the second most frequent malignancy in women and the third most common malignant disease in men, respectively. Although reinforced emphasis on CRC screening by means of immunochemical fecal occult blood test, colonoscopy or sigmoidoscopy has contributed to decrease cancer-related deaths, alternative diagnostic tests would be needed for establishing earlier and more potentially effective treatments. Innovative diagnostic techniques have recently emerged, some of which hold promises for screening and/or early CRC detection. Recent evidence suggests that the so-called "liquid biopsy", conventionally defined as detection and quantification of circulating tumor cells (CTCs) and cancer-related nucleic acids in peripheral blood, may allow earlier diagnosis of CRC combined with lower invasiveness and less patient inconvenience, higher throughput, faster turnaround time, inferior usage of healthcare resources and relatively low cost. Encouraging data have emerged from trials based on CTCs detection, though the sensitivity of the current diagnostic techniques is still perhaps insufficient for enabling early CRC diagnosis. Among the various biomarkers that can be detected with liquid biopsy, SEPT9 methylation displays good diagnostic performance and relatively high cancer detection rate (between 57-64% in patients with CRC stages 0-I), which would make this test a promising tool for population screening, alone or in combination with other conventional diagnostic investigations. Encouraging evidence has also been recently published for BCAT1/IKZF1 methylation. Regarding microRNA (miRNAs), the available evidence highlights that the combination of some of these biomarkers rather than the assessment of a single miRNA alone would enable efficient identification of early CRCs, though widespread clinical application is still challenged by a number of preanalytical, analytical and clinical issues.
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Affiliation(s)
- Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | | | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
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95
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Hissong E, Pittman ME. Colorectal carcinoma screening: Established methods and emerging technology. Crit Rev Clin Lab Sci 2019; 57:22-36. [PMID: 31603697 DOI: 10.1080/10408363.2019.1670614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Colorectal carcinoma screening programs have shown success in lowering both the incidence and mortality rate of colorectal carcinoma at a population level, in part because this carcinoma is relatively slow growing and has an identifiable premalignant lesion. Still, many patients do not undergo the recommended screening for colorectal carcinoma, and of those who do, a subset may be over- or under-diagnosed by the currently available testing methods. The primary purpose of this article is to review the data regarding currently available colorectal cancer screening modalities, which include fecal occult blood testing, direct colonic visualization, and noninvasive imaging techniques. In addition, readers will be introduced to a variety of biomarkers that may serve as stand-alone or adjunct tests in the future. Finally, there is a brief discussion of the current epidemiologic considerations that public health officials must address as they create population screening guidelines. The data we provide as laboratory physicians and scientists are critical to the construction of appropriate recommendations that ultimately decrease the burden of disease from colorectal carcinoma.
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Affiliation(s)
- Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Meredith E Pittman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
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96
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Zuluaga-Gomez J, Zerhouni N, Al Masry Z, Devalland C, Varnier C. A survey of breast cancer screening techniques: thermography and electrical impedance tomography. J Med Eng Technol 2019; 43:305-322. [DOI: 10.1080/03091902.2019.1664672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- J. Zuluaga-Gomez
- FEMTO-ST Institute, University Bourgogne Franche-Comté, CNRS, ENSMM, Besançon, France
- Department of Electrical Engineering, University of Oviedo, Gijon, Spain
- Universidad Autonoma Del Caribe, Barranquilla, Colombia
| | - N. Zerhouni
- FEMTO-ST Institute, University Bourgogne Franche-Comté, CNRS, ENSMM, Besançon, France
| | - Z. Al Masry
- FEMTO-ST Institute, University Bourgogne Franche-Comté, CNRS, ENSMM, Besançon, France
| | - C. Devalland
- Department of Pathology, Hospital Nord Franche-Comte, Belfort, France
| | - C. Varnier
- FEMTO-ST Institute, University Bourgogne Franche-Comté, CNRS, ENSMM, Besançon, France
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97
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Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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98
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Rafiei G, Shirkoohi R, Saffari M, Salehipour P, Modarressi MH. The Impact of Long-term Exposure to Low Levels of Inorganic Arsenic on the Hypomethylation of SEPT9 Promoter in Epithelial-Mesenchymal Transformed Colorectal Cancer Cell Lines. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2019; 8:130-138. [PMID: 32215264 DOI: 10.22088/ijmcm.bums.8.2.130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
Inorganic arsenicals are worldwide environmental contaminants that affect molecular characteristics in biological systems and lead to genomic and epigenomic instability as well as epithelial mesenchymal transition (EMT). In this study, we aimed to investigate whether low levels of sodium arsenite (iAsIII) can influence EMT and genomic instability through microsatellite analysis. We have also determined epigenomic instability by investigating the methylation status of SEPT9 tumor marker in colorectal cancer (CRC) cell lines, Caco2 and HCT116, which were treated with iAsIII to assess IC50s. Short-term and long-term exposure to low concentrations (1 µM and 0.1 µM) of iAsIII in two separate experiments was implemented to analyze EMT, microsatellite status and the methylation pattern of SEPT9 promoter. As expected, after 20 days of exposure to iAsIII, the expression of CDH1 was significantly decreased while the expression of CDH2, FIB1 and VIM was increased in Caco2 and HCT116, a finding that confirmed EMT induction. However, there was no detectable alteration in the size of microsatellites. As for the methylation pattern, SEPT9 promoter was hypomethylated as a result of long-term exposure to 0.1 µM iAsIII in Caco2. Long-term exposure of HCT116 to both concentrations could induce hypomethylation of SEPT9 promoter. Our findings indicate no linkage between EMT induction and microsatellite status in iAsIII-treated CRC cell lines. For the first time, the current study has shown that the induction of EMT by iAsIII is linked with SEPT9 promoter hypomethylation in Caco2 and HCT116 in a concentration- and time-dependent pattern.
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Affiliation(s)
- Gholamreza Rafiei
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shirkoohi
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojtaba Saffari
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Pouya Salehipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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99
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Nartowt BJ, Hart GR, Roffman DA, Llor X, Ali I, Muhammad W, Liang Y, Deng J. Scoring colorectal cancer risk with an artificial neural network based on self-reportable personal health data. PLoS One 2019; 14:e0221421. [PMID: 31437221 PMCID: PMC6705772 DOI: 10.1371/journal.pone.0221421] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is third in prevalence and mortality among all cancers in the US. Currently, the United States Preventative Services Task Force (USPSTF) recommends anyone ages 50-75 and/or with a family history to be screened for CRC. To improve screening specificity and sensitivity, we have built an artificial neural network (ANN) trained on 12 to 14 categories of personal health data from the National Health Interview Survey (NHIS). Years 1997-2016 of the NHIS contain 583,770 respondents who had never received a diagnosis of any cancer and 1409 who had received a diagnosis of CRC within 4 years of taking the survey. The trained ANN has sensitivity of 0.57 ± 0.03, specificity of 0.89 ± 0.02, positive predictive value of 0.0075 ± 0.0003, negative predictive value of 0.999 ± 0.001, and concordance of 0.80 ± 0.05 per the guidelines of Transparent Reporting of Multivariable Prediction Model for Individual Prognosis or Diagnosis (TRIPOD) level 2a, comparable to current risk-scoring methods. To demonstrate clinical applicability, both USPSTF guidelines and the trained ANN are used to stratify respondents to the 2017 NHIS into low-, medium- and high-risk categories (TRIPOD levels 4 and 2b, respectively). The number of CRC respondents misclassified as low risk is decreased from 35% by screening guidelines to 5% by ANN (in 60 cases). The number of non-CRC respondents misclassified as high risk is decreased from 53% by screening guidelines to 6% by ANN (in 25,457 cases). Our results demonstrate a robustly-tested method of stratifying CRC risk that is non-invasive, cost-effective, and easy to implement publicly.
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Affiliation(s)
- Bradley J. Nartowt
- Department of Therapeutic Radiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Gregory R. Hart
- Department of Therapeutic Radiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - David A. Roffman
- Sun Nuclear Corporation, Melbourne, FL, United States of America
| | - Xavier Llor
- Department of Digestive Diseases, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Issa Ali
- Department of Therapeutic Radiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Wazir Muhammad
- Department of Therapeutic Radiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Ying Liang
- Department of Therapeutic Radiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Jun Deng
- Department of Therapeutic Radiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America
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100
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Hu J, Hu B, Gui YC, Tan ZB, Xu JW. Diagnostic Value and Clinical Significance of Methylated SEPT9 for Colorectal Cancer: A Meta-Analysis. Med Sci Monit 2019; 25:5813-5822. [PMID: 31378778 PMCID: PMC6691747 DOI: 10.12659/msm.915472] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background This meta-analysis aimed to clarify the diagnostic role of plasma methylated SEPT9 (mSEPT9) in colorectal cancer (CRC) and examined its association with CRC. Material/Methods A systematic review was conducted prior to July 2018. Summary sensitivity, specificity, and positive and negative likelihood ratio (PLR/NLR) were calculated for the diagnostic value of mSEPT9 for CRC. The areas under the receiver operating curves (AUCs) were used to summarize the overall test performance. Results Twenty-two studies with 2271 CRC patients were enrolled. The summary sensitivity, specificity, PLR, NLR, DOR, and AUC of the overall analysis of mSEPT9 were 0.69, 0.92, 8.1, 0.34, 24, and 0.89, respectively. Subgroup and meta-regression analyses demonstrated that the diagnostic value was higher for the Epi proColon 2.0 assay, Asian ethnicity, and mSEPT9 test combined with fecal occult blood test (FOBT) or fecal immunochemical test (FIT) than for other test methods, white ethnicity, and mSEPT9 test alone. The rate of mSEPT9 positivity was higher in advanced CRC cases compared with early-stage CRC cases, and was higher in CRC cases than in adenoma cases. No significant difference in mSEPT9 positivity rate was found between left- and right-sided CRC. Conclusions Plasma mSEPT9 has a high diagnostic value for CRC, especially on the newly developed Epi proColon test 2.0 method. The diagnostic sensitivity is superior among Asians compared to whites, and the combination of mSEPT9 and FOBT/FIT has a better performance than mSEPT9 alone. Finally, the expression of mSEPT9 is associated with CRC stage but not with location.
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Affiliation(s)
- Jincui Hu
- Department of Physical Medicine and Rehabilitation, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Bangli Hu
- Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Yu-Chang Gui
- Department of Physical Medicine and Rehabilitation, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Zhi-Biao Tan
- Department of Physical Medicine and Rehabilitation, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Jian-Wen Xu
- Department of Physical Medicine and Rehabilitation, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
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