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Cao Q, Dan Z, Hou N, Yan L, Yuan X, Lu H, Yu S, Zhang J, Xiao H, Liu Q, Zhang X, Zhang M, Pang M. Discovery and validation of colorectal cancer tissue-specific methylation markers: a dual-center retrospective cohort study. Clin Epigenetics 2024; 16:122. [PMID: 39244604 PMCID: PMC11380779 DOI: 10.1186/s13148-024-01735-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 08/26/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND AND PURPOSE Early detection, diagnosis, and treatment of colorectal cancer and its precancerous lesions can significantly improve patients' survival rates. The purpose of this research is to identify methylation markers specific to colorectal cancer tissues and validate their diagnostic capability in colorectal cancer and precancerous changes by measuring the level of DNA methylation in stool samples. METHOD We analyzed samples from six cancer tissues and adjacent normal tissues and fecal samples from 758 participants, including 62 patients with interfering diseases. Bioinformatics databases were used to screen for candidate biomarkers for CRC, and quantitative methylation-specific PCR methods were applied for identification. The methylation levels of the candidate biomarkers in fecal and tissue samples were measured. Logistic regression and random forest models were built and validated using fecal sample data from one of the centers, and the independent or combined diagnostic value of the candidate biomarkers in fecal samples for CRC and precancerous lesions was analyzed. Finally, the diagnostic capability and stability of the model were validated at another medical center. RESULTS This study identified two colorectal cancer CpG sites with tissue specificity. These two biomarkers have certain diagnostic power when used individually, but their diagnostic value for colorectal cancer and colorectal adenoma is more significant when they are used in combination. CONCLUSION The results indicate that a DNA methylation biomarker combined diagnostic model based on two CpG sites, cg13096260 and cg12587766, has the potential for screening and diagnosing precancerous lesions and colorectal cancer. Additionally, compared to traditional diagnostic models, machine learning algorithms perform better but may yield more false-positive results, necessitating further investigation.
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Affiliation(s)
- Qinxing Cao
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Zhenjia Dan
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Nengyi Hou
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Li Yan
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Xingmei Yuan
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Hejiang Lu
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Song Yu
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Jiangping Zhang
- Chongqing Bohao Diagnostic Technology Co., Ltd, Chongqing, 410010, China
| | - Huasheng Xiao
- Shanghai Biotechnology Corporation, Ltd, Shanghai, 200126, China
| | - Qiang Liu
- Shanghai Biotechnology Corporation, Ltd, Shanghai, 200126, China
| | - Xiaoyong Zhang
- Shanghai Biotechnology Corporation, Ltd, Shanghai, 200126, China
| | - Min Zhang
- Department of Outpatient, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - Minghui Pang
- Department of Geriatric General Surgery, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China.
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Liu X, Zhang H, Fan Y, Cai D, Lei R, Wang Q, Li Y, Shen L, Gu Y, Zhang Q, Qi Z, Wang Z. SNORA28 Promotes Proliferation and Radioresistance in Colorectal Cancer Cells through the STAT3 Pathway by Increasing H3K9 Acetylation in the LIFR Promoter. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405332. [PMID: 38924373 PMCID: PMC11347989 DOI: 10.1002/advs.202405332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Radiotherapy is essential for treating colorectal cancer (CRC), especially in advanced rectal cancer. However, the low radiosensitivity of CRC cells greatly limits radiotherapy efficacy. Small nucleolar RNAs (snoRNAs) are a class of noncoding RNA that primarily direct post-transcriptional modifications of ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs), and other cellular RNAs. While snoRNAs are involved in tumor progression and chemoresistance, their association with radiosensitivity remains largely unknown. Herein, SNORA28 is shown highly expressed in CRC and is positively associated with poor prognosis. Furthermore, SNORA28 overexpression enhances the growth and radioresistance of CRC cells in vitro and in vivo. Mechanistically, SNORA28 acts as a molecular decoy that recruits bromodomain-containing protein 4 (BRD4), which increases the level of H3K9 acetylation at the LIFR promoter region. This stimulates LIFR transcription, which in turn triggers the JAK1/STAT3 pathway, enhancing the proliferation and radioresistance of CRC cells. Overall, these results highlight the ability of snoRNAs to regulate radiosensitivity in tumor cells and affect histone acetylation modification in the promoter region of target genes, thus broadening the current knowledge of snoRNA biological functions and the mechanism underlying target gene regulation.
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Affiliation(s)
- Xin Liu
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Hong Zhang
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Ying Fan
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Dan Cai
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
- Graduate Collaborative Training Base of Academy of Military SciencesHengyang Medical SchoolUniversity of South ChinaHengyangHunan421001China
| | - Ridan Lei
- Department of Epidemiology and Health StatisticsXiangya School of Public HealthCentral South UniversityChangshaHunan410078China
| | - Qi Wang
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Yaqiong Li
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Liping Shen
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Yongqing Gu
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Qingtong Zhang
- Department of Colorectal SurgeryLiaoning Cancer Hospital & InstituteCancer Hospital of China Medical UniversityCancer Hospital of Dalian University of TechnologyShenyang110042China
| | - Zhenhua Qi
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Zhidong Wang
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
- Graduate Collaborative Training Base of Academy of Military SciencesHengyang Medical SchoolUniversity of South ChinaHengyangHunan421001China
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Ryu H, Kim JH, Kim YJ, Jeon H, Kim BC, Jeon Y, Kim Y, Bak H, Kang Y, Kim C, Um H, Ahn JH, Hyun H, Kim BC, Song I, Jeon S, Bhak J, Han EC. Quantification method of ctDNA using cell-free DNA methylation profile for noninvasive screening and monitoring of colon cancer. Clin Epigenetics 2024; 16:95. [PMID: 39030645 PMCID: PMC11264732 DOI: 10.1186/s13148-024-01708-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 07/09/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Colon cancer ranks as the second most lethal form of cancer globally. In recent years, there has been active investigation into using the methylation profile of circulating tumor DNA (ctDNA), derived from blood, as a promising indicator for diagnosing and monitoring colon cancer. RESULTS We propose a liquid biopsy-based epigenetic method developed by utilizing 49 patients and 260 healthy controls methylation profile data to screen and monitor colon cancer. Our method initially identified 901 colon cancer-specific hypermethylated (CaSH) regions in the tissues of the 49 cancer patients. We then used these CaSH regions to accurately quantify the amount of circulating tumor DNA (ctDNA) in the blood samples of these same patients, utilizing cell-free DNA methylation profiles. Notably, the methylation profiles of ctDNA in the blood exhibited high sensitivity (82%) and specificity (93%) in distinguishing patients with colon cancer from the control group, with an area under the curve of 0.903. Furthermore, we confirm that our method for ctDNA quantification is effective for monitoring cancer patients and can serve as a valuable tool for postoperative prognosis. CONCLUSIONS This study demonstrated a successful application of the quantification of ctDNA among cfDNA using the original cancer tissue-derived CaSH region for screening and monitoring colon cancer.
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Affiliation(s)
- Hyojung Ryu
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | - Ji-Hoon Kim
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
- GenomeLab, Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yeo Jin Kim
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | - Hahyeon Jeon
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | | | - Yeonsu Jeon
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | | | - Hyebin Bak
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | | | - Changjae Kim
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | - Hyojin Um
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | - Ji-Hye Ahn
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | - Hwi Hyun
- Clinomics, Inc., Ulsan, 44919, Republic of Korea
| | | | - Inho Song
- Division of Colorectal Surgery, Department of Surgery, Dongnam Institute of Radiological and Medical Sciences, Busan, 46033, Republic of Korea
| | - Sungwon Jeon
- Clinomics, Inc., Ulsan, 44919, Republic of Korea.
- Geromics Inc., Suwon, 16229, Republic of Korea.
| | - Jong Bhak
- Clinomics, Inc., Ulsan, 44919, Republic of Korea.
- GenomeLab, Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Geromics Inc., Suwon, 16229, Republic of Korea.
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju, 28160, Republic of Korea.
| | - Eon Chul Han
- Division of Colorectal Surgery, Department of Surgery, Dongnam Institute of Radiological and Medical Sciences, Busan, 46033, Republic of Korea.
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Maekawa M, Tanaka A, Ogawa M, Roehrl MH. Propensity score matching as an effective strategy for biomarker cohort design and omics data analysis. PLoS One 2024; 19:e0302109. [PMID: 38696425 PMCID: PMC11065211 DOI: 10.1371/journal.pone.0302109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/27/2024] [Indexed: 05/04/2024] Open
Abstract
BACKGROUND Analysis of omics data that contain multidimensional biological and clinical information can be complex and make it difficult to deduce significance of specific biomarker factors. METHODS We explored the utility of propensity score matching (PSM), a statistical technique for minimizing confounding factors and simplifying the examination of specific factors. We tested two datasets generated from cohorts of colorectal cancer (CRC) patients, one comprised of immunohistochemical analysis of 12 protein markers in 544 CRC tissues and another consisting of RNA-seq profiles of 163 CRC cases. We examined the efficiency of PSM by comparing pre- and post-PSM analytical results. RESULTS Unlike conventional analysis which typically compares randomized cohorts of cancer and normal tissues, PSM enabled direct comparison between patient characteristics uncovering new prognostic biomarkers. By creating optimally matched groups to minimize confounding effects, our study demonstrates that PSM enables robust extraction of significant biomarkers while requiring fewer cancer cases and smaller overall patient cohorts. CONCLUSION PSM may emerge as an efficient and cost-effective strategy for multiomic data analysis and clinical trial design for biomarker discovery.
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Affiliation(s)
- Masaki Maekawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Atsushi Tanaka
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Makiko Ogawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Michael H. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
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Du Z, Jiang Y, Yang Y, Kang X, Yan J, Liu B, Yang M. A multi-omics analysis-based model to predict the prognosis of low-grade gliomas. Sci Rep 2024; 14:9427. [PMID: 38658591 PMCID: PMC11043340 DOI: 10.1038/s41598-024-58434-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024] Open
Abstract
Lower-grade gliomas (LGGs) exhibit highly variable clinical behaviors, while classic histology characteristics cannot accurately reflect the authentic biological behaviors, clinical outcomes, and prognosis of LGGs. In this study, we carried out analyses of whole exome sequencing, RNA sequencing and DNA methylation in primary vs. recurrent LGG samples, and also combined the multi-omics data to construct a prognostic prediction model. TCGA-LGG dataset was searched for LGG samples. 523 samples were used for whole exome sequencing analysis, 532 for transcriptional analysis, and 529 for DNA methylation analysis. LASSO regression was used to screen genes with significant association with LGG survival from the frequently mutated genes, differentially expressed genes, and differentially methylated genes, whereby a prediction model for prognosis of LGG was further constructed and validated. The most frequently mutated diver genes in LGGs were IDH1 (77%), TP53 (48%), ATRX (37%), etc. Top significantly up-regulated genes were C6orf15, DAO, MEOX2, etc., and top significantly down-regulated genes were DMBX1, GPR50, HMX2, etc. 2077 genes were more and 299 were less methylated in recurrent vs. primary LGG samples. Thirty-nine genes from the above analysis were included to establish a prediction model of survival, which showed that the high-score group had a very significantly shorter survival than the low-score group in both training and testing sets. ROC analysis showed that AUC was 0.817 for the training set and 0.819 for the testing set. This study will be beneficial to accurately predict the survival of LGGs to identify patients with poor prognosis to take specific treatment as early, which will help improve the treatment outcomes and prognosis of LGG.
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Affiliation(s)
- Zhijie Du
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuehui Jiang
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yueling Yang
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaoyu Kang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing Yan
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Baorui Liu
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Mi Yang
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
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Sun M, Xu B, Chen C, Zhu Y, Li X, Chen K. Tissue of origin prediction for cancer of unknown primary using a targeted methylation sequencing panel. Clin Epigenetics 2024; 16:25. [PMID: 38336771 PMCID: PMC10854167 DOI: 10.1186/s13148-024-01638-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
RATIONALE Cancer of unknown primary (CUP) is a group of rare malignancies with poor prognosis and unidentifiable tissue-of-origin. Distinct DNA methylation patterns in different tissues and cancer types enable the identification of the tissue of origin in CUP patients, which could help risk assessment and guide site-directed therapy. METHODS Using genome-wide DNA methylation profile datasets from The Cancer Genome Atlas (TCGA) and machine learning methods, we developed a 200-CpG methylation feature classifier for CUP tissue of origin prediction (MFCUP). MFCUP was further validated with public-available methylation array data of 2977 specimens and targeted methylation sequencing of 78 Formalin-fixed paraffin-embedded (FFPE) samples from a single center. RESULTS MFCUP achieved an accuracy of 97.2% in a validation cohort (n = 5923) representing 25 cancer types. When applied to an Infinium 450 K array dataset (n = 1052) and an Infinium EPIC (850 K) array dataset (n = 1925), MFCUP achieved an overall accuracy of 93.4% and 84.8%, respectively. Based on MFCUP, we established a targeted bisulfite sequencing panel and validated it with FFPE sections from 78 patients of 20 cancer types. This methylation sequencing panel correctly identified tissue of origin in 88.5% (69/78) of samples. We also found that the methylation levels of specific CpGs can distinguish one cancer type from others, indicating their potential as biomarkers for cancer diagnosis and screening. CONCLUSION Our methylation-based cancer classifier and targeted methylation sequencing panel can predict tissue of origin in diverse cancer types with high accuracy.
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Affiliation(s)
- Miaomiao Sun
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Xu
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Chao Chen
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Youjie Zhu
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Xiaomo Li
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China.
| | - Kuisheng Chen
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Ye J, Zhang J, Ding W. DNA methylation modulates epigenetic regulation in colorectal cancer diagnosis, prognosis and precision medicine. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:34-53. [PMID: 38464391 PMCID: PMC10918240 DOI: 10.37349/etat.2024.00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/11/2023] [Indexed: 03/12/2024] Open
Abstract
Colorectal cancer (CRC) is a multifaceted disease influenced by the interplay of genetic and environmental factors. The clinical heterogeneity of CRC cannot be attributed exclusively to genetic diversity and environmental exposures, and epigenetic markers, especially DNA methylation, play a critical role as key molecular markers of cancer. This review compiles a comprehensive body of evidence underscoring the significant involvement of DNA methylation modifications in the pathogenesis of CRC. Moreover, this review explores the potential utility of DNA methylation in cancer diagnosis, prognostics, assessment of disease activity, and prediction of drug responses. Recognizing the impact of DNA methylation will enhance the ability to identify distinct CRC subtypes, paving the way for personalized treatment strategies and advancing precision medicine in the management of CRC.
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Affiliation(s)
- Jingxin Ye
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
- Department of Gastroenterology, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian 223800, Jiangsu Province, China
| | - Jianfeng Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Weifeng Ding
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
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Sajibu S, Sonder E, Tiwari A, Orjuela S, Parker HR, Frans OT, Gubler C, Marra G, Robinson MD. Validation of hypermethylated DNA regions found in colorectal cancers as potential aging-independent biomarkers of precancerous colorectal lesions. BMC Cancer 2023; 23:998. [PMID: 37853362 PMCID: PMC10585861 DOI: 10.1186/s12885-023-11487-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND We previously identified 16,772 colorectal cancer-associated hypermethylated DNA regions that were also detectable in precancerous colorectal lesions (preCRCs) and unrelated to normal mucosal aging. We have now conducted a study to validate 990 of these differentially methylated DNA regions (DMRs) in a new series of preCRCs. METHODS We used targeted bisulfite sequencing to validate these 990 potential biomarkers in 59 preCRC tissue samples (41 conventional adenomas, 18 sessile serrated lesions), each with a patient-matched normal mucosal sample. Based on differential DNA methylation tests, a panel of candidate DMRs was chosen on a subset of our cohort and then validated on the remaining part of our cohort and two publicly available datasets with respect to their stratifying potential between preCRCs and normal mucosa. RESULTS Strong statistical significance for the difference in methylation levels was observed across the full set of 990 investigated DMRs. From these, a selected candidate panel of 30 DMRs correctly identified 58/59 tumors (area under the receiver operating curve: 0.998). CONCLUSIONS These validated DNA hypermethylation markers can be exploited to develop more accurate noninvasive colorectal tumor screening assays.
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Affiliation(s)
- Sija Sajibu
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Emanuel Sonder
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Amit Tiwari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Stephany Orjuela
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Hannah R Parker
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Christoph Gubler
- Division of Gastroenterology, Triemli Hospital, Zurich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
- SIB Swiss Institute of Bioinformatics, Vaud, Switzerland.
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