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Ravichandran SN, Kumar MM, Das A, Banerjee A, Veronica S, Sun-Zhang A, Zhang H, Anbalagan M, Sun XF, Pathak S. An Updated Review on Molecular Biomarkers in Diagnosis and Therapy of Colorectal Cancer. Curr Cancer Drug Targets 2024; 24:595-611. [PMID: 38031267 DOI: 10.2174/0115680096270555231113074003] [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: 07/26/2023] [Revised: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 12/01/2023]
Abstract
Colorectal cancer is one of the most common cancer types worldwide. Since colorectal cancer takes time to develop, its incidence and mortality can be treated effectively if it is detected in its early stages. As a result, non-invasive or invasive biomarkers play an essential role in the early diagnosis of colorectal cancer. Many experimental studies have been carried out to assess genetic, epigenetic, or protein markers in feces, serum, and tissue. It may be possible to find biomarkers that will help with the diagnosis of colorectal cancer by identifying the genes, RNAs, and/or proteins indicative of cancer growth. Recent advancements in the molecular subtypes of colorectal cancer, DNA methylation, microRNAs, long noncoding RNAs, exosomes, and their involvement in colorectal cancer have led to the discovery of novel biomarkers. In small-scale investigations, most biomarkers appear promising. However, large-scale clinical trials are required to validate their effectiveness before routine clinical implementation. Hence, this review focuses on small-scale investigations and results of big data analysis that may provide an overview of the biomarkers for the diagnosis, therapy, and prognosis of colorectal cancer.
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Affiliation(s)
- Shruthi Nagainallur Ravichandran
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Makalakshmi Murali Kumar
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Alakesh Das
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Suhanya Veronica
- Department of Medical Microbiology and NanoBiomedical Engineering, Medical University of Białystok, ul. Świerkowa, s20 B15-328, Białystok, Poland
| | - Alexander Sun-Zhang
- Department of Oncology- Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Hong Zhang
- School of Medicine, Department of Medical Sciences, Örebro University, Fakultetsgatan 1, 701 82 Örebro, Sweden
| | - Muralidharan Anbalagan
- School of Medicine, Tulane University School of Medicine, Tulane University, 1430 Tulane Ave, New Orleans, LA70112, United States
| | - Xiao-Feng Sun
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, 58183, Linköping, Sweden
| | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, Tamil Nadu, 603103, India
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Zhen Y, Pavez M, Li X. The role of Pcdh10 in neurological disease and cancer. J Cancer Res Clin Oncol 2023; 149:8153-8164. [PMID: 37058252 PMCID: PMC10374755 DOI: 10.1007/s00432-023-04743-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: 03/06/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
BACKGROUND Protocadherin 10 (PCDH 10), a member of the superfamily of protocadherins, is a Ca2+-dependent homophilic cell-cell adhesion molecule expressed on the surface of cell membranes. Protocadherin 10 plays a critical role in the central nervous system including in cell adhesion, formation and maintenance of neural circuits and synapses, regulation of actin assembly, cognitive function and tumor suppression. Additionally, Pcdh10 can serve as a non-invasive diagnostic and prognostic indicator for various cancers. METHODS This paper collects and reviews relevant literature in Pubmed. CONCLUSION This review describes the latest research understanding the role of Pcdh10 in neurological disease and human cancer, highlighting the importance of scrutinizing its properties for the development of targeted therapies and identifying a need for further research to explore Pcdh10 functions in other pathways, cell types and human pathologies.
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Affiliation(s)
- Yilan Zhen
- Menzies Institute for Medical Research, University of Tasmania, Liverpool street, Hobart, 7000, Australia
| | - Macarena Pavez
- Department of Anatomy, University of Otago, Dunedin, Otago, New Zealand.
| | - Xinying Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China.
- School of Life Sciences, Anhui Medical University, Hefei, People's Republic of China.
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3
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Dybska E, Nowak JK, Walkowiak J. Transcriptomic Context of RUNX3 Expression in Monocytes: A Cross-Sectional Analysis. Biomedicines 2023; 11:1698. [PMID: 37371794 DOI: 10.3390/biomedicines11061698] [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: 04/28/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The runt-related transcription factor 3 (RUNX3) regulates the differentiation of monocytes and their response to inflammation. However, the transcriptomic context of RUNX3 expression in blood monocytes remains poorly understood. We aim to learn about RUNX3 from its relationships within transcriptomes of bulk CD14+ cells in adults. This study used immunomagnetically sorted CD14+ cell gene expression microarray data from the Multi-Ethnic Study of Atherosclerosis (MESA, n = 1202, GSE56047) and the Correlated Expression and Disease Association Research (CEDAR, n = 281, E-MTAB-6667) cohorts. The data were preprocessed, subjected to RUNX3-focused correlation analyses and random forest modeling, followed by the gene ontology analysis. Immunity-focused differential ratio analysis with intermediary inference (DRAIMI) was used to integrate the data with protein-protein interaction network. Correlation analysis of RUNX3 expression revealed the strongest positive association for EVL (rmean = 0.75, pFDR-MESA = 5.37 × 10-140, pFDR-CEDAR = 5.52 × 10-80), ARHGAP17 (rmean = 0.74, pFDR-MESA = 1.13 × 10-169, pFDR-CEDAR = 9.20 × 10-59), DNMT1 (rmean = 0.74, pFDR-MESA = 1.10 × 10-169, pFDR-CEDAR = 1.67 × 10-58), and CLEC16A (rmean = 0.72, pFDR-MESA = 3.51 × 10-154, pFDR-CEDAR = 2.27 × 10-55), while the top negative correlates were C2ORF76 (rmean = -0.57, pFDR-MESA = 8.70 × 10-94, pFDR-CEDAR = 1.31 × 10-25) and TBC1D7 (rmean = -0.55, pFDR-MESA = 1.36 × 10-69, pFDR-CEDAR = 7.81 × 10-30). The RUNX3-associated transcriptome signature was involved in mRNA metabolism, signal transduction, and the organization of cytoskeleton, chromosomes, and chromatin, which may all accompany mitosis. Transcriptomic context of RUNX3 expression in monocytes hints at its relationship with cell growth, shape maintenance, and aspects of the immune response, including tyrosine kinases.
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Affiliation(s)
- Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, 60-572 Poznan, Poland
| | - Jan Krzysztof Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, 60-572 Poznan, Poland
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, 60-572 Poznan, Poland
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Zhang X, Hou H, Jiang M, Zhang X. Aberrant circulating tumor DNA methylation and exosomal microRNA biomarkers for early detection of colorectal cancer. Mol Biol Rep 2023; 50:2743-2750. [PMID: 36583782 DOI: 10.1007/s11033-022-08194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) became the third most commonly diagnosed malignancy and the second leading cause of cancer death in 2020. However, the rates of early screening and early diagnosis for CRC remain unsatisfactory. Thus, it is essential to explore the initiating factors of CRC and strategies for its early diagnosis. Research progress in liquid biopsy has led to the finding that circulating tumor-derived DNA (ctDNA) and exosomes play vital roles in early detection of CRC. THE APPLICATIONS OF LIQUID BIOPSY FOR EARLY DETECTION OF COLORECTAL CANCER: Moreover, the increased understanding of epigenetics has highlighted the role of ctDNA methylation in CRC carcinogenesis, and the detection of aberrant ctDNA methylation markers is a feasible strategy for diagnosis of early-stage CRC. Among exosomal markers, microRNAs (miRNAs) are abundant and are the most researched. Upregulated or downregulated expression of exosome-derived miRNAs can indicate the occurrence of early-stage CRC. FUTURE PERSPECTIVE The current research progress on aberrant ctDNA methylation and tumor exosomal miRNA biomarkers in early detection of CRC is summarized in this review, and the advantages and shortcomings of the methods are discussed.
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Affiliation(s)
- Xuchen Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China.,Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Helei Hou
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China.,Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Man Jiang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China.,Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Xiaochun Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China. .,Qingdao Cancer Institute, Qingdao University, Qingdao, China.
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Giannareas N, Zhang Q, Yang X, Na R, Tian Y, Yang Y, Ruan X, Huang D, Yang X, Wang C, Zhang P, Manninen A, Wang L, Wei GH. Extensive germline-somatic interplay contributes to prostate cancer progression through HNF1B co-option of TMPRSS2-ERG. Nat Commun 2022; 13:7320. [PMID: 36443337 PMCID: PMC9705428 DOI: 10.1038/s41467-022-34994-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Genome-wide association studies have identified 270 loci conferring risk for prostate cancer (PCa), yet the underlying biology and clinical impact remain to be investigated. Here we observe an enrichment of transcription factor genes including HNF1B within PCa risk-associated regions. While focused on the 17q12/HNF1B locus, we find a strong eQTL for HNF1B and multiple potential causal variants involved in the regulation of HNF1B expression in PCa. An unbiased genome-wide co-expression analysis reveals PCa-specific somatic TMPRSS2-ERG fusion as a transcriptional mediator of this locus and the HNF1B eQTL signal is ERG fusion status dependent. We investigate the role of HNF1B and find its involvement in several pathways related to cell cycle progression and PCa severity. Furthermore, HNF1B interacts with TMPRSS2-ERG to co-occupy large proportion of genomic regions with a remarkable enrichment of additional PCa risk alleles. We finally show that HNF1B co-opts ERG fusion to mediate mechanistic and biological effects of the PCa risk-associated locus 17p13.3/VPS53/FAM57A/GEMIN4. Taken together, we report an extensive germline-somatic interaction between TMPRSS2-ERG fusion and genetic variations underpinning PCa risk association and progression.
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Affiliation(s)
- Nikolaos Giannareas
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Qin Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiayun Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Rong Na
- Division of Urology, Department of Surgery, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China
| | - Yijun Tian
- Department of Tumour Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Yuehong Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiaohao Ruan
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Da Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoqun Yang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Peng Zhang
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Aki Manninen
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Liang Wang
- Department of Tumour Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
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6
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Zhang X, Li A, Wu J, Wu Y, Ma X, Liu Y, Chen Q, Zhang Y. Promoter methylation analysis of DKK2 may be a potential biomarker for early detection of cervical cancer. ASIAN BIOMED 2022; 16:181-189. [PMID: 37551167 PMCID: PMC10321177 DOI: 10.2478/abm-2022-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background Dickkopf 2 (DKK2) plays an important role in multiple cancers. Its potential value in the clinical diagnosis of cervical cancer has remained unclear. Objectives To investigate the expression and promoter methylation levels of DKK2 in cervical cancer and their clinicopathological associations. Methods We used the Gene Expression Omnibus, Oncomine, Cancer Genome Atlas, and University of ALabama at Birmingham CANcer data analysis databases, reverse transcription-PCR, and methylation-specific PCR analysis to predict and examine the expression of DKK2 mRNA and DKK2 methylation levels in cell lines and cervical cancer tissues from 79 patients with cervical cancer and 63 with cervical precancerous lesions including 25 with low-grade squamous intraepithelial lesions (LSIL) and 38 patients with high-grade squamous intraepithelial lesions (HSIL). Results DKK2 mRNA expression was downregulated in all cancer cell lines and cervical cancer tissues, whereas hypermethylation of DKK2 was higher in cervical cancer tissue samples. DKK2 methylation in cervical cancer was significantly higher than that in HSIL (χ2 = 8.346, P = 0.004), whereas DKK2 methylation in HSIL was significantly higher than that in normal cervical samples (χ2 = 7.934, P = 0.005) and in LSIL samples (χ2 = 4.375, P = 0.037). DKK2 silencing caused by its promoter hypermethylation was confirmed by treatment with the methyltransferase inhibitor 5-Aza-dC in cell lines. Patients with lymph node metastasis exhibited increased promoter methylation frequency (χ2 = 5.239, P = 0.022) and low DKK2 mRNA expression (χ2 = 3.958, P = 0.047) compared with patients with no lymph node metastasis. Patients with high-risk human papillomavirus infection exhibited increased promoter methylation frequency (χ2 = 6.279, P = 0.015). Conclusions DKK2 epigenetic changes of DKK2 may play a key role in the development of cervical cancer, suggesting that DKK2 hypermethylation could be used as a triage test for screening, early diagnosis, or risk prediction of cervical cancer.
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Affiliation(s)
- Xian Zhang
- Department of Gynecology and Obstetrics, Liaocheng People's Hospital and Liaocheng Clinical School of Shandong First Medical University, Liaocheng, Shandong252000, China
| | - Aihua Li
- Department of Gynecology and Obstetrics, Liaocheng People's Hospital and Liaocheng Clinical School of Shandong First Medical University, Liaocheng, Shandong252000, China
| | - Jie Wu
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, Shandong266000, China
| | - Yu Wu
- Department of Gynecology and Obstetrics, Liaocheng People's Hospital and Liaocheng Clinical School of Shandong First Medical University, Liaocheng, Shandong252000, China
| | - Xiaoping Ma
- Department of Gynecology and Obstetrics, Liaocheng People's Hospital and Liaocheng Clinical School of Shandong First Medical University, Liaocheng, Shandong252000, China
| | - Yanjun Liu
- Department of Gynecology and Obstetrics, Liaocheng People's Hospital and Liaocheng Clinical School of Shandong First Medical University, Liaocheng, Shandong252000, China
| | - Qingfa Chen
- Institute of Tissue Engineering and Regenerative Medicine, Liaocheng People's Hospital and Liaocheng Clinical School of Shandong First Medical University, Liaocheng, Shandong252000, China
| | - Yan Zhang
- Department of Gynecology and Obstetrics, Liaocheng People's Hospital and Liaocheng Clinical School of Shandong First Medical University, Liaocheng, Shandong252000, China
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7
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Feng Z, Oberije CJG, van de Wetering AJP, Koch A, Wouters KAD, Vaes N, Masclee AAM, Carvalho B, Meijer GA, Zeegers MP, Herman JG, Melotte V, van Engeland M, Smits KM. Lessons From a Systematic Literature Search on Diagnostic DNA Methylation Biomarkers for Colorectal Cancer: How to Increase Research Value and Decrease Research Waste? Clin Transl Gastroenterol 2022; 13:e00499. [PMID: 35584320 PMCID: PMC9236597 DOI: 10.14309/ctg.0000000000000499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To improve colorectal cancer (CRC) survival and lower incidence rates, colonoscopy and/or fecal immunochemical test screening are widely implemented. Although candidate DNA methylation biomarkers have been published to improve or complement the fecal immunochemical test, clinical translation is limited. We describe technical and methodological problems encountered after a systematic literature search and provide recommendations to increase (clinical) value and decrease research waste in biomarker research. In addition, we present current evidence for diagnostic CRC DNA methylation biomarkers. METHODS A systematic literature search identified 331 diagnostic DNA methylation marker studies published before November 2020 in PubMed, EMBASE, Cochrane Library, and Google Scholar. For 136 bodily fluid studies, extended data extraction was performed. STARD criteria and level of evidence were registered to assess reporting quality and strength for clinical translation. RESULTS Our systematic literature search revealed multiple issues that hamper the development of DNA methylation biomarkers for CRC diagnosis, including methodological and technical heterogeneity and lack of validation or clinical translation. For example, clinical translation and independent validation were limited, with 100 of 434 markers (23%) studied in bodily fluids, 3 of 434 markers (0.7%) translated into clinical tests, and independent validation for 92 of 411 tissue markers (22%) and 59 of 100 bodily fluids markers (59%). DISCUSSION This systematic literature search revealed that major requirements to develop clinically relevant diagnostic CRC DNA methylation markers are often lacking. To avoid the resulting research waste, clinical needs, intended biomarker use, and independent validation should be better considered before study design. In addition, improved reporting quality would facilitate meta-analysis, thereby increasing the level of evidence and enabling clinical translation.
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Affiliation(s)
- Zheng Feng
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Cary J. G. Oberije
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands;
| | - Alouisa J. P. van de Wetering
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Alexander Koch
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Kim. A. D. Wouters
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Nathalie Vaes
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Ad A. M. Masclee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands;
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;
| | - Gerrit A. Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;
| | - Maurice P. Zeegers
- Department of Complex Genetics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands;
- Department of Complex Genetics, CAPHRI – Care and Public Health Research Institute, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - James G. Herman
- Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Veerle Melotte
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Department of Clinical Genetics, Erasmus University Medical Center, University of Rotterdam, Rotterdam, the Netherlands;
| | - Manon van Engeland
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
| | - Kim M. Smits
- Department of Pathology, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands;
- Division of Medical Oncology, Department of Internal Medicine, GROW – School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands.
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Sánchez-Maldonado JM, Collado R, Cabrera-Serrano AJ, Ter Horst R, Gálvez-Montosa F, Robles-Fernández I, Arenas-Rodríguez V, Cano-Gutiérrez B, Bakker O, Bravo-Fernández MI, García-Verdejo FJ, López JAL, Olivares-Ruiz J, López-Nevot MÁ, Fernández-Puerta L, Cózar-Olmo JM, Li Y, Netea MG, Jurado M, Lorente JA, Sánchez-Rovira P, Álvarez-Cubero MJ, Sainz J. Type 2 Diabetes-Related Variants Influence the Risk of Developing Prostate Cancer: A Population-Based Case-Control Study and Meta-Analysis. Cancers (Basel) 2022; 14:cancers14102376. [PMID: 35625981 PMCID: PMC9139180 DOI: 10.3390/cancers14102376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
In this study, we have evaluated whether 57 genome-wide association studies (GWAS)-identified common variants for type 2 diabetes (T2D) influence the risk of developing prostate cancer (PCa) in a population of 304 Caucasian PCa patients and 686 controls. The association of selected single nucleotide polymorphisms (SNPs) with the risk of PCa was validated through meta-analysis of our data with those from the UKBiobank and FinnGen cohorts, but also previously published genetic studies. We also evaluated whether T2D SNPs associated with PCa risk could influence host immune responses by analysing their correlation with absolute numbers of 91 blood-derived cell populations and circulating levels of 103 immunological proteins and 7 steroid hormones. We also investigated the correlation of the most interesting SNPs with cytokine levels after in vitro stimulation of whole blood, peripheral mononuclear cells (PBMCs), and monocyte-derived macrophages with LPS, PHA, Pam3Cys, and Staphylococcus Aureus. The meta-analysis of our data with those from six large cohorts confirmed that each copy of the FTOrs9939609A, HNF1Brs7501939T, HNF1Brs757210T, HNF1Brs4430796G, and JAZF1rs10486567A alleles significantly decreased risk of developing PCa (p = 3.70 × 10-5, p = 9.39 × 10-54, p = 5.04 × 10-54, p = 1.19 × 10-71, and p = 1.66 × 10-18, respectively). Although it was not statistically significant after correction for multiple testing, we also found that the NOTCH2rs10923931T and RBMS1rs7593730 SNPs associated with the risk of developing PCa (p = 8.49 × 10-4 and 0.004). Interestingly, we found that the protective effect attributed to the HFN1B locus could be mediated by the SULT1A1 protein (p = 0.00030), an arylsulfotransferase that catalyzes the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. In addition to these results, eQTL analysis revealed that the HNF1Brs7501939, HNF1Brs757210, HNF1Brs4430796, NOTCH2rs10923931, and RBMS1rs7593730 SNPs influence the risk of PCa through the modulation of mRNA levels of their respective genes in whole blood and/or liver. These results confirm that functional TD2-related variants influence the risk of developing PCa, but also highlight the need of additional experiments to validate our functional results in a tumoral tissue context.
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Affiliation(s)
- José Manuel Sánchez-Maldonado
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
- Hematology Department, Virgen de las Nieves University Hospital, 18012 Granada, Spain;
- Instituto de Investigación Biosanataria IBs. Granada, 18012 Granada, Spain
| | - Ricardo Collado
- Medical Oncology Department, Hospital de San Pedro Alcántara, 10003 Cáceres, Spain; (R.C.); (M.I.B.-F.); (J.O.-R.)
| | - Antonio José Cabrera-Serrano
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
- Hematology Department, Virgen de las Nieves University Hospital, 18012 Granada, Spain;
- Instituto de Investigación Biosanataria IBs. Granada, 18012 Granada, Spain
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Nijmegen Medical Center, 6525 GA Nijmegen, The Netherlands; (R.T.H.); (Y.L.); (M.G.N.)
| | - Fernando Gálvez-Montosa
- Department of Medical Oncology, Complejo Hospitalario de Jaén, 23007 Jaén, Spain; (F.G.-M.); (F.J.G.-V.); (J.A.L.L.); (P.S.-R.)
| | - Inmaculada Robles-Fernández
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
| | - Verónica Arenas-Rodríguez
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
- Department of Biochemistry and Molecular Biology III, Faculty of Medicine, University of Granada, 18016 Granada, Spain;
| | - Blanca Cano-Gutiérrez
- Department of Biochemistry and Molecular Biology III, Faculty of Medicine, University of Granada, 18016 Granada, Spain;
| | - Olivier Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | | | - Francisco José García-Verdejo
- Department of Medical Oncology, Complejo Hospitalario de Jaén, 23007 Jaén, Spain; (F.G.-M.); (F.J.G.-V.); (J.A.L.L.); (P.S.-R.)
| | - José Antonio López López
- Department of Medical Oncology, Complejo Hospitalario de Jaén, 23007 Jaén, Spain; (F.G.-M.); (F.J.G.-V.); (J.A.L.L.); (P.S.-R.)
| | - Jesús Olivares-Ruiz
- Medical Oncology Department, Hospital de San Pedro Alcántara, 10003 Cáceres, Spain; (R.C.); (M.I.B.-F.); (J.O.-R.)
| | | | | | | | - Yang Li
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Nijmegen Medical Center, 6525 GA Nijmegen, The Netherlands; (R.T.H.); (Y.L.); (M.G.N.)
- Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Nijmegen Medical Center, 6525 GA Nijmegen, The Netherlands; (R.T.H.); (Y.L.); (M.G.N.)
- Department for Immunology & Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Manuel Jurado
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
- Hematology Department, Virgen de las Nieves University Hospital, 18012 Granada, Spain;
- Instituto de Investigación Biosanataria IBs. Granada, 18012 Granada, Spain
- Department of Medicine, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Jose Antonio Lorente
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
- Department of Legal Medicine, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Pedro Sánchez-Rovira
- Department of Medical Oncology, Complejo Hospitalario de Jaén, 23007 Jaén, Spain; (F.G.-M.); (F.J.G.-V.); (J.A.L.L.); (P.S.-R.)
| | - María Jesús Álvarez-Cubero
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
- Department of Biochemistry and Molecular Biology III, Faculty of Medicine, University of Granada, 18016 Granada, Spain;
| | - Juan Sainz
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (J.M.S.-M.); (A.J.C.-S.); (I.R.-F.); (V.A.-R.); (M.J.); (J.A.L.); (M.J.Á.-C.)
- Hematology Department, Virgen de las Nieves University Hospital, 18012 Granada, Spain;
- Instituto de Investigación Biosanataria IBs. Granada, 18012 Granada, Spain
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18071 Granada, Spain
- Correspondence: ; Tel.: +34-95871-5500 (ext. 126); Fax: +34-9-5863-7071
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9
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Jafarpour S, Saberi F, Yazdi M, Nedaeinia R, Amini G, Ferns GA, Salehi R. Association between colorectal cancer and the degree of ITGA4 promoter methylation in peripheral blood mononuclear cells. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Shao X, Wang H, Yu Y, Zhou C. Combined detection of stool-based methylation indicators for early screening of colorectal neoplasm. Am J Transl Res 2021; 13:11597-11607. [PMID: 34786085 PMCID: PMC8581910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
In the past two decades, several methylated DNA targets, including gene promoters and other intronic markers have been explored in tumors and benign lesions. Therefore, it can be expected that a panel of stool-based biomarkers will become a screening method for colorectal cancer (CRC) and adenoma with better sensitivity and specificity, aiming to decrease the incidence and mortality of CRC. In this study, the methylation of secreted frizzled-related protein 1 (SFRP1), hyperplastic polyposis protein 1 (HPP1), α-internexin (INA), Wnt inhibitory factor 1 (WIF1), tissue factor pathway inhibitor 2 (TFPI2), ikaros family zinc finger protein 1 (IKZF1), and spastic paraplegia 20 (SPG20) were detected in stool samples from patients with CRC, adenoma, polyps, and healthy controls, respectively, and these biomarkers were used to establish a logistic regression model for classification. Receiver operating characteristic (ROC) curves were drawn to assess the importance of each biomarker. Subsequently, a biomarker or combination of biomarkers was analyzed for early screening of high-risk neoplasm. The data showed that when a single biomarker was used for CRC screening, the sensitivity ranged from 63.9% to 76.8%, the area under the curve (AUC) ranged from 0.821 to 0.875, and the accuracy ranged from 77.0% to 84.5%. Finally, the methylation of SFRP1, HPP1, TFPI2, and IKZF1 was selected using a backward stepwise method in the multivariate logistic analysis according to the Akaike Information Criterion. These findings indicate that stool DNA biomarkers have good diagnostic power in discriminating high-risk level of neoplasm from healthy population.
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Affiliation(s)
- Xinyu Shao
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
| | - Huiyu Wang
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
| | - Yang Yu
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
| | - Chunli Zhou
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University Suzhou, Jiangsu, China
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11
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Baranova I, Kovarikova H, Laco J, Sedlakova I, Vrbacky F, Kovarik D, Hejna P, Palicka V, Chmelarova M. Identification of a four-gene methylation biomarker panel in high-grade serous ovarian carcinoma. Clin Chem Lab Med 2021; 58:1332-1340. [PMID: 32145055 DOI: 10.1515/cclm-2019-1319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/04/2020] [Indexed: 12/31/2022]
Abstract
Background The lack of effective biomarkers for the screening and early detection of ovarian cancer (OC) is one of the most pressing problems in oncogynecology. Because epigenetic alterations occur early in the cancer development, they provide great potential to serve as such biomarkers. In our study, we investigated a potential of a four-gene methylation panel (including CDH13, HNF1B, PCDH17 and GATA4 genes) for the early detection of high-grade serous ovarian carcinoma (HGSOC). Methods For methylation detection we used methylation sensitive high-resolution melting analysis and real-time methylation specific analysis. We also investigated the relation between gene hypermethylation and gene relative expression using the 2-ΔΔCt method. Results The sensitivity of the examined panel reached 88.5%. We were able to detect methylation in 85.7% (12/14) of early stage tumors and in 89.4% (42/47) of late stage tumors. The total efficiency of the panel was 94.4% and negative predictive value reached 90.0%. The specificity and positive predictive value achieved 100% rates. Our results showed lower gene expression in the tumor samples in comparison to control samples. The more pronounced downregulation was measured in the group of samples with detected methylation. Conclusions In our study we designed the four-gene panel for HGSOC detection in ovarian tissue with 100% specificity and sensitivity of 88.5%. The next challenge is translation of the findings to the less invasive source for biomarker examination, such as plasma. Our results indicate that combination of examined genes deserve consideration for further testing in clinical molecular diagnosis of HGSOC.
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Affiliation(s)
- Ivana Baranova
- Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Helena Kovarikova
- Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Laco
- The Fingerland Department of Pathology, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Iva Sedlakova
- Department of Obstetrics and Gynecology, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Filip Vrbacky
- The 4th Department of Internal Medicine - Hematology, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Dalibor Kovarik
- Department of Forensic Medicine, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Petr Hejna
- Department of Forensic Medicine, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Vladimir Palicka
- Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Marcela Chmelarova
- Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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12
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Dobre M, Salvi A, Pelisenco IA, Vasilescu F, De Petro G, Herlea V, Milanesi E. Crosstalk Between DNA Methylation and Gene Mutations in Colorectal Cancer. Front Oncol 2021; 11:697409. [PMID: 34277443 PMCID: PMC8281955 DOI: 10.3389/fonc.2021.697409] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/14/2021] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is often characterized by mutations and aberrant DNA methylation within the promoters of tumor suppressor genes and proto-oncogenes. The most frequent somatic mutations occur within KRAS and BRAF genes. Mutations of the KRAS gene have been detected in approximately 40% of patients, while mutations in BRAF have been detected less frequently at a rate of 10%. In this study, the DNA methylation levels of 22 candidate genes were evaluated in three types of tissue: mucosal tumoral tissue from 18 CRC patients, normal adjacent tissues from 10 CRC patients who underwent surgical resection, and tissue from a control group of six individuals with normal colonoscopies. A differential methylation profile of nine genes (RUNX3, SFRP1, WIF1, PCDH10, DKK2, DKK3, TMEFF2, OPCML, and SFRP2) presenting high methylation levels in tumoral compared to normal tissues was identified. KRAS mutations (codons 12 or 13) were detected in eight CRC cases, and BRAF mutations (codon 600) in four cases. One of the CRC patients presented concomitant mutations in KRAS codon 12 and BRAF, whereas seven patients did not present these mutations (WT). When comparing the methylation profile according to mutation status, we found that six genes (SFRP2, DKK2, PCDH10, TMEFF2, SFRP1, HS3ST2) showed a methylation level higher in BRAF positive cases than BRAF negative cases. The molecular sub-classification of CRC according to mutations and epigenetic modifications may help to identify epigenetic biomarkers useful in designing personalized strategies to improve patient outcomes.
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Affiliation(s)
- Maria Dobre
- Laboratory of Histopathology and Immunohistochemistry, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Florina Vasilescu
- Laboratory of Histopathology and Immunohistochemistry, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Giuseppina De Petro
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Vlad Herlea
- Department of Pathology, Fundeni Clinical Institute, Bucharest, Romania
| | - Elena Milanesi
- Laboratory of Radiobiology, Victor Babes National Institute of Pathology, Bucharest, Romania
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13
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Yin L, Zhu Z, Huang L, Luo X, Li Y, Xiao C, Yang J, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.). HORTICULTURE RESEARCH 2021; 8:142. [PMID: 34193846 PMCID: PMC8245426 DOI: 10.1038/s41438-021-00576-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/29/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.
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Affiliation(s)
- Liqin Yin
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Xuan Luo
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Yun Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Chaowen Xiao
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Maolin Wang
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
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14
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Ahn B, Chae YS, Lee SK, Kim M, Kim HS, Moon JW, Park SH. Identification of novel DNA hypermethylation of the adenylate kinase 5 promoter in colorectal adenocarcinoma. Sci Rep 2021; 11:12626. [PMID: 34135408 PMCID: PMC8209216 DOI: 10.1038/s41598-021-92147-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/28/2021] [Indexed: 11/09/2022] Open
Abstract
Adenylate kinase 5 (AK5) belongs to the adenylate kinase family that catalyses reversible phosphate transfer between adenine nucleotides, and it is related to various energetic signalling mechanisms. However, the role of AK5 in colorectal cancer (CRC) has not been reported. In this study, AK5 was significantly hypermethylated in CRC compared to adjacent normal tissues (P < 0.0001) and normal tissues (P = 0.0015). Although the difference in mRNA expression was not statistically significant in all of them, the selected 49 cases of CRC tissues with AK5 hypermethylation with the cut off value of 40% showed a significant inverse correlation with mRNA expression (P = 0.0003). DNA methylation of AK5 promoter significantly decreased and AK5 expression recovered by 5-aza-2'-deoxycytidine, DNA methyltransferase inhibitor in CRC cell lines. In addition, AK5 promoter activity significantly decreased due to DNA methyltransferase, and it increased due to 5-aza. Moreover, AK5 regulated the phosphorylated AMPK and mTOR phosphorylation and inhibited the cell migration and cell invasion in CRC cell lines. Furthermore, low AK5 expression is associated with poor differentiation (P = 0.014). These results demonstrate that the AK5 promoter is frequently hypermethylated and induced methylation-mediated gene down-regulation. AK5 expression regulates AMPK/mTOR signalling and may be closely related to metastasis in colorectal adenocarcinoma.
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Affiliation(s)
- Bokyung Ahn
- Department of Pathology, Asan Medical Center, Seoul, Republic of Korea.,Department of Pathology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yang Seok Chae
- Department of Pathology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Kyung Lee
- Medicine and Life Sciences, Journal, Springer Nature, Seoul, Republic of Korea
| | - Moa Kim
- Institute of Human Genetics, Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyeon Soo Kim
- Institute of Human Genetics, Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Wook Moon
- Institute of Human Genetics, Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea. .,BK21Plus Medical Science, Korea University College of Medicine, Seoul, Republic of Korea.
| | - Sun-Hwa Park
- Institute of Human Genetics, Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
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15
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Quilichini E, Fabre M, Nord C, Dirami T, Le Marec A, Cereghini S, Pasek RC, Gannon M, Ahlgren U, Haumaitre C. Insights into the etiology and physiopathology of MODY5/HNF1B pancreatic phenotype with a mouse model of the human disease. J Pathol 2021; 254:31-45. [PMID: 33527355 PMCID: PMC8251562 DOI: 10.1002/path.5629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/18/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
Maturity-onset diabetes of the young type 5 (MODY5) is due to heterozygous mutations or deletion of HNF1B. No mouse models are currently available to recapitulate the human MODY5 disease. Here, we investigate the pancreatic phenotype of a unique MODY5 mouse model generated by heterozygous insertion of a human HNF1B splicing mutation at the intron-2 splice donor site in the mouse genome. This Hnf1bsp2/+ model generated with targeted mutation of Hnf1b mimicking the c.544+1G>T (T) mutation identified in humans, results in alternative transcripts and a 38% decrease of native Hnf1b transcript levels. As a clinical feature of MODY5 patients, the hypomorphic mouse model Hnf1bsp2/+ displays glucose intolerance. Whereas Hnf1bsp2/+ isolated islets showed no altered insulin secretion, we found a 65% decrease in pancreatic insulin content associated with a 30% decrease in total large islet volume and a 20% decrease in total β-cell volume. These defects were associated with a 30% decrease in expression of the pro-endocrine gene Neurog3 that we previously identified as a direct target of Hnf1b, showing a developmental etiology. As another clinical feature of MODY5 patients, the Hnf1bsp2/+ pancreases display exocrine dysfunction with hypoplasia. We observed chronic pancreatitis with loss of acinar cells, acinar-to-ductal metaplasia, and lipomatosis, with upregulation of signaling pathways and impaired acinar cell regeneration. This was associated with ductal cell deficiency characterized by shortened primary cilia. Importantly, the Hnf1bsp2/+ mouse model reproduces the pancreatic features of the human MODY5/HNF1B disease, providing a unique in vivo tool for molecular studies of the endocrine and exocrine defects and to advance basic and translational research. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Evans Quilichini
- Centre National de la Recherche Scientifique (CNRS)UMR7622, Institut de Biologie Paris‐Seine (IBPS)ParisFrance
| | - Mélanie Fabre
- Centre National de la Recherche Scientifique (CNRS)UMR7622, Institut de Biologie Paris‐Seine (IBPS)ParisFrance
| | | | - Thassadite Dirami
- Centre National de la Recherche Scientifique (CNRS)UMR7622, Institut de Biologie Paris‐Seine (IBPS)ParisFrance
- Sorbonne UniversitéUMR7622‐IBPSParisFrance
| | - Axelle Le Marec
- Centre National de la Recherche Scientifique (CNRS)UMR7622, Institut de Biologie Paris‐Seine (IBPS)ParisFrance
- Sorbonne UniversitéUMR7622‐IBPSParisFrance
| | - Silvia Cereghini
- Centre National de la Recherche Scientifique (CNRS)UMR7622, Institut de Biologie Paris‐Seine (IBPS)ParisFrance
- Sorbonne UniversitéUMR7622‐IBPSParisFrance
| | - Raymond C Pasek
- Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Maureen Gannon
- Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Ulf Ahlgren
- Umeå Centre for Molecular MedicineUmeå UniversityUmeåSweden
| | - Cécile Haumaitre
- Centre National de la Recherche Scientifique (CNRS)UMR7622, Institut de Biologie Paris‐Seine (IBPS)ParisFrance
- Sorbonne UniversitéUMR7622‐IBPSParisFrance
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16
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Mamelli RE, Felipe AV, Silva TD, Hinz V, Forones NM. RNAM EXPRESSION AND DNA METHYLATION OF DKK2 GENE IN COLORECTAL CÂNCER. ARQUIVOS DE GASTROENTEROLOGIA 2021; 58:55-60. [PMID: 33909798 DOI: 10.1590/s0004-2803.202100000-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/28/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Colorectal cancer is the third most common neoplasm in the world. Methylation of tumor related genes in CpG islands can cause gene silencing and been involved in the development of cancer. The potential role of DKK2 as a biomarker for early diagnosis of colorectal cancer remains unclear. OBJECTIVE The aim of the study was to evaluate the profile of methylation and RNAm expression of DKK2 as potential predictors of colorectal cancer diagnosis and prognosis. METHODS Expression of mRNAs encoding DKK2 in 35 colorectal cancer tissues was quantified using real-time polymerase chain reaction analysis. The DNA methylation was studied by high resolution melting analysis. The general characteristics of the patients were collected. DKK2 methylation and expression were compared to clinical, pathological aspects and overall survival. RESULTS Among the 35 patients studied, 18 were male, 10 were on right colon and 25 on left colon. Among the 20 patients with high hypermethylation, 15 of them had mRNA low expression of DKK2. There was no significant association between DKK2 promoter methylation and mRNA DKK2 expression and clinical or pathological features. DKK2 promoter methylation (P=0.154) and DKK2 RNA expression (P=0.345) did not show significant correlation with overall survival. CONCLUSION DKK2 promoter methylation and DKK2 RNA status appear to be biomarkers of cancer diagnosis but not predictors of prognosis.
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Affiliation(s)
- Ronaldo Eliezer Mamelli
- Universidade Federal de São Paulo, Escola Paulista de Medicina (UNIFESP-EPM), São Paulo, SP, Brasil
| | - Aledson Vitor Felipe
- Universidade Federal de São Paulo, Escola Paulista de Medicina (UNIFESP-EPM), São Paulo, SP, Brasil
| | - Tiago Donizetti Silva
- Universidade Federal de São Paulo, Escola Paulista de Medicina (UNIFESP-EPM), São Paulo, SP, Brasil
| | - Vanessa Hinz
- Universidade Federal de São Paulo, Escola Paulista de Medicina (UNIFESP-EPM), São Paulo, SP, Brasil
| | - Nora Manoukian Forones
- Universidade Federal de São Paulo, Escola Paulista de Medicina (UNIFESP-EPM), São Paulo, SP, Brasil
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17
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Chandra S, Srinivasan S, Batra J. Hepatocyte nuclear factor 1 beta: A perspective in cancer. Cancer Med 2021; 10:1791-1804. [PMID: 33580750 PMCID: PMC7940219 DOI: 10.1002/cam4.3676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/17/2022] Open
Abstract
Hepatocyte nuclear factor 1 beta (HNF1 β/B) exists as a homeobox transcription factor having a vital role in the embryonic development of organs mainly liver, kidney and pancreas. Initially described as a gene causing maturity‐onset diabetes of the young (MODY), HNF1β expression deregulation and single nucleotide polymorphisms in HNF1β have now been associated with several tumours including endometrial, prostate, ovarian, hepatocellular, renal and colorectal cancers. Its function has been studied either as homodimer or heterodimer with HNF1α. In this review, the role of HNF1B in different cancers will be discussed along with the role of its splice variants, and its emerging role as a potential biomarker in cancer.
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Affiliation(s)
- Shubhra Chandra
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Woolloongabba, QLD, Australia
| | - Srilakshmi Srinivasan
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Woolloongabba, QLD, Australia
| | - Jyotsna Batra
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Woolloongabba, QLD, Australia
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Bártů M, Hojný J, Hájková N, Michálková R, Krkavcová E, Simon K, Frýba V, Stružinská I, Němejcová K, Dundr P. Expression, Epigenetic, and Genetic Changes of HNF1B in Colorectal Lesions: an Analysis of 145 Cases. Pathol Oncol Res 2020; 26:2337-2350. [PMID: 32488808 DOI: 10.1007/s12253-020-00830-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022]
Abstract
Hepatocyte nuclear factor 1 beta (HNF1B) is transcription factor which plays a crucial role in the regulation of the development of several organs, but also seems to be implicated in the development of certain tumours, especially the subset of clear cell carcinomas of the ovary and kidney. Depending on the type of the tumour, HNF1B may act as either a tumour suppressor or an oncogene, although the exact mechanism by which HNF1B participates in the process of cancerogenesis is unknown. Using immunohistochemical approach and methylation and mutation analysis, we have investigated the expression, epigenetic, and genetic changes of HNF1B on 40 cases of colorectal adenomas and 105 cases of colorectal carcinomas. The expression of HNF1B was correlated with the benign or malignant behaviour of the lesion, given that carcinomas showed significantly lower levels of expression compared to adenomas. In carcinomas, lower levels of HNF1B expression were associated with recurrence and shortened disease-free survival. The mutation analysis revealed three somatic mutations (two frameshift and one nonsense) in the carcinoma sample set. Promoter methylation was detected in three carcinomas. These results suggest that in colorectal cancer, HNF1B may play a part in the pathogenesis and act in a tumour suppressive fashion.
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Affiliation(s)
- Michaela Bártů
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Jan Hojný
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Nikola Hájková
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Romana Michálková
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Eva Krkavcová
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Karol Simon
- First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800, Prague, Czech Republic
| | - Vladimír Frýba
- 1st Department of Surgery - Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, 12808, Prague, Czech Republic
| | - Ivana Stružinská
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Kristýna Němejcová
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Pavel Dundr
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic.
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Hojny J, Bartu M, Krkavcova E, Nemejcova K, Sevcik J, Cibula D, Fryba V, Plincelnerova L, Dundr P, Struzinska I. Identification of novel HNF1B mRNA splicing variants and their qualitative and semi-quantitative profile in selected healthy and tumour tissues. Sci Rep 2020; 10:6958. [PMID: 32332782 PMCID: PMC7181708 DOI: 10.1038/s41598-020-63733-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte nuclear factor-1-beta (HNF1B) is a transcription factor crucial for the development of several tissues, and a promising biomarker of certain solid tumours. Thus far, two HNF1B alternative splicing variants (ASVs) have been described, however, the complete spectrum, prevalence and role of HNF1B ASVs in tumorigenesis are unclear. Considering the equivocal data about HNF1B ASVs and expression presented in literature, our aim was to characterize the spectrum of HNF1B mRNA splicing variants across different tissues. Here, we characterize HNF1B ASVs with high sensitivity in carcinomas of the uterine corpus, large intestine, kidney, pancreas, and prostate, with selected paired healthy tissues, using the previously described multiplex PCR and NGS approach. We identified 45 ASVs, of which 43 were novel. The spectrum and relative quantity of expressed ASVs mRNA differed among the analysed tissue types. Two known (3p, Δ7_8) and two novel (Δ7, Δ8) ASVs with unknown biological functions were detected in all the analysed tissues in a higher proportion. Our study reveals the wide spectrum of HNF1B ASVs in selected tissues. Characterization of the HNF1B ASVs is an important prerequisite for further expression studies to delineate the HNF1B splicing pattern, potential ASVs functional impact, and eventual refinement of HNF1B's biomarker role.
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Affiliation(s)
- Jan Hojny
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Michaela Bartu
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Eva Krkavcova
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Kristyna Nemejcova
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Jan Sevcik
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, 12853, Czech Republic
| | - David Cibula
- Gynecological Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12851, Czech Republic
| | - Vladimir Fryba
- 1st Department of Surgery - Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Lenka Plincelnerova
- Department of Urology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Pavel Dundr
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic
| | - Ivana Struzinska
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12808, Czech Republic.
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Yang C, Zhang Y, Xu X, Li W. Molecular subtypes based on DNA methylation predict prognosis in colon adenocarcinoma patients. Aging (Albany NY) 2019; 11:11880-11892. [PMID: 31852837 PMCID: PMC6949097 DOI: 10.18632/aging.102492] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/17/2019] [Indexed: 12/25/2022]
Abstract
Tumor heterogeneity makes early diagnosis and effective treatment of colon adenocarcinoma difficult. As an important regulator of gene expression, DNA methylation can influence tumor heterogeneity. In this study, we explored the prognostic value of subtypes based on DNA methylation status in 424 colon adenocarcinoma samples from the Cancer Genome Atlas database. Differences in DNA methylation levels were associated with differences in T, N, and M category, age, stage, and prognosis. Seven subgroups were identified based on consensus clustering using 356 CpG sites that significantly influenced survival. Finally, a prognostic model was constructed and used to classify samples in a testing dataset into seven DNA methylation subgroups based on the classification results of a training dataset. These specific classifications based on DNA methylation may help account for heterogeneity within previously established molecular subgroups of colon adenocarcinoma and could potentially aid in the development of more effective personalized treatments.
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Affiliation(s)
- Changshun Yang
- Department of Surgical Oncology, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Yu Zhang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350001, China
| | - Xiaoqin Xu
- School of Public Health, Fujian Medical University, Fuzhou 350001, China
| | - Weihua Li
- Department of Surgical Oncology, Fujian Provincial Hospital, Fuzhou 350001, China
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Kasprzak A, Adamek A. Insulin-Like Growth Factor 2 (IGF2) Signaling in Colorectal Cancer-From Basic Research to Potential Clinical Applications. Int J Mol Sci 2019; 20:ijms20194915. [PMID: 31623387 PMCID: PMC6801528 DOI: 10.3390/ijms20194915] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers in men and women worldwide as well as is the leading cause of death in the western world. Almost a third of the patients has or will develop liver metastases. While genetic as well as epigenetic mechanisms are important in CRC pathogenesis, the basis of the most cases of cancer is unknown. High spatial and inter-patient variability of the molecular alterations qualifies this cancer in the group of highly heterogeneous tumors, which makes it harder to elucidate the mechanisms underlying CRC progression. Determination of highly sensitive and specific early diagnosis markers and understanding the cellular and molecular mechanism(s) of cancer progression are still a challenge of the current era in oncology of solid tumors. One of the accepted risk factors for CRC development is overexpression of insulin-like growth factor 2 (IGF2), a 7.5-kDa peptide produced by liver and many other tissues. IGF2 is the first gene discovered to be parentally imprinted. Loss of imprinting (LOI) or aberrant imprinting of IGF2 could lead to IGF2 overexpression, increased cell proliferation, and CRC development. IGF2 as a mitogen is associated with increased risk of developing colorectal neoplasia. Higher serum IGF2 concentration as well as its tissue overexpression in CRC compared to control are associated with metastasis. IGF2 protein was one of the three candidates for a selective marker of CRC progression and staging. Recent research indicates dysregulation of different micro- and long non-coding RNAs (miRNAs and lncRNAs, respectively) embedded within the IGF2 gene in CRC carcinogenesis, with some of them indicated as potential diagnostic and prognostic CRC biomarkers. This review systematises the knowledge on the role of genetic and epigenetic instabilities of IGF2 gene, free (active form of IGF2) and IGF-binding protein (IGFBP) bound (inactive form), paracrine/autocrine secretion of IGF2, as well as mechanisms of inducing dysplasia in vitro and tumorigenicity in vivo. We have tried to answer which molecular changes of the IGF2 gene and its regulatory mechanisms have the most significance in initiation, progression (including liver metastasis), prognosis, and potential anti-IGF2 therapy in CRC patients.
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Affiliation(s)
- Aldona Kasprzak
- Department of Histology and Embryology, University of Medical Sciences, Swiecicki Street 6, 60-781 Poznan, Poland.
| | - Agnieszka Adamek
- Department of Infectious Diseases, Hepatology and Acquired Immunodeficiencies, University of Medical Sciences, Szwajcarska Street 3, 61-285 Poznan, Poland.
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A Novel Prognostic DNA Methylation Panel for Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20194672. [PMID: 31547144 PMCID: PMC6801964 DOI: 10.3390/ijms20194672] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers and the second leading cause of cancer-related deaths. Discrepancies in clinical outcomes are observed even among patients with same-stage CRC due to molecular heterogeneity. Thus, biomarkers for predicting prognosis in CRC patients are urgently needed. We previously demonstrated that stage II CRC patients with NKX6.1 methylation had poor 5-year overall survival. However, the methylation frequency of NKX6.1 was only 23% in 151 pairs of CRC tissues. Thus, we aimed to develop a more robust prognostic panel for CRC using NKX6.1 in combination with three genes: LIM homeobox transcription factor 1α (LMX1A), sex-determining region Y-box 1 (SOX1), and zinc finger protein 177 (ZNF177). Through quantitative methylation analysis, we found that LMX1A, SOX1, and ZNF177 were hypermethylated in CRC tissues. LMX1A methylation was significantly associated with poor 5-year overall, and disease-free survivals in stage I and II CRC patients. Sensitivity and specificity analyses of the four-gene combination revealed the best sensitivity and optimal specificity. Moreover, patients with the four-gene methylation profile exhibited poorer disease-free survival than those without methylation. A significant effect of the four-gene methylation status on overall survival and disease-free survival was observed in early stage I and II CRC patients (p = 0.0016 and p = 0.0230, respectively). Taken together, these results demonstrate that the combination of the methylation statuses of NKX6.1, LMX1A, SOX1, and ZNF177 creates a novel prognostic panel that could be considered a molecular marker for outcomes in CRC patients.
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A novel panel of stool-based DNA biomarkers for early screening of colorectal neoplasms in a Chinese population. J Cancer Res Clin Oncol 2019; 145:2423-2432. [PMID: 31456088 DOI: 10.1007/s00432-019-02992-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/27/2019] [Indexed: 01/05/2023]
Abstract
PURPOSE The mortality of colorectal cancer ranked fifth in China according to cancer statistics in 2015. Cancer screening had been repeatedly proved to play a vital role in decreasing the incidence and mortality of colorectal cancer, but the existing screening methods could not meet the requirements. So it is of urgent need to develop a non-invasive, convenient and accurate screening method. METHODS In this study, stool samples were collected from 102 colorectal cancer, 20 colorectal adenoma, 6 hyperplastic polyps patients and 105 normal controls, and stool DNA was extracted for detection of methylation (BMP3, NDRG4, SDC2 and SFRP2) and KRAS mutations. Meanwhile, hemoglobin in stool samples was detected by immunoassays. Then, the logistic regression model used for classification was built with these biomarkers, and a ROC curve was drawn to evaluate the performance of each biomarker and the panel of them. Meanwhile, conventional serum biomarkers were detected for the comparison of positive rate in colorectal cancer between serum biomarkers and stool DNA biomarkers. RESULTS As a result, a classification model built with methylation of SDC2 and SFRP2, KRAS mutations and hemoglobin showed a sensitivity of 91.4% for colorectal cancer and 60% for adenoma with the specificity of 86.1%. Compared with it, most of the conventional serum biomarkers showed a sensitivity of less than 20% for colorectal cancer which was significantly lower than stool DNA biomarkers. CONCLUSIONS A novel panel comprised of stool DNA biomarkers was of much higher sensitivity and specificity in early screening of colorectal neoplasms than conventional serum biomarkers.
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Liang Y, Zhang C, Dai DQ. Identification of differentially expressed genes regulated by methylation in colon cancer based on bioinformatics analysis. World J Gastroenterol 2019; 25:3392-3407. [PMID: 31341364 PMCID: PMC6639549 DOI: 10.3748/wjg.v25.i26.3392] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/09/2019] [Accepted: 06/01/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND DNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncogenes and downregulate tumor suppressor genes without changing the sequences. However, studies of methylation in the control of gene expression are still inadequate. In the present research, we performed bioinformatics analysis to clarify the function of methylation and supply candidate methylation-related biomarkers and drivers for colon cancer.
AIM To identify and analyze methylation-regulated differentially expressed genes (MeDEGs) in colon cancer by bioinformatics analysis.
METHODS We downloaded RNA expression profiles, Illumina Human Methylation 450K BeadChip data, and clinical data of colon cancer from The Cancer Genome Atlas project. MeDEGs were identified by analyzing the gene expression and methylation levels using the edgeR and limma package in R software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in the DAVID database and KEGG Orthology-Based Annotation System 3.0, respectively. We then conducted Kaplan–Meier survival analysis to explore the relationship between methylation and expression and prognosis. Gene set enrichment analysis (GSEA) and investigation of protein-protein interactions (PPI) were performed to clarify the function of prognosis-related genes.
RESULTS A total of 5 up-regulated and 81 down-regulated genes were identified as MeDEGs. GO and KEGG pathway analyses indicated that MeDEGs were enriched in multiple cancer-related terms. Furthermore, Kaplan–Meier survival analysis showed that the prognosis was negatively associated with the methylation status of glial cell-derived neurotrophic factor (GDNF) and reelin (RELN). In PPI networks, GDNF and RELN interact with neural cell adhesion molecule 1. Besides, GDNF can interact with GDNF family receptor alpha (GFRA1), GFRA2, GFRA3, and RET. RELN can interact with RAFAH1B1, disabled homolog 1, very low-density lipoprotein receptor, lipoprotein receptor-related protein 8, and NMDA 2B. Based on GSEA, hypermethylation of GDNF and RELN were both significantly associated with pathways including “RNA degradation,” “ribosome,” “mismatch repair,” “cell cycle” and “base excision repair.”
CONCLUSION Aberrant DNA methylation plays an important role in colon cancer progression. MeDEGs that are associated with the overall survival of patients may be potential targets in tumor diagnosis and treatment.
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Affiliation(s)
- Yu Liang
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Cheng Zhang
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Dong-Qiu Dai
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
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V Subramaniam A, Yehya AHS, Cheng WK, Wang X, Oon CE. Epigenetics: The master control of endothelial cell fate in cancer. Life Sci 2019; 232:116652. [PMID: 31302197 DOI: 10.1016/j.lfs.2019.116652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/07/2023]
Abstract
The development of new blood vessels from pre-existing vasculature is called angiogenesis. The growth of tumors depends on a network of supplying vessels that provide them with oxygen and nutrients. Pro-angiogenic factors that are secreted by tumors will trigger the sprouting of nearby existing blood vessels towards themselves and therefore researchers have developed targeted therapy towards these pro-angiogenic proteins to inhibit angiogenesis. However, certain pro-angiogenic proteins tend to bypass the inhibition. Thus, instead of targeting these expressed proteins, research towards angiogenesis inhibition had been focused on a deeper scale, epigenetic modifications. Epigenetic regulatory mechanisms are a heritable change in a sequence of stable but reversible gene function modification yet do not affect the DNA primary sequence directly. Methylation of DNA, modification of histone and silencing of micro-RNA (miRNA)-associated gene are currently considered to initiate and sustain epigenetic changes. Recent findings on the subject matter have provided an insight into the mechanism of epigenetic modifications, thus this review aims to present an update on the latest studies.
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Affiliation(s)
- Ayappa V Subramaniam
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, Pulau Pinang, Malaysia
| | - Ashwaq Hamid Salem Yehya
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, Pulau Pinang, Malaysia
| | - Wei Kang Cheng
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, Pulau Pinang, Malaysia.
| | - Xiaomeng Wang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 639798, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore 138632, Singapore; Department of Cell Biology, Institute of Ophthalmology, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
| | - Chern Ein Oon
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, Pulau Pinang, Malaysia.
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Quilichini E, Fabre M, Dirami T, Stedman A, De Vas M, Ozguc O, Pasek RC, Cereghini S, Morillon L, Guerra C, Couvelard A, Gannon M, Haumaitre C. Pancreatic Ductal Deletion of Hnf1b Disrupts Exocrine Homeostasis, Leads to Pancreatitis, and Facilitates Tumorigenesis. Cell Mol Gastroenterol Hepatol 2019; 8:487-511. [PMID: 31229598 PMCID: PMC6722301 DOI: 10.1016/j.jcmgh.2019.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS The exocrine pancreas consists of acinar cells that produce digestive enzymes transported to the intestine through a branched ductal epithelium. Chronic pancreatitis is characterized by progressive inflammation, fibrosis, and loss of acinar tissue. These changes of the exocrine tissue are risk factors for pancreatic cancer. The cause of chronic pancreatitis cannot be identified in one quarter of patients. Here, we investigated how duct dysfunction could contribute to pancreatitis development. METHODS The transcription factor Hnf1b, first expressed in pancreatic progenitors, is strictly restricted to ductal cells from late embryogenesis. We previously showed that Hnf1b is crucial for pancreas morphogenesis but its postnatal role still remains unelucidated. To investigate the role of pancreatic ducts in exocrine homeostasis, we inactivated the Hnf1b gene in vivo in mouse ductal cells. RESULTS We uncovered that postnatal Hnf1b inactivation in pancreatic ducts leads to chronic pancreatitis in adults. Hnf1bΔduct mutants show dilatation of ducts, loss of acinar cells, acinar-to-ductal metaplasia, and lipomatosis. We deciphered the early events involved, with down-regulation of cystic disease-associated genes, loss of primary cilia, up-regulation of signaling pathways, especially the Yap pathway, which is involved in acinar-to-ductal metaplasia. Remarkably, Hnf1bΔduct mutants developed pancreatic intraepithelial neoplasia and promote pancreatic intraepithelial neoplasia progression in concert with KRAS. We further showed that adult Hnf1b inactivation in pancreatic ducts is associated with impaired regeneration after injury, with persistent metaplasia and initiation of neoplasia. CONCLUSIONS Loss of Hnf1b in ductal cells leads to chronic pancreatitis and neoplasia. This study shows that Hnf1b deficiency may contribute to diseases of the exocrine pancreas and gains further insight into the etiology of pancreatitis and tumorigenesis.
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Affiliation(s)
- Evans Quilichini
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Mélanie Fabre
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Thassadite Dirami
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Aline Stedman
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Matias De Vas
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Ozge Ozguc
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Raymond C. Pasek
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Silvia Cereghini
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Lucie Morillon
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France
| | - Carmen Guerra
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Anne Couvelard
- Hôpital Bichat, Département de Pathologie, Assistance Publique-Hôpitaux de Paris, Université Paris Diderot, Paris, France
| | - Maureen Gannon
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cécile Haumaitre
- UMR7622 Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Paris, France,Correspondence Address correspondence to: Cecile Haumaitre, PhD, Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, 9 Quai Saint-Bernard, Batiment C-7eme Etage-Case 24, 75252 Paris Cedex 05, France. fax: (33) 1-44-27-34-45.
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Association of Folate and Vitamins Involved in the 1-Carbon Cycle with Polymorphisms in the Methylenetetrahydrofolate Reductase Gene (MTHFR) and Global DNA Methylation in Patients with Colorectal Cancer. Nutrients 2019; 11:nu11061368. [PMID: 31216671 PMCID: PMC6627304 DOI: 10.3390/nu11061368] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 01/09/2023] Open
Abstract
Folate, vitamin B2, vitamin B6, vitamin B12, choline, and betaine are nutrients involved in the 1-carbon cycle that can alter the levels of DNA methylation and influence genesis and/or tumor progression. Thus, the objective of this study was to evaluate the association of folate and vitamins involved in the 1-carbon cycle and MTHFR polymorphisms in global DNA methylation in patients with colorectal cancer gene. The study included 189 patients with colorectal adenocarcinoma answering a clinical evaluation questionnaire and the Food Frequency Questionnaire (FFQ) validated for patients with colon and rectal cancer. Blood samples were collected for evaluation of MTHFR gene polymorphisms in global DNA methylation in blood and in tumor. The values for serum folate were positively correlated with the equivalent total dietary folate (total DFE) (rho = 0.51, p = 0.03) and global DNA methylation (rho = 0.20, p = 0.03). Individuals aged over 61 years (p = 0.01) in clinicopathological staging III and IV (p = 0.01) and with + heterozygous mutated homozygous genotypes for the MTHFR A1298C gene had higher levels of global DNA methylation (p = 0.04). The association between dietary intake of folate, serum folate, and tumor stage were predictive of global DNA methylation in patients’ blood. The levels of serum folate, the dietary folate and the status of DNA methylation can influence clinicopathological staging.
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Molnár B, Galamb O, Péterfia B, Wichmann B, Csabai I, Bodor A, Kalmár A, Szigeti KA, Barták BK, Nagy ZB, Valcz G, Patai ÁV, Igaz P, Tulassay Z. Gene promoter and exon DNA methylation changes in colon cancer development - mRNA expression and tumor mutation alterations. BMC Cancer 2018; 18:695. [PMID: 29945573 PMCID: PMC6020382 DOI: 10.1186/s12885-018-4609-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/18/2018] [Indexed: 12/28/2022] Open
Abstract
Background DNA mutations occur randomly and sporadically in growth-related genes, mostly on cytosines. Demethylation of cytosines may lead to genetic instability through spontaneous deamination. Aims were whole genome methylation and targeted mutation analysis of colorectal cancer (CRC)-related genes and mRNA expression analysis of TP53 pathway genes. Methods Long interspersed nuclear element-1 (LINE-1) BS-PCR followed by pyrosequencing was performed for the estimation of global DNA metlyation levels along the colorectal normal-adenoma-carcinoma sequence. Methyl capture sequencing was done on 6 normal adjacent (NAT), 15 adenomatous (AD) and 9 CRC tissues. Overall quantitative methylation analysis, selection of top hyper/hypomethylated genes, methylation analysis on mutation regions and TP53 pathway gene promoters were performed. Mutations of 12 CRC-related genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53) were evaluated. mRNA expression of TP53 pathway genes was also analyzed. Results According to the LINE-1 methylation results, overall hypomethylation was observed along the normal-adenoma-carcinoma sequence. Within top50 differential methylated regions (DMRs), in AD-N comparison TP73, NGFR, PDGFRA genes were hypermethylated, FMN1, SLC16A7 genes were hypomethylated. In CRC-N comparison DKK2, SDC2, SOX1 genes showed hypermethylation, while ERBB4, CREB5, CNTN1 genes were hypomethylated. In certain mutation hot spot regions significant DNA methylation alterations were detected. The TP53 gene body was addressed by hypermethylation in adenomas. APC, TP53 and KRAS mutations were found in 30, 15, 21% of adenomas, and in 29, 53, 29% of CRCs, respectively. mRNA expression changes were observed in several TP53 pathway genes showing promoter methylation alterations. Conclusions DNA methylation with consecutive phenotypic effect can be observed in a high number of promoter and gene body regions through CRC development. Electronic supplementary material The online version of this article (10.1186/s12885-018-4609-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary. .,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.,Institute of Mathematics and Informatics, Faculty of Sciences, University of Pécs, Ifjúság útja 6, Pécs, H-7624, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Krisztina Andrea Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barbara Kinga Barták
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsófia Brigitta Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
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Heparan Sulfate Proteoglycans in Human Colorectal Cancer. Anal Cell Pathol (Amst) 2018; 2018:8389595. [PMID: 30027065 PMCID: PMC6031075 DOI: 10.1155/2018/8389595] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/14/2018] [Accepted: 05/20/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is the third most common cancer worldwide, accounting for more than 610,000 mortalities every year. Prognosis of patients is highly dependent on the disease stage at diagnosis. Therefore, it is crucial to investigate molecules involved in colorectal cancer tumorigenesis, with possible use as tumor markers. Heparan sulfate proteoglycans are complex molecules present in the cell membrane and extracellular matrix, which play vital roles in cell adhesion, migration, proliferation, and signaling pathways. In colorectal cancer, the cell surface proteoglycan syndecan-2 is upregulated and increases cell migration. Moreover, expression of syndecan-1 and syndecan-4, generally antitumor molecules, is reduced. Levels of glypicans and perlecan are also altered in colorectal cancer; however, their role in tumor progression is not fully understood. In addition, studies have reported increased heparan sulfate remodeling enzymes, as the endosulfatases. Therefore, heparan sulfate proteoglycans are candidate molecules to clarify colorectal cancer tumorigenesis, as well as important targets to therapy and diagnosis.
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Laporte GA, Leguisamo NM, Kalil AN, Saffi J. Clinical importance of DNA repair in sporadic colorectal cancer. Crit Rev Oncol Hematol 2018; 126:168-185. [PMID: 29759559 DOI: 10.1016/j.critrevonc.2018.03.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 03/05/2018] [Accepted: 03/22/2018] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is the third major cause of cancer-related deaths worldwide. However, despite the scientific efforts to provide a molecular classification to improve CRC clinical practice management, prognosis and therapeutic decision are still strongly dependent on the TNM staging system. Mismatch repair system deficiencies can occur in many organs, but it is mainly a hallmark of CRC influencing clinical outcomes and response to therapy. This review will discuss the effect of the modulation of other DNA repair pathways (direct, excision and double strand break repairs) in the clinical and pathological aspects of colorectal cancer and its potential as prognostic and predictive biomarkers.
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Affiliation(s)
- Gustavo A Laporte
- Surgical Oncology Service, Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Natalia M Leguisamo
- Institute of Cardiology/University Foundation of Cardiology, Porto Alegre, Rio Grande do Sul, Brazil; Laboratory of Genetic Toxicology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Antonio N Kalil
- Surgical Oncology Service, Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil.
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31
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Li S, Han Z, Zhao N, Zhu B, Zhang Q, Yang X, Sheng D, Hou J, Guo S, Wei L, Zhang L. Inhibition of DNMT suppresses the stemness of colorectal cancer cells through down-regulating Wnt signaling pathway. Cell Signal 2018; 47:79-87. [PMID: 29601907 DOI: 10.1016/j.cellsig.2018.03.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/19/2018] [Accepted: 03/25/2018] [Indexed: 12/19/2022]
Abstract
Cancer stem cell (CSC) theory reveals a new insight into the understanding of tumorigenesis and metastasis. Recently, DNA methylation is suggested to be a potential epigenetic mechanism for maintenance of CSCs. What's more, studies have shown that DNA methyltransferase (DNMT) is essential for CSCs and deletion of DNMT can reduce tumorigenesis by limiting CSC pool. Therefore, targeting the epigenetic modifiers especially DNA methylation offers an optional strategy for treating human cancers. In the present study we found that DNMT inhibitor 5-Aza-2'-deoxycytidine (5-AzaDC) markedly reduced colorectal CSC abundance in vitro and suppressed liver metastatic tumor growth in vivo. And 5-AzaDC inhibited the expression of active β-catenin and down-regulated the Wnt signaling pathway. The Wnt inhibitors were frequently inactivated by promoter methylation in colorectal cancer; however analysis of TCGA data base showed that only the expression of SFRP1 was significantly reduced in tumors compared to normal tissues. In addition, restoring of SFRP1 expression inhibited the stem cell-like potential of colorectal cancer cells. Our results indicated that inhibition of DNMT blocked the self-renewal of colorectal CSCs and SFRP1 was essential for the maintenance of colorectal CSCs.
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Affiliation(s)
- Shanxin Li
- Department of Pharmacy, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Zhipeng Han
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China
| | - Naping Zhao
- Department of Pharmacy, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Bing Zhu
- Department of Pharmacy, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Qianwen Zhang
- Department of Pharmacology, Fudan University School of Pharmacy, Shanghai, China
| | - Xue Yang
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China
| | - Dandan Sheng
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China
| | - Jing Hou
- Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiwei Guo
- Third Department of General Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Lixin Wei
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China.
| | - Li Zhang
- Department of Pharmacy, Changhai Hospital, The Second Military Medical University, Shanghai, China.
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Zeng J, Hu J, Lian Y, Jiang Y, Chen B. SFRP5 is a target gene transcriptionally regulated by PPARγ in 3T3-L1 adipocytes. Gene 2017; 641:190-195. [PMID: 29066306 DOI: 10.1016/j.gene.2017.10.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 12/12/2022]
Abstract
Secreted frizzled-related protein 5 (SFRP5) is a newly identified adipokine. SFRP5 expression increases during the differentiation and maturation of adipocytes, but the factors regulating SFRP5 expression during this process remain unclear. This study showed that peroxisome proliferator-activated receptor γ (PPARγ) adenovirus transfection could enhance the SFRP5 expression of 3T3-L1 adipocytes. Three potential binding sites of PPARγ in the SFRP5 promoter domain were found by bioinformatics analysis. Luciferase reporter gene assay demonstrated that PPARγ regulated the activity of the SFRP5 promoter through cis-acting elements at -2,284--1,500bp. Further experiments verified that PPARγ could specifically bind to the SFRP5 promoter at -2,284--2,263bp using chromatin immunoprecipitation and electrophoretic mobility shift assay. These results suggest that SFRP5 be a target gene of PPARγ, and its expression may be under the transcriptional regulation of PPARγ.
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Affiliation(s)
- Jun Zeng
- Department of Endocrinology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Jiongyu Hu
- Department of Endocrinology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yu Lian
- Department of Endocrinology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Youzhao Jiang
- Department of Endocrinology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China.
| | - Bing Chen
- Department of Endocrinology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China.
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Zhong X, Shen H, Mao J, Zhang J, Han W. Epigenetic silencing of protocadherin 10 in colorectal cancer. Oncol Lett 2017; 13:2449-2453. [PMID: 28454418 PMCID: PMC5403191 DOI: 10.3892/ol.2017.5733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common types of malignant tumor in the world and occurs through a multi-step process resulting from the accumulation of genetic and epigenetic alterations of the genome. Although the molecular mechanisms of the pathogenesis of CRC remain unclear, the inactivation of tumor suppressor genes (TSGs) through promoter methylation serves an important role. Aberrant methylation is a well-defined marker of CRC. At present, the epigenetic silencing of protocadherin 10 (PCDH10) has been identified as an important TSG with key roles in colorectal carcinogenesis, invasion and metastasis as a frequent and early event. Advances in gene methylation detection in tumor tissues and body fluids have led to the development of non-invasive screening methods for CRC. The present study aimed to review the epigenetic alteration of PCDH10 in CRC development, and the potential of PCDH10 to be a non-invasive biomarker for CRC.
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Affiliation(s)
- Xian Zhong
- Department of Medical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
- Department of Medical Oncology, Hangzhou Binjiang Hospital, Hangzhou, Zhejiang 310052, P.R. China
| | - Hong Shen
- Department of Medical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Jianshan Mao
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Jiawei Zhang
- Cancer Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, P.R. China
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34
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Next-Generation Sequencing Approach in Methylation Analysis of HNF1B and GATA4 Genes: Searching for Biomarkers in Ovarian Cancer. Int J Mol Sci 2017; 18:ijms18020474. [PMID: 28241454 PMCID: PMC5344006 DOI: 10.3390/ijms18020474] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is well-known to be associated with ovarian cancer (OC) and has great potential to serve as a biomarker in monitoring response to therapy and for disease screening. The purpose of this study was to investigate methylation of HNF1B and GATA4 and correlate detected methylation with clinicopathological characteristic of OC patients. The study group consisted of 64 patients with OC and 35 control patients. To determine the most important sites of HNF1B and GATA4, we used next-generation sequencing. For further confirmation of detected methylation of selected regions, we used high-resolution melting analysis and methylation-specific real-time polymerase chain reaction (PCR). Selected regions of HNF1B and GATA4 were completely methylation free in all control samples, whereas methylation-positive pattern was observed in 32.8% (HNF1B) and 45.3% (GATA4) of OC samples. Evaluating both genes together, we were able to detect methylation in 65.6% of OC patients. We observed a statistically significant difference in HNF1B methylation between samples with different stages of OC. We also detected subtype specific methylation in GATA4 and a decrease of methylation in late stages of OC. The combination of unmethylated HNF1B and methylated GATA4 was associated with longer overall survival. In our study, we employed innovative approach of methylation analysis of HNF1B and GATA4 to search for possible epigenetic biomarkers. We confirmed the significance of the HNF1B and GATA4 hypermethylation with emphasis on the need of selecting the most relevant sites for analysis. We suggest selected CpGs to be further examined as a potential positive prognostic factor.
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Alexander M, Burch JB, Steck SE, Chen CF, Hurley TG, Cavicchia P, Shivappa N, Guess J, Zhang H, Youngstedt SD, Creek KE, Lloyd S, Jones K, Hébert JR. Case-control study of candidate gene methylation and adenomatous polyp formation. Int J Colorectal Dis 2017; 32:183-192. [PMID: 27771773 PMCID: PMC5288296 DOI: 10.1007/s00384-016-2688-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/12/2016] [Indexed: 02/04/2023]
Abstract
PURPOSE Colorectal cancer (CRC) is one of the most common and preventable forms of cancer but remains the second leading cause of cancer-related death. Colorectal adenomas are precursor lesions that develop in 70-90 % of CRC cases. Identification of peripheral biomarkers for adenomas would help to enhance screening efforts. This exploratory study examined the methylation status of 20 candidate markers in peripheral blood leukocytes and their association with adenoma formation. METHODS Patients recruited from a local endoscopy clinic provided informed consent and completed an interview to ascertain demographic, lifestyle, and adenoma risk factors. Cases were individuals with a histopathologically confirmed adenoma, and controls included patients with a normal colonoscopy or those with histopathological findings not requiring heightened surveillance (normal biopsy, hyperplastic polyp). Methylation-specific polymerase chain reaction was used to characterize candidate gene promoter methylation. Odds ratios (ORs) and 95 % confidence intervals (95% CIs) were calculated using unconditional multivariable logistic regression to test the hypothesis that candidate gene methylation differed between cases and controls, after adjustment for confounders. RESULTS Complete data were available for 107 participants; 36 % had adenomas (men 40 %, women 31 %). Hypomethylation of the MINT1 locus (OR 5.3, 95% CI 1.0-28.2) and the PER1 (OR 2.9, 95% CI 1.1-7.7) and PER3 (OR 11.6, 95% CI 1.6-78.5) clock gene promoters was more common among adenoma cases. While specificity was moderate to high for the three markers (71-97 %), sensitivity was relatively low (18-45 %). CONCLUSION Follow-up of these epigenetic markers is suggested to further evaluate their utility for adenoma screening or surveillance.
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Affiliation(s)
- M Alexander
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - J B Burch
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA.
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA.
- William Jennings Bryant Dorn Department of Veterans Affairs Medical Center, Columbia, SC, USA.
| | - S E Steck
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - C-F Chen
- Center for Molecular Studies, Greenwood Genetic Center, Greenwood, SC, USA
| | - T G Hurley
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
| | - P Cavicchia
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
- Division of Community Health Promotion, Florida Department of Health, Tallahassee, FL, USA
| | - N Shivappa
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - J Guess
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
| | - H Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - S D Youngstedt
- College of Nursing and Health Innovation, College of Health Solutions, Arizona State University and Phoenix VA Health Care System, Phoenix, AZ, USA
| | - K E Creek
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - S Lloyd
- South Carolina Medical Endoscopy Center, and Department of Family Medicine, University of South Carolina School of Medicine, Columbia, SC, USA
| | - K Jones
- Center for Molecular Studies, Greenwood Genetic Center, Greenwood, SC, USA
| | - J R Hébert
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene St, Room 228, Columbia, SC, 29209, USA
- Department of Family and Preventive Medicine, School of Medicine, University of South Carolin, Columbia, SC, USA
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Galamb O, Kalmár A, Barták BK, Patai &AV, Leiszter K, Péterfia B, Wichmann B, Valcz G, Veres G, Tulassay Z, Molnár B. Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma. World J Gastroenterol 2016; 22:10325-10340. [PMID: 28058013 PMCID: PMC5175245 DOI: 10.3748/wjg.v22.i47.10325] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/20/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites.
METHODS In silico DNA methylation analysis of 353 epigenetic clock CpG sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples [64 colorectal cancer (CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684]. Among the differentially methylated age-related genes, secreted frizzled related protein 1 (SFRP1) promoter methylation was further investigated in colonic tissue from 8 healthy adults, 19 normal children, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specific high resolution melting (MS-HRM) analysis. mRNA expression of age-related “epigenetic clock” genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples (49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children) (GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267). Whole promoter methylation analysis of genes showing inverse DNA methylation-gene expression data was performed on 30 colonic samples using methyl capture sequencing.
RESULTS Fifty-seven age-related CpG sites including hypermethylated PPP1R16B, SFRP1, SYNE1 and hypomethylated MGP, PIPOX were differentially methylated between CRC and normal tissues (P < 0.05, Δβ≥ 10%). In the adenoma vs normal comparison, 70 CpG sites differed significantly, including hypermethylated DKK3, SDC2, SFRP1, SYNE1 and hypomethylated CEMIP, SPATA18 (P < 0.05, Δβ≥ 10%). In MS-HRM analysis, the SFRP1 promoter region was significantly hypermethylated in CRC (55.0% ± 8.4 %) and adenoma tissue samples (49.9% ± 18.1%) compared to normal adult (5.2% ± 2.7%) and young (2.2% ± 0.7%) colonic tissue (P < 0.0001). DNA methylation of SFRP1 promoter was slightly, but significantly increased in healthy adults compared to normal young samples (P < 0.02). This correlated with significantly increased SFRP1 mRNA levels in children compared to normal adult samples (P < 0.05). In CRC tissue the mRNA expression of 117 age-related genes were changed, while in adenoma samples 102 genes showed differential expression compared with normal colonic tissue (P < 0.05, logFC > 0.5). The change of expression for several genes including SYNE1, CLEC3B, LTBP3 and SFRP1, followed the same pattern in aging and carcinogenesis, though not for all genes (e.g., MGP).
CONCLUSION Several age-related DNA methylation alterations can be observed during CRC development and progression affecting the mRNA expression of certain CRC- and adenoma-related key control genes.
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Kim BR, Kang MH, Kim JL, Na YJ, Park SH, Lee SI, Kang S, Joung SY, Lee SY, Lee DH, Min BW, Oh SC. RUNX3 inhibits the metastasis and angiogenesis of colorectal cancer. Oncol Rep 2016; 36:2601-2608. [DOI: 10.3892/or.2016.5086] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/09/2016] [Indexed: 11/05/2022] Open
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The variation trends of SFRP2 methylation of tissue, feces, and blood detection in colorectal cancer development. Eur J Cancer Prev 2016; 25:288-98. [DOI: 10.1097/cej.0000000000000185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Galamb O, Kalmár A, Péterfia B, Csabai I, Bodor A, Ribli D, Krenács T, Patai ÁV, Wichmann B, Barták BK, Tóth K, Valcz G, Spisák S, Tulassay Z, Molnár B. Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer. Epigenetics 2016; 11:588-602. [PMID: 27245242 DOI: 10.1080/15592294.2016.1190894] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The WNT signaling pathway has an essential role in colorectal carcinogenesis and progression, which involves a cascade of genetic and epigenetic changes. We aimed to analyze DNA methylation affecting the WNT pathway genes in colorectal carcinogenesis in promoter and gene body regions using whole methylome analysis in 9 colorectal cancer, 15 adenoma, and 6 normal tumor adjacent tissue (NAT) samples by methyl capture sequencing. Functional methylation was confirmed on 5-aza-2'-deoxycytidine-treated colorectal cancer cell line datasets. In parallel with the DNA methylation analysis, mutations of WNT pathway genes (APC, β-catenin/CTNNB1) were analyzed by 454 sequencing on GS Junior platform. Most differentially methylated CpG sites were localized in gene body regions (95% of WNT pathway genes). In the promoter regions, 33 of the 160 analyzed WNT pathway genes were differentially methylated in colorectal cancer vs. normal, including hypermethylated AXIN2, CHP1, PRICKLE1, SFRP1, SFRP2, SOX17, and hypomethylated CACYBP, CTNNB1, MYC; 44 genes in adenoma vs. NAT; and 41 genes in colorectal cancer vs. adenoma comparisons. Hypermethylation of AXIN2, DKK1, VANGL1, and WNT5A gene promoters was higher, while those of SOX17, PRICKLE1, DAAM2, and MYC was lower in colon carcinoma compared to adenoma. Inverse correlation between expression and methylation was confirmed in 23 genes, including APC, CHP1, PRICKLE1, PSEN1, and SFRP1. Differential methylation affected both canonical and noncanonical WNT pathway genes in colorectal normal-adenoma-carcinoma sequence. Aberrant DNA methylation appears already in adenomas as an early event of colorectal carcinogenesis.
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Affiliation(s)
- Orsolya Galamb
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Alexandra Kalmár
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Bálint Péterfia
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - István Csabai
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - András Bodor
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Dezső Ribli
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Tibor Krenács
- d 1st Department of Pathology and Experimental Cancer Research , Semmelweis University , Budapest , Hungary.,e Tumor Progression Research Group , Hungarian Academy of Sciences - Semmelweis University , Budapest , Hungary
| | - Árpád V Patai
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Barnabás Wichmann
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Barbara Kinga Barták
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Kinga Tóth
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Gábor Valcz
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Sándor Spisák
- f Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Zsolt Tulassay
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.,b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Béla Molnár
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
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Epigenetics in diagnosis of colorectal cancer. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2016; 5:49-57. [PMID: 27844020 PMCID: PMC5019333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Colorectal cancer (CRC) is a third most common epithelial carcinoma. CRC is known to develop from the early precancerous lesion to full blown malignancy via definite phases due to cumulative mutations and aberrant methylation of number of genes. The use of serum biomarkers that is non-invasive to discriminate cancer patients from healthy persons will prove to be an important tool to improve the early diagnosis of CRC. This will serve as the boon to the clinical management of the disease.
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Cacabelos R, Torrellas C. Epigenetics of Aging and Alzheimer's Disease: Implications for Pharmacogenomics and Drug Response. Int J Mol Sci 2015; 16:30483-543. [PMID: 26703582 PMCID: PMC4691177 DOI: 10.3390/ijms161226236] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/16/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic variability (DNA methylation/demethylation, histone modifications, microRNA regulation) is common in physiological and pathological conditions. Epigenetic alterations are present in different tissues along the aging process and in neurodegenerative disorders, such as Alzheimer’s disease (AD). Epigenetics affect life span and longevity. AD-related genes exhibit epigenetic changes, indicating that epigenetics might exert a pathogenic role in dementia. Epigenetic modifications are reversible and can potentially be targeted by pharmacological intervention. Epigenetic drugs may be useful for the treatment of major problems of health (e.g., cancer, cardiovascular disorders, brain disorders). The efficacy and safety of these and other medications depend upon the efficiency of the pharmacogenetic process in which different clusters of genes (pathogenic, mechanistic, metabolic, transporter, pleiotropic) are involved. Most of these genes are also under the influence of the epigenetic machinery. The information available on the pharmacoepigenomics of most drugs is very limited; however, growing evidence indicates that epigenetic changes are determinant in the pathogenesis of many medical conditions and in drug response and drug resistance. Consequently, pharmacoepigenetic studies should be incorporated in drug development and personalized treatments.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
| | - Clara Torrellas
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
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Sun Y, Li S, Shen K, Ye S, Cao D, Yang J. DAPK1, MGMT and RARB promoter methylation as biomarkers for high-grade cervical lesions. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:14939-14945. [PMID: 26823825 PMCID: PMC4713611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
Gene promoter methylation may be used a potential biomarker for detecting solid tumor including cervical cancer. Here, we used methylation sensitive-high resolution melting (MS-HRM) analysis to detecting promoter methylation ratios of DAPK1, MGMT and RARB gene in patients with different cervical disease grade. The detection of gene promoter methylation was conducted in two hundred fifty patients' samples including normal cytology (n=48), cervical intraepithelial neoplasia grade 1 (CIN1, n=54), cervical intraepithelial neoplasia grade 2 (CIN2, n=47), cervical intraepithelial neoplasia grade 3 (CIN3, n=56) and cervical squamous cell carcinomas (SCS, n=45). We found there were a significant positive correlation between the promoter methylation status of DAPK1 and cervical disease grade (P=0.022). In addition, the methylated promoters of DAPK1 combined with MGMT, MGMT combined with RARB, DAPK1 combined with RARB were positive correlated with cervical disease grade (P < 0.05). All three genes promoters methylated were positive correlated with cervical disease grade (P < 0.001). Receiver operating characteristic (ROC) curves was conducted to evaluate whether the three genes methylation could be used to be a potential marker for diagnosing high grade cervical disease (HSIL and SCC). The cutoff values for the methylation rates of all these genes were 0-5%. Regrettably, only the methylation of MGMT combined with DAPK1 gave 43.4% sensitivity and 68.6% specificity. The current results indicated that MS-HRM-based testing for DNA methylations of MGMT plus DAPK1 genes holds some promise for high grade cervical disease screening.
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Affiliation(s)
- Yin Sun
- Department of O&G, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science & Peking Union Medical CollegeChina
| | - Shu Li
- Department of O&G, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science & Peking Union Medical CollegeChina
| | - Keng Shen
- Department of O&G, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science & Peking Union Medical CollegeChina
| | - Shuang Ye
- Fudan University Shanghai Cancer Center, OncologyChina
| | - Dongyan Cao
- Fudan University Shanghai Cancer Center, OncologyChina
| | - Jiaxin Yang
- Fudan University Shanghai Cancer Center, OncologyChina
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Yu DD, Guo SW, Jing YY, Dong YL, Wei LX. A review on hepatocyte nuclear factor-1beta and tumor. Cell Biosci 2015; 5:58. [PMID: 26464794 PMCID: PMC4603907 DOI: 10.1186/s13578-015-0049-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/01/2015] [Indexed: 01/06/2023] Open
Abstract
Hepatocyte nuclear factor-1beta (HNF1β) was initially identified as a liver-specific transcription factor. It is a homeobox transcription factor that functions as a homodimer or heterodimer with HNF1α. HNF1β plays an important role in organogenesis during embryonic stage, especially of the liver, kidney, and pancreas. Mutations in the HNF1β gene cause maturity-onset diabetes of the young type 5 (MODY5), renal cysts, genital malformations, and pancreas atrophy. Recently, it has been shown that the expression of HNF1β is associated with cancer risk in several tumors, including hepatocellular carcinoma, pancreatic carcinoma, renal cancer, ovarian cancer, endometrial cancer, and prostate cancer. HNF1β also regulates the expression of genes associated with stem/progenitor cells, which indicates that HNF1β may play an important role in stem cell regulation. In this review, we discuss some of the current developments about HNF1β and tumor, the relationship between HNF1β and stem/progenitor cells, and the potential pathogenesis of HNF1β in various tumors.
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Affiliation(s)
- Dan-Dan Yu
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Shi-Wei Guo
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Ying-Ying Jing
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Yu-Long Dong
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Li-Xin Wei
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
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Wu X, Zhao B, Cheng Y, Yang Y, Huang C, Meng X, Wu B, Zhang L, Lv X, Li J. Melittin induces PTCH1 expression by down-regulating MeCP2 in human hepatocellular carcinoma SMMC-7721 cells. Toxicol Appl Pharmacol 2015; 288:74-83. [PMID: 26189965 DOI: 10.1016/j.taap.2015.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/29/2015] [Accepted: 07/15/2015] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) has a high mortality rate worldwide and still remains to be a noticeable public health problem. Therefore, new remedies are urgently needed. Melittin, a major component of bee venom, is known to suppress cell growth in various cancers including HCC. However, the mechanism of the anticancer effect of melittin on HCC has not been fully elucidated. It has been reported that Methyl-CpG binding protein 2 (MeCP2) plays a key role in tumor proliferation, apoptosis, migration and invasion. In the present study, we found the high expression of MeCP2 in human HCC tissues and in the SMMC-7721 cell line. MeCP2 silencing inhibited cell proliferation, while over-expression of MeCP2 promoted cell growth in SMMC-7721 cells. It indicates that MeCP2 may be an attractive target for human HCC. We further found that melittin could inhibit cell proliferation by reducing MeCP2 expression in vitro. Interestingly, the inhibitory effect of melittin on cell proliferation was due to a delay in G0/G1 cell cycle progression, without influencing cell apoptosis. Next, we investigated the potential molecular mechanisms and found that MeCP2 could modulate Shh signaling in SMMC-7721 cells. Further study indicates that melittin may induce the demethylation of PTCH1 promoter, resulting in the increased expression of PTCH1. Furthermore, the expression of Shh and GLI1 was significantly lowered upon treatment of melittin. These results suggest that melittin can block Shh signaling in vitro. In short, these results indicate that melittin inhibits cell proliferation by down-regulating MeCP2 through Shh signaling in SMMC-7721 cells.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Cycle Checkpoints/drug effects
- Cell Line, Tumor
- Cell Proliferation/drug effects
- DNA Methylation
- Dose-Response Relationship, Drug
- Gene Expression Regulation, Neoplastic
- Hedgehog Proteins/metabolism
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Melitten/pharmacology
- Methyl-CpG-Binding Protein 2/genetics
- Methyl-CpG-Binding Protein 2/metabolism
- Patched Receptors
- Patched-1 Receptor
- Promoter Regions, Genetic
- RNA Interference
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Resting Phase, Cell Cycle/drug effects
- Signal Transduction/drug effects
- Time Factors
- Transcription Factors/metabolism
- Transfection
- Zinc Finger Protein GLI1
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Affiliation(s)
- Xiaoqin Wu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Bin Zhao
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Yahui Cheng
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Yang Yang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Cheng Huang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Xiaoming Meng
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Baoming Wu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Lei Zhang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Xiongwen Lv
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University, ILD-AMU, Anhui Medical University, Hefei 230032, China.
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Lee HS, Yun JH, Jung J, Yang Y, Kim BJ, Lee SJ, Yoon JH, Moon Y, Kim JM, Kwon YI. Identification of differentially-expressed genes by DNA methylation in cervical cancer. Oncol Lett 2015; 9:1691-1698. [PMID: 25789025 PMCID: PMC4356325 DOI: 10.3892/ol.2015.2917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/08/2014] [Indexed: 01/03/2023] Open
Abstract
To identify novel cervical cancer-related genes that are regulated by DNA methylation, integrated analyses of genome-wide DNA methylation and RNA expression profiles were performed using the normal and tumor regions of tissues from four patients; two with cervical cancer and two with pre-invasive cancer. The present study identified 19 novel cervical cancer-related genes showing differential RNA expression by DNA methylation. A number of the identified genes were novel cervical cancer-related genes and their differential expression was confirmed in a publicly available database. Among the candidate genes, the epigenetic regulation and expression of three genes, CAMK2N1, ALDH1A3 and PPP1R3C, was validated in HeLa cells treated with a demethylating reagent using methylation-specific polymerase chain reaction (PCR) and quantitative PCR, respectively. From these results, the expression of the CAMK2N1, ALDH1A3 and PPP1R3C genes are were shown to be suppressed in cervical cancers by DNA methylation. These genes may be involved in the progression or initiation of cervical cancer.
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Affiliation(s)
- Heun-Sik Lee
- Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Chungcheongbuk-do 363-951, Republic of Korea
| | - Jun Ho Yun
- Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Chungcheongbuk-do 363-951, Republic of Korea
| | | | - Young Yang
- Center for Women's Disease, Department of Biological Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Bong-Jo Kim
- Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Chungcheongbuk-do 363-951, Republic of Korea
| | - Sung-Jong Lee
- Department of Obstetrics and Gynecology, Saint Vincent's Hospital, the Catholic University, Suwon, Gyeonggi-do 442-723, Republic of Korea
| | - Joo Hee Yoon
- Department of Obstetrics and Gynecology, Saint Vincent's Hospital, the Catholic University, Suwon, Gyeonggi-do 442-723, Republic of Korea
| | - Yong Moon
- Department of Public Health Administration, Namseoul University, Cheonan, Chungcheongnam-do 331-707, Republic of Korea
| | - Jeong-Min Kim
- Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Chungcheongbuk-do 363-951, Republic of Korea
| | - Yong-Il Kwon
- Department of Obstetrics and Gynecology, Kangdong Sacred Heart Hospital, Hallym University Medical Center, Seoul 134-701, Republic of Korea
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Meng G, Li Y, Lv Y, Dai H, Zhang X, Guo QN. Preliminary screening of differentially expressed genes involved in methyl-CpG-binding protein 2 gene-mediated proliferation in human osteosarcoma cells. Tumour Biol 2015; 36:3009-15. [PMID: 25613065 DOI: 10.1007/s13277-014-2935-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/03/2014] [Indexed: 12/27/2022] Open
Abstract
Methyl-CpG-binding protein 2 (MeCP2) is essential in human brain development and has been linked to several cancer types and neuro-developmental disorders. This study aims to screen the MeCP2 related differentially expressed genes and discover the therapeutic targets for osteosarcoma. CCK8 assay was used to detect the proliferation and SaOS2 and U2OS cells. Apoptosis of cells was detected by flow cytometry analysis that monitored Annexin V-APC/7-DD binding and 7-ADD uptake simultaneously. Denaturing formaldehyde agarose gel electrophoresis was employed to examine the quality of total RNA 18S and 28S units. Gene chip technique was utilized to discover the differentially expressed genes correlated with MeCP2 gene. Differential gene screening criteria were used to screen the changed genes. The gene up-regulation or down-regulation more than 1.5 times was regarded as significant differential expression genes. The CCK8 results indicated that the cell proliferation of MeCP2 silencing cells (LV-MeCP2-RNAi) was significantly decreased compared to non-silenced cells (LV-MeCP2-RNAi-CN) (P < 0.05). MeCP2 silencing could also induce significant apoptosis compared to non-silenced cells (P < 0.05); 107 expression changed genes were screened from a total of 49,395 transcripts. Among the total 107 transcripts, 34 transcripts were up-regulated and 73 transcripts were down-regulated. There were five significant differentially expressed genes, including IGFBP4, HOXC8, LMO4, MDK, and CTGF, which correlated with the MeCP2 gene. The methylation frequency of CpG in IGFBP4 gene could achieve 55%. In conclusion, the differentially expressed IGFBP4, HOXC8, LMO4, MDK, and CTGF genes may be involved in MeCP2 gene-mediated proliferation and apoptosis in osteosarcoma cells.
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Affiliation(s)
- Gang Meng
- Department of Pathology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
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47
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Estécio MRH, Maddipoti S, Bueso-Ramos C, DiNardo CD, Yang H, Wei Y, Kondo K, Fang Z, Stevenson W, Chang KS, Pierce SA, Bohannan Z, Borthakur G, Kantarjian H, Garcia-Manero G. RUNX3 promoter hypermethylation is frequent in leukaemia cell lines and associated with acute myeloid leukaemia inv(16) subtype. Br J Haematol 2015; 169:344-51. [PMID: 25612675 DOI: 10.1111/bjh.13299] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/08/2014] [Indexed: 01/15/2023]
Abstract
Correlative and functional studies support the involvement of the RUNX gene family in haematological malignancies. To elucidate the role of epigenetics in RUNX inactivation, we evaluated promoter DNA methylation of RUNX1, 2, and 3 in 23 leukaemia cell lines and samples from acute myeloid leukaemia (AML), acute lymphocytic leukaemia (ALL) and myelodysplatic syndromes (MDS) patients. RUNX1 and RUNX2 gene promoters were mostly unmethylated in cell lines and clinical samples. Hypermethylation of RUNX3 was frequent among cell lines (74%) and highly variable among patient samples, with clear association to cytogenetic status. High frequency of RUNX3 hypermethylation (85% of the 20 studied cases) was found in AML patients with inv(16)(p13.1q22) compared to other AML subtypes (31% of the other 49 cases). RUNX3 hypermethylation was also frequent in ALL (100% of the six cases) but low in MDS (21%). In support of a functional role, hypermethylation of RUNX3 was correlated with low levels of protein, and treatment of cell lines with the DNA demethylating agent, decitabine, resulted in mRNA re-expression. Furthermore, relapse-free survival of non-inv(16)(p13.1q22) AML patients without RUNX3 methylation was significantly better (P = 0·016) than that of methylated cases. These results suggest that RUNX3 silencing is an important event in inv(16)(p13.1q22) leukaemias.
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Affiliation(s)
- Marcos R H Estécio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Ding Z, Jiang T, Piao Y, Han T, Han Y, Xie X. Meta-analysis of the association between APC promoter methylation and colorectal cancer. Onco Targets Ther 2015; 8:211-22. [PMID: 25632237 PMCID: PMC4304602 DOI: 10.2147/ott.s75827] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Previous studies investigating the association between adenomatous polyposis coli (APC) gene promoter methylation and colorectal cancer (CRC) have yielded conflicting results. The aim of this study was to comprehensively evaluate the potential application of the detection of APC promoter methylation to the prevention and treatment of CRC. PubMed, Embase, and MEDLINE (results updated to October 2014) were searched for relevant studies. The effect size was defined as the weighted odds ratio (OR), which was calculated using either the fixed-effects or random-effects model. Prespecified subgroup and sensitivity analyses were conducted to evaluate potential heterogeneity among the included studies. Nineteen studies comprising 2,426 participants were selected for our meta-analysis. The pooled results of nine studies comprising a total of 740 subjects indicated that APC promoter methylation was significantly associated with CRC risk (pooled OR 5.53; 95% confidence interval [CI] 3.50–8.76; P<0.01). Eleven studies with a total of 1,219 patients evaluated the association between APC promoter methylation and the presence of CRC metastasis, and the pooled OR was 0.80 (95% CI 0.44–1.46; P=0.47). A meta-analysis conducted with four studies with a total of 467 patients found no significant correlation between APC promoter methylation and the presence of colorectal adenoma (pooled OR 1.85; 95% CI 0.67–5.10; P=0.23). No significant correlation between APC promoter methylation and patients’ Dukes’ stage, TNM stage, differentiation grade, age, or sex was identified. In conclusion, APC promoter methylation was found to be significantly associated with a higher risk of developing CRC. The findings indicate that APC promoter methylation may be a potential biomarker for the carcinogenesis of CRC.
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Affiliation(s)
- Zhenyu Ding
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Tong Jiang
- Laboratory of Military Health in Cold Region, Center for Disease Control and Prevention of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Ying Piao
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Tao Han
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Yaling Han
- Institute of Cardiovascular Disease, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Xiaodong Xie
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
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Liu F, Ji F, Ji Y, Jiang Y, Sun X, Lu Y, Zhang L, Han Y, Liu X. Dissecting the mechanism of colorectal tumorigenesis based on RNA-sequencing data. Exp Mol Pathol 2015; 98:246-53. [PMID: 25576648 DOI: 10.1016/j.yexmp.2015.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/26/2014] [Accepted: 01/05/2015] [Indexed: 02/07/2023]
Abstract
OBJECTIVE This study aimed to identify the differentially expressed genes (DEGs), mutated genes and fusion genes in colorectal cancer. MATERIALS AND METHODS RNA-sequencing data (ID: SRP009386) from cancerous, paracancerous non-tumor and distant normal tissue from one Chinese patient with stage III colorectal cancer were downloaded from Sequence Read Archive. Quality control was checked using FastQC, followed by sequence alignment against the hg19 reference genome using TopHat v1.3.3. The expression levels were quantified using Cufflinks, followed by DEGs screening using NOISeq. Enrichment analysis was performed using DAVID. Transcription factors were screened using TRANSFA. Mutated loci were identified using SAMTools and VCFTools. Gene fusion events were detected by TopHat-fusion. RESULTS In total 2440, 1887 and 834 DEGs were respectively detected in cancerous vs. normal tissue, cancerous vs. paracancerous tissue and paracancerous vs. normal tissue. The up-regulated genes from cancerous and paracancerous tissue compared with normal tissue were enriched in "extracellular matrix receptor interaction" and "focal adhesion pathway" as well as some biological processes except for "negative regulation of programmed cell death" uniquely presenting in cancer. Dysregulated transcription factors including SOX4, BCL6, CEBPB and MSX2 were enriched in the unique biological process. Trp53 was identified with one mutated locus 7577142 (C → T) on chromosome 17. BCL6 also experienced missense mutation. Additionally, COL1A1-PPP2R2C and EXPH5-COL1A2 were observed fusion genes in cancer tissue. CONCLUSIONS The unique biological process in cancer tissue may be the cause for colorectal carcinogenesis. The screened transcription factors, mutated genes and fusion genes may contribute to the progression of colorectal cancer.
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Affiliation(s)
- Fuguo Liu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Fengzhi Ji
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yuling Ji
- Statistics Division, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yueping Jiang
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Xueguo Sun
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yanyan Lu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Lingyun Zhang
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Yue Han
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
| | - Xishuang Liu
- Department of Gastroenterology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, Shandong Province, China.
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Nishihara R, Wang M, Qian ZR, Baba Y, Yamauchi M, Mima K, Sukawa Y, Kim SA, Inamura K, Zhang X, Wu K, Giovannucci EL, Chan AT, Fuchs CS, Ogino S, Schernhammer ES. Alcohol, one-carbon nutrient intake, and risk of colorectal cancer according to tumor methylation level of IGF2 differentially methylated region. Am J Clin Nutr 2014; 100:1479-88. [PMID: 25411283 PMCID: PMC4232016 DOI: 10.3945/ajcn.114.095539] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/19/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Although a higher consumption of alcohol, which is a methyl-group antagonist, was previously associated with colorectal cancer risk, mechanisms remain poorly understood. OBJECTIVE We hypothesized that excess alcohol consumption might increase risk of colorectal carcinoma with hypomethylation of insulin-like growth factor 2 (IGF2) differentially methylated region-0 (DMR0), which was previously associated with a worse prognosis. DESIGN With the use of a molecular pathologic epidemiology database in 2 prospective cohort studies, the Nurses' Health Study and Health Professionals Follow-up Study, we examined the association between alcohol intake and incident colorectal cancer according to the tumor methylation level of IGF2 DMR0. Duplication-method Cox proportional cause-specific hazards regression for competing risk data were used to compute HRs and 95% CIs. In addition, we investigated intakes of vitamin B-6, vitamin B-12, methionine, and folate as exposures. RESULTS During 3,206,985 person-years of follow-up, we identified 993 rectal and colon cancer cases with an available tumor DNA methylation status. Compared with no alcohol consumption, the consumption of ≥15 g alcohol/d was associated with elevated risk of colorectal cancer with lower levels of IGF2 DMR0 methylation [within the first and second quartiles: HRs of 1.55 (95% CI: 1.08, 2.24) and 2.11 (95% CI: 1.44, 3.07), respectively]. By contrast, alcohol consumption was not associated with cancer with higher levels of IGF2 DMR0 methylation. The association between alcohol and cancer risk differed significantly by IGF2 DMR0 methylation level (P-heterogeneity = 0.006). The association of vitamin B-6, vitamin B-12, and folate intakes with cancer risk did not significantly differ according to IGF2 DMR0 methylation level (P-heterogeneity > 0.2). CONCLUSIONS Higher alcohol consumption was associated with risk of colorectal cancer with IGF2 DMR0 hypomethylation but not risk of cancer with high-level IGF2 DMR0 methylation. The association between alcohol intake and colorectal cancer risk may differ by tumor epigenetic features.
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Affiliation(s)
- Reiko Nishihara
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Molin Wang
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Zhi Rong Qian
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Yoshifumi Baba
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Mai Yamauchi
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Kosuke Mima
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Yasutaka Sukawa
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Sun A Kim
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Kentaro Inamura
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Xuehong Zhang
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Kana Wu
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Edward L Giovannucci
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Andrew T Chan
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Charles S Fuchs
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Shuji Ogino
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
| | - Eva S Schernhammer
- From the Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (RN, ZRQ, MY, KM, YS, SAK, KI, CSF, and SO); the Departments of Nutrition (RN, KW, and ELG), Epidemiology (MW, ELG, SO, and ESS), and Biostatistics (MW), Harvard School of Public Health, Boston, MA; the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA (MW, XZ, KW, ELG, ATC, CSF, and ESS); the Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan (YB); the Division of Gastroenterology, Massachusetts General Hospital, Boston, MA (ATC); and Applied Cancer Research-Institution for Translational Research Vienna, Vienna, Austria (ESS)
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