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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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Tocan V, Nakamura-Utsunomiya A, Sonoda Y, Matsuoka W, Mizuguchi S, Muto Y, Hijioka T, Nogami M, Sasaoka D, Nagamatsu F, Oba U, Kawakubo N, Hamada H, Mushimoto Y, Chong PF, Kaku N, Koga Y, Sakai Y, Oda Y, Tajiri T, Ohga S. High-Titer Anti-ZSCAN1 Antibodies in a Toddler Clinically Diagnosed with Apparent Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation Syndrome. Int J Mol Sci 2024; 25:2820. [PMID: 38474067 DOI: 10.3390/ijms25052820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Severe obesity in young children prompts for a differential diagnosis that includes syndromic conditions. Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD) syndrome is a potentially fatal disorder characterized by rapid-onset obesity associated with hypoventilation, neural crest tumors, and endocrine and behavioral abnormalities. The etiology of ROHHAD syndrome remains to be established, but recent research has been focusing on autoimmunity. We report on a 2-year-old girl with rapid-onset obesity during the first year of life who progressed to hypoventilation and encephalitis in less than four months since the start of accelerated weight gain. The patient had a high titer of anti-ZSCAN1 antibodies (348; reference range < 40), and the increased values did not decline after acute phase treatment. Other encephalitis-related antibodies, such as the anti-NDMA antibody, were not detected. The rapid progression from obesity onset to central hypoventilation with encephalitis warns about the severe consequences of early-onset ROHHAD syndrome. These data indicate that serial measurements of anti-ZSCAN1 antibodies might be useful for the diagnosis and estimation of disease severity. Further research is needed to determine whether it can predict the clinical course of ROHHAD syndrome and whether there is any difference in antibody production between patients with and without tumors.
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Affiliation(s)
- Vlad Tocan
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akari Nakamura-Utsunomiya
- Department of Genetic Medicine/Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8511, Japan
- Department of Pediatrics, Hiroshima City North Medical Center Asa Citizens Hospital, Hiroshima 731-0293, Japan
- Division of Neonatal Screening, National Center for Child Health and Development, Tokyo 157-8535, Japan
| | - Yuri Sonoda
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Wakato Matsuoka
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Soichi Mizuguchi
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Yuichiro Muto
- Department of Pediatrics, Japanese Red Cross Kumamoto Hospital, Kumamoto 861-8520, Japan
| | - Takaaki Hijioka
- Department of Pediatrics, Japanese Red Cross Kumamoto Hospital, Kumamoto 861-8520, Japan
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Masao Nogami
- Department of Pediatrics, Japanese Red Cross Kumamoto Hospital, Kumamoto 861-8520, Japan
| | - Daiki Sasaoka
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Fusa Nagamatsu
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Utako Oba
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Naonori Kawakubo
- Department of Pediatric Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroshi Hamada
- Department of Pediatric Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuichi Mushimoto
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Pin Fee Chong
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Noriyuki Kaku
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Yuhki Koga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tatsuro Tajiri
- Department of Pediatric Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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Hosseiniyan Khatibi SM, Rahbar Saadat Y, Hejazian SM, Sharifi S, Ardalan M, Teshnehlab M, Zununi Vahed S, Pirmoradi S. Decoding the Possible Molecular Mechanisms in Pediatric Wilms Tumor and Rhabdoid Tumor of the Kidney through Machine Learning Approaches. Fetal Pediatr Pathol 2023; 42:825-844. [PMID: 37548233 DOI: 10.1080/15513815.2023.2242979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
Objective: Wilms tumor (WT) and Rhabdoid tumor (RT) are pediatric renal tumors and their differentiation is based on histopathological and molecular analysis. The present study aimed to introduce the panels of mRNAs and microRNAs involved in the pathogenesis of these cancers using deep learning algorithms. Methods: Filter, graph, and association rule mining algorithms were applied to the mRNAs/microRNAs data. Results: Candidate miRNAs and mRNAs with high accuracy (AUC: 97%/93% and 94%/97%, respectively) could differentiate the WT and RT classes in training and test data. Let-7a-2 and C19orf24 were identified in the WT, while miR-199b and RP1-3E10.2 were detected in the RT by analysis of Association Rule Mining. Conclusion: The application of the machine learning methods could identify mRNA/miRNA patterns to discriminate WT from RT. The identified miRNAs/mRNAs panels could offer novel insights into the underlying molecular mechanisms that are responsible for the initiation and development of these cancers. They may provide further insight into the pathogenesis, prognosis, diagnosis, and molecular-targeted therapy in pediatric renal tumors.
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Affiliation(s)
- Seyed Mahdi Hosseiniyan Khatibi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Simin Sharifi
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz Iran
| | | | - Mohammad Teshnehlab
- Department of Electrical and Computer Engineering, K.N. Toosi University of Technology, Tehran, Iran
| | | | - Saeed Pirmoradi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
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Chu J, Li Y, He M, Zhang H, Yang L, Yang M, Liu J, Cui C, Hong L, Hu X, Zhou L, Li T, Li C, Fan H, Jiang G, Lang T. Zinc finger and SCAN domain containing 1, ZSCAN1, is a novel stemness-related tumor suppressor and transcriptional repressor in breast cancer targeting TAZ. Front Oncol 2023; 13:1041688. [PMID: 36923432 PMCID: PMC10009259 DOI: 10.3389/fonc.2023.1041688] [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: 09/11/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
Introduction Cancer stem cells (CSCs) targeted therapy holds the potential for improving cancer management; identification of stemness-related genes in CSCs is necessary for its development. Methods The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) datasets were used for survival analysis. ZSCAN1 correlated genes was identified by Spearman correlation analysis. Breast cancer stem-like cells (BCSLCs) were isolated by sorting CD44+CD24- cells from suspension cultured breast cancer (BC) spheroids. The sphere-forming capacity and sphere- and tumor-initiating capacities were determined by sphere formation and limiting dilution assays. The relative gene expression was determined by qRT-PCR, western blot. Lentivirus system was used for gene manipulation. Nuclear run-on assay was employed to examine the levels of nascent mRNAs. DNA pull-down and Chromatin immunoprecipitation (ChIP) assays were used for determining the interaction between protein and target DNA fragments. Luciferase reporter assay was used for evaluating the activity of the promoter. Results and discussion ZSCAN1 is aberrantly suppressed in BC, and this suppression indicates a bad prognosis. Ectopic expression of ZSCAN1 inhibited the proliferation, clonogenicity, and tumorigenicity of BC cells. ZSCAN1-overexpressing BCSLCs exhibited weakened stemness properties. Normal human mammary epithelial (HMLE) cells with ZSCAN1 depletion exhibited enhanced stemness properties. Mechanistic studies showed that ZSCAN1 directly binds to -951 ~ -925bp region of WWTR1 (encodes TAZ) promoter, inhibits WWTR1 transcription, thereby inhibiting the stemness of BCSCs. Our work thus revealed ZSCAN1 as a novel stemness-related tumor suppressor and transcriptional repressor in BC.
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Affiliation(s)
- Jian Chu
- Department of Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yunzhe Li
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Misi He
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Hui Zhang
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Lingling Yang
- School of Medicine, Chongqing University, Chongqing, China
| | - Muyao Yang
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Jingshu Liu
- Obstetrics and Gynecology Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chenxi Cui
- School of Medicine, Chongqing University, Chongqing, China
| | - Liquan Hong
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xingchi Hu
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, Jiangsu, China
| | - Lei Zhou
- School of Optometry, Department of Applied Biology and Chemical Technology, Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China.,Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, Hong Kong SAR, China
| | - Tangya Li
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, Jiangsu, China
| | - Changchun Li
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, Jiangsu, China
| | - Huiwen Fan
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, Jiangsu, China
| | - Guoqin Jiang
- Department of Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tingyuan Lang
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China.,Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Drosouni A, Panagopoulou M, Aidinis V, Chatzaki E. Autotaxin in Breast Cancer: Role, Epigenetic Regulation and Clinical Implications. Cancers (Basel) 2022; 14:5437. [PMID: 36358855 PMCID: PMC9658281 DOI: 10.3390/cancers14215437] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 08/02/2023] Open
Abstract
Autotaxin (ATX), the protein product of Ectonucleotide Pyrophosphatase Phosphodiesterase 2 (ENPP2), is a secreted lysophospholipase D (lysoPLD) responsible for the extracellular production of lysophosphatidic acid (LPA). ATX-LPA pathway signaling participates in several normal biological functions, but it has also been connected to cancer progression, metastasis and inflammatory processes. Significant research has established a role in breast cancer and it has been suggested as a therapeutic target and/or a clinically relevant biomarker. Recently, ENPP2 methylation was described, revealing a potential for clinical exploitation in liquid biopsy. The current review aims to gather the latest findings about aberrant signaling through ATX-LPA in breast cancer and discusses the role of ENPP2 expression and epigenetic modification, giving insights with translational value.
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Affiliation(s)
- Andrianna Drosouni
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Maria Panagopoulou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, 71410 Heraklion, Greece
| | - Vassilis Aidinis
- Institute of BioInnovation, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, 71410 Heraklion, Greece
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Londra D, Mastoraki S, Bournakis E, Zavridou M, Thanos A, Rampias T, Lianidou ES. USP44 Promoter Methylation in Plasma Cell-Free DNA in Prostate Cancer. Cancers (Basel) 2021; 13:cancers13184607. [PMID: 34572834 PMCID: PMC8467003 DOI: 10.3390/cancers13184607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Liquid biopsy provides real-time monitoring of tumor evolution and response to therapy through analysis of circulating tumor cells (CTCs) and plasma-circulating tumor DNA (ctDNA). USP44 is a member of family proteins deubiquitinases, and plays an important role in cell growth; however, its accurate role in other cellular networks is under research. In this study, we examined for the first time USP44 promoter methylation in plasma cell-free DNA (cfDNA) of patients with prostate cancer (early stage n = 32, metastatic n = 39) and 10 healthy donors (HD). USP44 promoter methylation was detected in plasma cell-free DNA by a newly developed highly specific and sensitive real-time MSP method. We report for the first time that detection of USP44 promoter methylation in plasma cell free DNA provides significant prognostic information in metastatic prostate cancer. Abstract Liquid biopsy provides real-time monitoring of tumor evolution and response to therapy through analysis of circulating tumor cells (CTCs) and plasma-circulating tumor DNA (ctDNA). USP44 is a critical gene which plays an important role in cell proliferation; however, its accurate role in other cellular networks is under research. USP44 promoter methylation has been so far reported in colorectal neoplasia and metastatic breast cancer. In this study, we examined for the first time USP44 promoter methylation in plasma cell-free DNA (cfDNA) of patients with prostate cancer (early stage n = 32, metastatic n = 39) and 10 healthy donors (HD). USP44 promoter methylation was detected in plasma cell-free DNA by a newly developed highly specific and sensitive real-time MSP method. Our findings indicate that USP44 promoter is methylated in plasma cell-free DNA of metastatic prostate cancer patients and that detection of USP44 promoter methylation is significantly associated with overall survival (OS) (p = 0.008). We report for the first time that detection of USP44 promoter methylation in plasma cell free DNA provides significant prognostic information in metastatic prostate cancer.
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Affiliation(s)
- Dora Londra
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (D.L.); (S.M.); (M.Z.)
| | - Sophia Mastoraki
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (D.L.); (S.M.); (M.Z.)
| | - Evangelos Bournakis
- Oncology Unit, 2nd Department of Surgery, Aretaieio Hospital, Medical School, National and Kapodistrian University of Athens, 11528 Athens, Greece;
| | - Martha Zavridou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (D.L.); (S.M.); (M.Z.)
| | - Anastasios Thanos
- Mutual Health Fund of National Bank of Greece Personnel, 11473 Athens, Greece;
| | - Theodoros Rampias
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Evi S. Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (D.L.); (S.M.); (M.Z.)
- Correspondence: ; Tel.: +30-210-7274-311
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