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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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2
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Fakhri S, Moradi SZ, Abbaszadeh F, Faraji F, Amirian R, Sinha D, McMahon EG, Bishayee A. Targeting the key players of phenotypic plasticity in cancer cells by phytochemicals. Cancer Metastasis Rev 2024; 43:261-292. [PMID: 38169011 DOI: 10.1007/s10555-023-10161-8] [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: 07/13/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Plasticity of phenotypic traits refers to an organism's ability to change in response to environmental stimuli. As a result, the response may alter an organism's physiological state, morphology, behavior, and phenotype. Phenotypic plasticity in cancer cells describes the considerable ability of cancer cells to transform phenotypes through non-genetic molecular signaling activities that promote therapy evasion and tumor metastasis via amplifying cancer heterogeneity. As a result of metastable phenotypic state transitions, cancer cells can tolerate chemotherapy or develop transient adaptive resistance. Therefore, new findings have paved the road in identifying factors and agents that inhibit or suppress phenotypic plasticity. It has also investigated novel multitargeted agents that may promise new effective strategies in cancer treatment. Despite the efficiency of conventional chemotherapeutic agents, drug toxicity, development of resistance, and high-cost limit their use in cancer therapy. Recent research has shown that small molecules derived from natural sources are capable of suppressing cancer by focusing on the plasticity of phenotypic responses. This systematic, comprehensive, and critical review analyzes the current state of knowledge regarding the ability of phytocompounds to target phenotypic plasticity at both preclinical and clinical levels. Current challenges/pitfalls, limitations, and future perspectives are also discussed.
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Affiliation(s)
- Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, 6734667149, Iran
| | - Seyed Zachariah Moradi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, 6734667149, Iran
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, 6734667149, Iran
| | - Fatemeh Abbaszadeh
- Department of Neuroscience, Faculty of Advanced Technologies in Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
- Neurobiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farahnaz Faraji
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, 6517838678, Iran
| | - Roshanak Amirian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, 6734667149, Iran
| | - Dona Sinha
- Department of Receptor Biology and Tumor Metastasis, Chittaranjan National Cancer Institute, Kolkata, 700 026, West Bengal, India
| | - Emily G McMahon
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL, 34211, USA
| | - Anupam Bishayee
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL, 34211, USA.
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Shi ZD, Pang K, Wu ZX, Dong Y, Hao L, Qin JX, Wang W, Chen ZS, Han CH. Tumor cell plasticity in targeted therapy-induced resistance: mechanisms and new strategies. Signal Transduct Target Ther 2023; 8:113. [PMID: 36906600 PMCID: PMC10008648 DOI: 10.1038/s41392-023-01383-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/07/2022] [Accepted: 02/20/2023] [Indexed: 03/13/2023] Open
Abstract
Despite the success of targeted therapies in cancer treatment, therapy-induced resistance remains a major obstacle to a complete cure. Tumor cells evade treatments and relapse via phenotypic switching driven by intrinsic or induced cell plasticity. Several reversible mechanisms have been proposed to circumvent tumor cell plasticity, including epigenetic modifications, regulation of transcription factors, activation or suppression of key signaling pathways, as well as modification of the tumor environment. Epithelial-to-mesenchymal transition, tumor cell and cancer stem cell formation also serve as roads towards tumor cell plasticity. Corresponding treatment strategies have recently been developed that either target plasticity-related mechanisms or employ combination treatments. In this review, we delineate the formation of tumor cell plasticity and its manipulation of tumor evasion from targeted therapy. We discuss the non-genetic mechanisms of targeted drug-induced tumor cell plasticity in various types of tumors and provide insights into the contribution of tumor cell plasticity to acquired drug resistance. New therapeutic strategies such as inhibition or reversal of tumor cell plasticity are also presented. We also discuss the multitude of clinical trials that are ongoing worldwide with the intention of improving clinical outcomes. These advances provide a direction for developing novel therapeutic strategies and combination therapy regimens that target tumor cell plasticity.
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Affiliation(s)
- Zhen-Duo Shi
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China.,School of Life Sciences, Jiangsu Normal University, Jiangsu, China.,Department of Urology, Heilongjiang Provincial Hospital, Heilongjiang, China
| | - Kun Pang
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Yang Dong
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Lin Hao
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Jia-Xin Qin
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Wei Wang
- Department of Medical College, Southeast University, Nanjing, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA.
| | - Cong-Hui Han
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Jiangsu, China. .,Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China. .,School of Life Sciences, Jiangsu Normal University, Jiangsu, China. .,Department of Urology, Heilongjiang Provincial Hospital, Heilongjiang, China.
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4
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Hussmann D, Starnawska A, Kristensen L, Daugaard I, Cédile O, Nguyen VQ, Kjeldsen TE, Hansen CS, Bybjerg-Grauholm J, Kristensen T, Larsen TS, Møller MB, Nyvold CG, Hansen LL, Wojdacz TK. Methylation microarray-based detection of clinical copy-number aberrations in CLL benchmarked to standard FISH analysis. Genomics 2022; 114:110510. [PMID: 36272495 DOI: 10.1016/j.ygeno.2022.110510] [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: 05/16/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 01/15/2023]
Abstract
Copy-number aberrations (CNAs) are assessed using FISH analysis in diagnostics of chronic lymphocytic leukemia (CLL), but CNAs can also be extrapolated from Illumina BeadChips developed for genome-wide methylation microarray screening. Increasing numbers of microarray data-sets are available from diagnostic samples, making it useful to assess the potential in CNA diagnostics. We benchmarked the limitations of CNA testing from two Illumina BeadChips (EPIC and 450k) and using two common packages for analysis (conumee and ChAMP) to FISH-based assessment of 11q, 13q, and 17p deletions in 202 CLL samples. Overall, the two packages predicted CNAs with similar accuracy regardless of the microarray type, but lower than FISH-based assessment. We showed that the bioinformatics analysis needs to be adjusted to the specific CNA, as no general settings were identified. Altogether, we were able to predict CNAs using methylation microarray data, however, with limited accuracy, making FISH-based assessment of deletions the superior diagnostic choice.
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Affiliation(s)
- Dianna Hussmann
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Centre for Genomics and Personalized Medicine, CGPM, Aarhus University, Aarhus, Denmark
| | - Louise Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Iben Daugaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Oriane Cédile
- Haematology-Pathology Research Laboratory, Research Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Vivi Quoc Nguyen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Tina E Kjeldsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Christine Søholm Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark; Department of Psychiatry, Mount Sinai, New York, NY, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark; Department of Clinical Development, Odense University Hospital, Odense, Denmark
| | | | - Michael Boe Møller
- Department of Pathology, Odense University Hospital, Odense, Denmark; Haematology-Pathology Research Laboratory, Research Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Charlotte Guldborg Nyvold
- Haematology-Pathology Research Laboratory, Research Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | | | - Tomasz K Wojdacz
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark; Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Szczecin, Poland.
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Stupnikov A, Sizykh A, Budkina A, Favorov A, Afsari B, Wheelan S, Marchionni L, Medvedeva Y. Hobotnica: exploring molecular signature quality. F1000Res 2022; 10:1260. [PMID: 36204675 PMCID: PMC9513410 DOI: 10.12688/f1000research.74846.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
A Molecular Features Set (MFS), is a result of a vast diversity of bioinformatics pipelines. The lack of a “gold standard” for most experimental data modalities makes it difficult to provide valid estimation for a particular MFS's quality. Yet, this goal can partially be achieved by analyzing inner-sample Distance Matrices (DM) and their power to distinguish between phenotypes. The quality of a DM can be assessed by summarizing its power to quantify the differences of inner-phenotype and outer-phenotype distances. This estimation of the DM quality can be construed as a measure of the MFS's quality. Here we propose Hobotnica, an approach to estimate MFSs quality by their ability to stratify data, and assign them significance scores, that allow for collating various signatures and comparing their quality for contrasting groups.
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Affiliation(s)
- Alexey Stupnikov
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
- National Medical Research Center for Endocrinology, Moscow, Russian Federation
| | - Alexey Sizykh
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Anna Budkina
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Alexander Favorov
- Johns Hopkins University, Baltimore, USA
- Vavilov Institute for General Genetics RAS, Moscow, Russian Federation
| | | | | | | | - Yulia Medvedeva
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
- National Medical Research Center for Endocrinology, Moscow, Russian Federation
- Center of Biotechnology RAS, Moscow, Russian Federation
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6
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Marney CB, Anderson ES, Adnan M, Peng KL, Hu Y, Weinhold N, Schmitt AM. p53-intact cancers escape tumor suppression through loss of long noncoding RNA Dino. Cell Rep 2021; 35:109329. [PMID: 34192538 PMCID: PMC8287872 DOI: 10.1016/j.celrep.2021.109329] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/15/2021] [Accepted: 06/09/2021] [Indexed: 02/08/2023] Open
Abstract
Many long noncoding RNA (lncRNA) genes exist near cancer-associated loci, yet evidence connecting lncRNA functions to recurrent genetic alterations in cancer are lacking. Here, we report that DINO, the lncRNA transcribed from the cancer-associated DINO/CDKN1A locus, suppresses tumor formation independent of p21, the protein encoded at the locus. Loss of one or two alleles of Dino impairs p53 signaling and apoptosis, resulting in a haplo-insufficient tumor suppressor phenotype in genetically defined mouse models of tumorigenesis. A discrete region of the DINO/CDKN1A locus is recurrently hypermethylated in human cancers, silencing DINO but not CDKN1A, the gene encoding p21. Hypermethylation silences DINO, impairs p53 signaling pathway in trans, and is mutually exclusive with TP53 alterations, indicating that DINO and TP53 comprise a common tumor suppressor module. Therefore, DINO encodes a lncRNA essential for tumor suppression that is recurrently silenced in human cancers as a mechanism to escape p53-dependent tumor suppression.
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Affiliation(s)
- Christina B Marney
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Erik S Anderson
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Mutayyaba Adnan
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Kai-Lin Peng
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Ya Hu
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Nils Weinhold
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA
| | - Adam M Schmitt
- Division of Translational Oncology, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10128, USA.
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