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Terrazzan A, Vanini R, Ancona P, Bianchi N, Taccioli C, Aguiari G. State-of-the-art in transposable element modulation affected by drugs in malignant prostatic cancer cells. J Cell Biochem 2024; 125:e30557. [PMID: 38501160 DOI: 10.1002/jcb.30557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Over recent years, the investigation of transposable elements (TEs) has granted researchers a deeper comprehension of their characteristics and functions, particularly regarding their significance in the mechanisms contributing to cancer development. This manuscript focuses on prostate carcinoma cell lines and offers a comprehensive review intended to scrutinize the associations and interactions between TEs and genes, as well as their response to treatment using various chemical drugs, emphasizing their involvement in cancer progression. We assembled a compendium of articles retrieved from the PubMed database to construct networks demonstrating correlations with genes and pharmaceuticals. In doing so, we linked the transposition of certain TE types to the expression of specific transcripts directly implicated in carcinogenesis. Additionally, we underline that treatment employing different drugs revealed unique patterns of TE reactivation. Our hypothesis gathers the current understanding and guides research toward evidence-based investigations, emphasizing the association between antiviral drugs, chemotherapy, and the reduced expression of TEs in patients affected by prostate cancer.
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Affiliation(s)
- Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, Ferrara, Italy
| | - Riccardo Vanini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Pietro Ancona
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Gianluca Aguiari
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
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Gao J, Shi W, Wang J, Guan C, Dong Q, Sheng J, Zou X, Xu Z, Ge Y, Yang C, Li J, Bao H, Zhong X, Cui Y. Research progress and applications of epigenetic biomarkers in cancer. Front Pharmacol 2024; 15:1308309. [PMID: 38681199 PMCID: PMC11048075 DOI: 10.3389/fphar.2024.1308309] [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: 10/06/2023] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
Epigenetic changes are heritable changes in gene expression without changes in the nucleotide sequence of genes. Epigenetic changes play an important role in the development of cancer and in the process of malignancy metastasis. Previous studies have shown that abnormal epigenetic changes can be used as biomarkers for disease status and disease prediction. The reversibility and controllability of epigenetic modification changes also provide new strategies for early disease prevention and treatment. In addition, corresponding drug development has also reached the clinical stage. In this paper, we will discuss the recent progress and application status of tumor epigenetic biomarkers from three perspectives: DNA methylation, non-coding RNA, and histone modification, in order to provide new opportunities for additional tumor research and applications.
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Affiliation(s)
- Jianjun Gao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wujiang Shi
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiangang Wang
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Canghai Guan
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qingfu Dong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialin Sheng
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinlei Zou
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhaoqiang Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yifei Ge
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengru Yang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiehan Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haolin Bao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangyu Zhong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Katoh H, Honda T. Roles of Human Endogenous Retroviruses and Endogenous Virus-Like Elements in Cancer Development and Innate Immunity. Biomolecules 2023; 13:1706. [PMID: 38136578 PMCID: PMC10741599 DOI: 10.3390/biom13121706] [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: 10/28/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections in the host genome. Although mutations and silencing mechanisms impair their original role in viral replication, HERVs are believed to play roles in various biological processes. Long interspersed nuclear elements (LINEs) are non-LTR retrotransposons that have a lifecycle resembling that of retroviruses. Although LINE expression is typically silenced in somatic cells, it also contributes to various biological processes. The aberrant expression of HERVs and LINEs is closely associated with the development of cancer and/or immunological diseases, suggesting that they are integrated into various pathways related to the diseases. HERVs/LINEs control gene expression depending on the context as promoter/enhancer elements. Some RNAs and proteins derived from HERVs/LINEs have oncogenic potential, whereas others stimulate innate immunity. Non-retroviral endogenous viral elements (nrEVEs) are a novel type of virus-like element in the genome. nrEVEs may also be involved in host immunity. This article provides a current understanding of how these elements impact cellular physiology in cancer development and innate immunity, and provides perspectives for future studies.
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Affiliation(s)
- Hirokazu Katoh
- Department of Virology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Tomoyuki Honda
- Department of Virology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
- Department of Virology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
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Erenpreisa J, Giuliani A, Cragg MS. Special Issue "Advances in Genome Regulation in Cancer". Int J Mol Sci 2023; 24:14567. [PMID: 37834014 PMCID: PMC10572122 DOI: 10.3390/ijms241914567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Cancer is globally increasing [...].
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Affiliation(s)
- Jekaterina Erenpreisa
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Mark Steven Cragg
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
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Fontana A. Unravelling the nexus: Towards a unified model of development, ageing, and cancer. Biosystems 2023; 231:104966. [PMID: 37419274 DOI: 10.1016/j.biosystems.2023.104966] [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: 05/23/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023]
Abstract
This work presents a comprehensive model that aims to unify our understanding of embryogenesis, ageing, and cancer. While there have been previous attempts to construct models separately for two of these phenomena (such as embryogenesis and cancer, ageing and cancer), models encompassing all three are relatively scarce, if not entirely absent. The model's most notable feature is the presence of driver cells throughout the body, which may correspond to Spemann's organisers. These driver cells play a vital role in propelling development as they dynamically emerge from non-driver cells and inhabit specialised niches. Remarkably, this continuous process persists throughout an organism's entire lifespan, signifying that development unfolds from conception to the end of life. Driver cells orchestrate change events through the induction of distinctive epigenetic patterns of gene activation. Events occurring at young age drive development, are subject to high evolutionary pressure and hence carefully optimised. Events occurring after reproduction age are subject to decreasing evolutionary pressure: for this reason, such events are "pseudorandom" -deterministic but erratic. Some of these events lead to age-related benign conditions, such as gray hair. Some lead to serious age-related diseases, such as diabetes and Alzheimer's disease. Furthermore, some of these events might perturb epigenetically key pathways involved in driver activation and formation, leading to cancer. In our model, this driver cell-based mechanism represents the backbone of multicellular biology: understanding and correcting its functioning may give the chance to solve a wide range of conditions at once.
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Erenpreisa J, Vainshelbaum NM, Lazovska M, Karklins R, Salmina K, Zayakin P, Rumnieks F, Inashkina I, Pjanova D, Erenpreiss J. The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer. Int J Mol Sci 2023; 24:11660. [PMID: 37511419 PMCID: PMC10380301 DOI: 10.3390/ijms241411660] [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: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.
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Affiliation(s)
| | | | - Marija Lazovska
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Roberts Karklins
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Dace Pjanova
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Juris Erenpreiss
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
- Clinic iVF-Riga, Zala 1, LV-1010 Riga, Latvia
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Sirbu O, Helmy M, Giuliani A, Selvarajoo K. Globally invariant behavior of oncogenes and random genes at population but not at single cell level. NPJ Syst Biol Appl 2023; 9:28. [PMID: 37355674 DOI: 10.1038/s41540-023-00290-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/15/2023] [Indexed: 06/26/2023] Open
Abstract
Cancer is widely considered a genetic disease. Notably, recent works have highlighted that every human gene may possibly be associated with cancer. Thus, the distinction between genes that drive oncogenesis and those that are associated to the disease, but do not play a role, requires attention. Here we investigated single cells and bulk (cell-population) datasets of several cancer transcriptomes and proteomes in relation to their healthy counterparts. When analyzed by machine learning and statistical approaches in bulk datasets, both general and cancer-specific oncogenes, as defined by the Cancer Genes Census, show invariant behavior to randomly selected gene sets of the same size for all cancers. However, when protein-protein interaction analyses were performed, the oncogenes-derived networks show higher connectivity than those relative to random genes. Moreover, at single-cell scale, we observe variant behavior in a subset of oncogenes for each considered cancer type. Moving forward, we concur that the role of oncogenes needs to be further scrutinized by adopting protein causality and higher-resolution single-cell analyses.
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Affiliation(s)
- Olga Sirbu
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Republic of Singapore
| | - Mohamed Helmy
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Republic of Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Roma, Italy
| | - Kumar Selvarajoo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Republic of Singapore.
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore (NUS), Singapore, 117456, Republic of Singapore.
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore, 639798, Republic of Singapore.
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