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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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Talley MJ, Longworth MS. Retrotransposons in embryogenesis and neurodevelopment. Biochem Soc Trans 2024; 52:1159-1171. [PMID: 38716891 PMCID: PMC11346457 DOI: 10.1042/bst20230757] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024]
Abstract
Retrotransposable elements (RTEs) are genetic elements that can replicate and insert new copies into different genomic locations. RTEs have long been identified as 'parasitic genes', as their mobilization can cause mutations, DNA damage, and inflammation. Interestingly, high levels of retrotransposon activation are observed in early embryogenesis and neurodevelopment, suggesting that RTEs may possess functional roles during these stages of development. Recent studies demonstrate that RTEs can function as transcriptional regulatory elements through mechanisms such as chromatin organization and noncoding RNAs. It is clear, however, that RTE expression and activity must be restrained at some level during development, since overactivation of RTEs during neurodevelopment is associated with several developmental disorders. Further investigation is needed to understand the importance of RTE expression and activity during neurodevelopment and the balance between RTE-regulated development and RTE-mediated pathogenesis.
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Affiliation(s)
- Mary Jo Talley
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
| | - Michelle S. Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, U.S.A
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Arriagada G, Quezada J, Merino-Veliz N, Avilés F, Tapia-Cammas D, Gomez J, Curotto D, Valdes JA, Oyarzún PA, Gallardo-Escárate C, Metzger MJ, Alvarez M. Identification and expression analysis of two steamer-like retrotransposons in the Chilean blue mussel (Mytilus chilensis). Biol Res 2024; 57:17. [PMID: 38664786 PMCID: PMC11046912 DOI: 10.1186/s40659-024-00498-x] [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: 10/26/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Disseminated neoplasia (DN) is a proliferative cell disorder of the circulatory system of bivalve mollusks. The disease is transmitted between individuals and can also be induced by external chemical agents such as bromodeoxyuridine. In Mya arenaria, we have cloned and characterized an LTR-retrotransposon named Steamer. Steamer mRNA levels and gene copy number correlates with DN and can be used as a marker of the disease. So far, the only mollusk where a retrotransposon expression relates to DN is Mya arenaria. On the other hand, it has been reported that the Chilean blue mussel Mytilus chilensis can also suffers DN. Our aim was to identify retrotransposons in Mytilus chilensis and to study their expression levels in the context of disseminated neoplasia. RESULTS Here we show that 7.1% of individuals collected in August 2018, from two farming areas, presents morphological characteristics described in DN. Using Steamer sequence to interrogate the transcriptome of M. chilensis we found two putative retrotransposons, named Steamer-like elements (MchSLEs). MchSLEs are present in the genome of M. chilensis and MchSLE1 is indeed an LTR-retrotransposon. Neither expression, nor copy number of the reported MchSLEs correlate with DN status but both are expressed at different levels among individual animals. We also report that in cultured M. chilensis haemocytes MchSLEs1 expression can be induced by bromodeoxyuridine. CONCLUSIONS We conclude that SLEs present in Mytilus chilensis are differentially expressed among individuals and do not correlate with disseminated neoplasia. Treatment of haemocytes with a stressor like bromodeoxyuridine induces expression of MchSLE1 suggesting that in Mytilus chilensis environmental stressors can induce activation of LTR-retrotransposon.
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Affiliation(s)
- Gloria Arriagada
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Johan Quezada
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Nicolas Merino-Veliz
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Fernando Avilés
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Diana Tapia-Cammas
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Gomez
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Daniela Curotto
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan A Valdes
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile
| | - Pablo A Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay, Chile
| | | | | | - Marco Alvarez
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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Crawford BI, Talley MJ, Russman J, Riddle J, Torres S, Williams T, Longworth MS. Condensin-mediated restriction of retrotransposable elements facilitates brain development in Drosophila melanogaster. Nat Commun 2024; 15:2716. [PMID: 38548759 PMCID: PMC10978865 DOI: 10.1038/s41467-024-47042-9] [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: 12/22/2022] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Neural stem and progenitor cell (NSPC) maintenance is essential for ensuring that organisms are born with proper brain volumes and head sizes. Microcephaly is a disorder in which babies are born with significantly smaller head sizes and cortical volumes. Mutations in subunits of the DNA organizing complex condensin have been identified in microcephaly patients. However, the molecular mechanisms by which condensin insufficiency causes microcephaly remain elusive. We previously identified conserved roles for condensins in repression of retrotransposable elements (RTEs). Here, we show that condensin subunit knockdown in NSPCs of the Drosophila larval central brain increases RTE expression and mobility which causes cell death, and significantly decreases adult head sizes and brain volumes. These findings suggest that unrestricted RTE expression and activity may lead to improper brain development in condensin insufficient organisms, and lay the foundation for future exploration of causative roles for RTEs in other microcephaly models.
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Affiliation(s)
- Bert I Crawford
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Mary Jo Talley
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Joshua Russman
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - James Riddle
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Sabrina Torres
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Troy Williams
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44195, USA.
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Annapragada AV, Niknafs N, White JR, Bruhm DC, Cherry C, Medina JE, Adleff V, Hruban C, Mathios D, Foda ZH, Phallen J, Scharpf RB, Velculescu VE. Genome-wide repeat landscapes in cancer and cell-free DNA. Sci Transl Med 2024; 16:eadj9283. [PMID: 38478628 PMCID: PMC11323656 DOI: 10.1126/scitranslmed.adj9283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but characterizing these has been challenging using standard sequencing approaches. We developed a de novo kmer finding approach, called ARTEMIS (Analysis of RepeaT EleMents in dISease), to identify repeat elements from whole-genome sequencing. Using this method, we analyzed 1.2 billion kmers in 2837 tissue and plasma samples from 1975 patients, including those with lung, breast, colorectal, ovarian, liver, gastric, head and neck, bladder, cervical, thyroid, or prostate cancer. We identified tumor-specific changes in these patients in 1280 repeat element types from the LINE, SINE, LTR, transposable element, and human satellite families. These included changes to known repeats and 820 elements that were not previously known to be altered in human cancer. Repeat elements were enriched in regions of driver genes, and their representation was altered by structural changes and epigenetic states. Machine learning analyses of genome-wide repeat landscapes and fragmentation profiles in cfDNA detected patients with early-stage lung or liver cancer in cross-validated and externally validated cohorts. In addition, these repeat landscapes could be used to noninvasively identify the tissue of origin of tumors. These analyses reveal widespread changes in repeat landscapes of human cancers and provide an approach for their detection and characterization that could benefit early detection and disease monitoring of patients with cancer.
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Affiliation(s)
- Akshaya V. Annapragada
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - James R. White
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel C. Bruhm
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christopher Cherry
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jamie E. Medina
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vilmos Adleff
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Carolyn Hruban
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dimitrios Mathios
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zachariah H. Foda
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jillian Phallen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert B. Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Victor E. Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Mathavarajah S, Dellaire G. LINE-1: an emerging initiator of cGAS-STING signalling and inflammation that is dysregulated in disease. Biochem Cell Biol 2024; 102:38-46. [PMID: 37643478 DOI: 10.1139/bcb-2023-0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
The cGAS-STING (cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING)) axis integrates DNA damage and cellular stress with type I interferon (IFN) signalling to facilitate transcriptional changes underlying inflammatory stress responses. The cGAS-STING pathway responds to cytosolic DNA in the form of double-stranded DNA, micronuclei, and long interspersed nuclear element 1 (L1) retroelements. L1 retroelements are a class of self-propagating non-long terminal repeat transposons that have remained highly active in mammalian genomes. L1 retroelements are emerging as important inducers of cGAS-STING and IFN signalling, which are often dysregulated in several diseases, including cancer. A key repressor of cGAS-STING and L1 activity is the exonuclease three prime repair exonuclease 1 (TREX1), and loss of TREX1 promotes the accumulation of L1. In addition, L1 dysregulation is a common theme among diseases with chronic induction of type I IFN signalling through cGAS-STING, such as Aicardi-Goutières syndrome, Fanconi anemia, and dermatomyositis. Although TREX1 is highly conserved in tetrapod species, other suppressor proteins exist that inhibit L1 retrotransposition. These suppressor genes when mutated are often associated with diseases characterized by unchecked inflammation that is associated with high cGAS-STING activity and elevated levels of L1 expression. In this review, we discuss these interconnected pathways of L1 suppression and their role in the regulation of cGAS-STING and inflammation in disease.
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Affiliation(s)
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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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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Altered expression of DNA methyltransferases and methylation status of the TLR4 and TNF-α promoters in COVID-19. Arch Virol 2023; 168:95. [PMID: 36840831 PMCID: PMC9959945 DOI: 10.1007/s00705-023-05722-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/10/2023] [Indexed: 02/26/2023]
Abstract
Epigenetic modifications play a significant role in the host's immune response to viral infection. Two epigenetic events, DNA methylation and histone acetylation, are crucial for modifying the chromatin architecture and the location of regulatory elements such as promoters and enhancers. In this case-control study, we evaluated the expression of genes involved in epigenetic machinery (DNMT1, DNMT3A, DNMT3B, HDAC2, and HDAC3) and the degree of methylation of promoters of immune response genes (IFITM1/2/3, TLR3/4, TNF-α, NF-κB, and MYD88) as well as global methylation (LINE-1 and global 5-mC) in blood samples from 120 COVID-19 patients (30 mild, 30 moderate, 30 severe, and 30 critical) and 30 healthy subjects without COVID-19. In contrast to previous reports, DNMT3A and DNMT3B expression was found to be significantly downregulated in COVID-19 cases, whereas DNMT1, HDAC2, and HDAC3 expression did not change. DNMT1 and DNMT3A were negatively correlated with COVID-19 severity. Critically ill patients had lower HDAC3 expression levels. TLR4 and TNF-α had increased promoter methylation, whereas IFITM1/2/3, TLR3, NF-κB, MYD88, and LINE-1 did not differ between cases and controls. Methylation of the TNF-α promoter increased as disease severity increased. Significantly less methylation of the TLR3 promoter was observed in patients with a positive outcome (recovery). We also found a correlation between the expression of DNMT3B and the methylation level of the TLR4 promoter. In milder cases, the global 5-mC levels were lower than that in more severe cases. Our findings suggest the exclusion of DNMTs inhibitors previously recommended for COVID-19 treatment and the need for additional research in this area.
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Nishikawa S, Iwakuma T. Drugs Targeting p53 Mutations with FDA Approval and in Clinical Trials. Cancers (Basel) 2023; 15:429. [PMID: 36672377 PMCID: PMC9856662 DOI: 10.3390/cancers15020429] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/01/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Mutations in the tumor suppressor p53 (p53) promote cancer progression. This is mainly due to loss of function (LOS) as a tumor suppressor, dominant-negative (DN) activities of missense mutant p53 (mutp53) over wild-type p53 (wtp53), and wtp53-independent oncogenic activities of missense mutp53 by interacting with other tumor suppressors or oncogenes (gain of function: GOF). Since p53 mutations occur in ~50% of human cancers and rarely occur in normal tissues, p53 mutations are cancer-specific and ideal therapeutic targets. Approaches to target p53 mutations include (1) restoration or stabilization of wtp53 conformation from missense mutp53, (2) rescue of p53 nonsense mutations, (3) depletion or degradation of mutp53 proteins, and (4) induction of p53 synthetic lethality or targeting of vulnerabilities imposed by p53 mutations (enhanced YAP/TAZ activities) or deletions (hyperactivated retrotransposons). This review article focuses on clinically available FDA-approved drugs and drugs in clinical trials that target p53 mutations and summarizes their mechanisms of action and activities to suppress cancer progression.
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Affiliation(s)
- Shigeto Nishikawa
- Department of Pediatrics, Division of Hematology & Oncology, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
| | - Tomoo Iwakuma
- Department of Pediatrics, Division of Hematology & Oncology, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Lou C, Qiang R, Wu H, Zhang L, Li W, Jia T, Liu X. Expression of LINE-1 retrotransposon in early human spontaneous abortion tissues. Medicine (Baltimore) 2022; 101:e31964. [PMID: 36626466 PMCID: PMC9750690 DOI: 10.1097/md.0000000000031964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The aim of this study is to investigate a new mechanism that may affect spontaneous abortions (SA): Can long interspersed nuclear element-1 (LINE-1) insertions in embryo cells lead to early SA? METHODS The method involves prospective study on new mechanism of human early SA. Twenty SA tissues and 10 induced abortion (IA) tissues were utilized for this experiment. Western Blot, Immunohistochemistry (IHC), and reverse transcription-polymerase chain reaction were used to analyze different LINE-1 proteins and mRNA expression between early SA tissues and early IA tissues. SPSS software version 21.0 was used for statistical analysis. RESULTS Western Blot demonstrated that the LINE-1 protein expression in SA tissues (Mean: 60.2%) is higher than in IA tissues (Mean: 30.3%) in 91% of the compared samples. reverse transcription-polymerase chain reaction showed that LINE-1 mRNA expression in SA tissues (Mean: 64.2%) is higher than in IA tissues (Mean: 29.2%) in 6 primer pairs in 89% of the compared samples. IHC showed that the LINE-1 protein expression in SA tissues (Mean: 59.2%) is higher than in IA tissues (Mean: 28.8%) in 83% of the compared samples. CONCLUSIONS Expression of LINE-1 in early SA tissues is higher than in IA tissues, LINE-1 may lead to early SA and LINE-1 plays a role in early SA, this shows that a new mechanism may be involved in SA.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Hanzhi Wu
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Liping Zhang
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Wei Li
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Ting Jia
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Xing Liu
- Department of Obstetrics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
- * Correspondence: Xing Liu, Department of Obstetrics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province, China (e-mail: )
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Inflammatory response to retrotransposons drives tumor drug resistance that can be prevented by reverse transcriptase inhibitors. Proc Natl Acad Sci U S A 2022; 119:e2213146119. [PMID: 36449545 PMCID: PMC9894111 DOI: 10.1073/pnas.2213146119] [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] [Indexed: 12/05/2022] Open
Abstract
Activation of endogenous retrotransposons frequently occurs in cancer cells and contributes to tumor genomic instability. To test whether inhibition of retrotranspositions has an anticancer effect, we used treatment with the nucleoside reverse transcriptase inhibitor (NRTI) stavudine (STV) in mouse cancer models, MMTV-HER2/Neu and Th-MYCN, that spontaneously develop breast cancer and neuroblastoma, respectively. In both cases, STV in drinking water did not affect tumor incidence nor demonstrate direct antitumor effects. However, STV dramatically extended progression-free survival in both models following an initial complete response to chemotherapy. To approach the mechanism underlying this phenomenon, we analyzed the effect of NRTI on the selection of treatment-resistant variants in tumor cells in culture. Cultivation of mouse breast carcinoma 4T1 in the presence of STV dramatically reduced the frequency of cells capable of surviving treatment with anticancer drugs. Global transcriptome analysis demonstrated that the acquisition of drug resistance by 4T1 cells was accompanied by an increase in the constitutive activity of interferon type I and NF-κB pathways and an elevated expression of LINE-1 elements, which are known to induce inflammatory responses via their products of reverse transcription. Treatment with NRTI reduced NF-κB activity and reverted drug resistance. Furthermore, the inducible expression of LINE-1 stimulated inflammatory response and increased the frequency of drug-resistant variants in a tumor cell population. These results indicate a mechanism by which retrotransposon desilencing can stimulate tumor cell survival during treatment and suggest reverse transcriptase inhibition as a potential therapeutic approach for targeting the development of drug-resistant cancers.
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Issah I, Arko-Mensah J, Rozek LS, Rentschler K, Agyekum TP, Dwumoh D, Batterman S, Robins TG, Fobil JN. Association between global DNA methylation (LINE-1) and occupational particulate matter exposure among informal electronic-waste recyclers in Ghana. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:2406-2424. [PMID: 34404291 DOI: 10.1080/09603123.2021.1969007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
This study examined the associations between PM (2.5 and 10) and global DNA methylation among 100 e-waste workers and 51 non-e-waste workers serving as controls. Long interspersed nucleotide repetitive elements-1 (LINE-1) was measured by pyrosequencing. Personal PM2.5 and PM10 were measured over a 4-hour work-shift using real-time particulate monitors incorporated into a backpack . Linear regression models were used to assess the association between PM and LINE-1 DNA methylation. The concentrations of PM2.5 and PM10 were significantly higher among the e-waste workers than the controls (77.32 vs 34.88, p < 0.001 and 210.21 vs 121.92, p < 0.001, respectively). PM2.5 exposure was associated with increased LINE-1 CpG2 DNA methylation (β = 0.003; 95% CI; 0.001, 0.006; p = 0.022) but not with the average of all 4 CpG sites of LINE-1. In summary, high levels of PM2.5 exposure was associated with increased levels of global DNA methylation in a site-specific manner.
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Affiliation(s)
- Ibrahim Issah
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
| | - John Arko-Mensah
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Katie Rentschler
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Thomas P Agyekum
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
| | - Duah Dwumoh
- Department of Biostatistics, University of Ghana School of Public Health, Legon, Ghana
| | - Stuart Batterman
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Thomas G Robins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Julius N Fobil
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
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13
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Kosushkin SA, Ustyantsev IG, Borodulina OR, Vassetzky NS, Kramerov DA. Tail Wags Dog’s SINE: Retropositional Mechanisms of Can SINE Depend on Its A-Tail Structure. BIOLOGY 2022; 11:biology11101403. [PMID: 36290307 PMCID: PMC9599045 DOI: 10.3390/biology11101403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary The genomes of higher organisms including humans are invaded by millions of repetitive elements (transposons), which can sometimes be deleterious or beneficial for hosts. Many aspects of the mechanisms underlying the expansion of transposons in the genomes remain unclear. Short retrotransposons (SINEs) are one of the most abundant classes of genomic repeats. Their amplification relies on two major processes: transcription and reverse transcription. Here, short retrotransposons of dogs and other canids called Can SINE were analyzed. Their amplification was extraordinarily active in the wolf and, particularly, dog breeds relative to other canids. We also studied a variation of their transcription mechanism involving the polyadenylation of transcripts. An analysis of specific signals involved in this process allowed us to conclude that Can SINEs could alternate amplification with and without polyadenylation in their evolution. Understanding the mechanisms of transposon replication can shed light on the mechanisms of genome function. Abstract SINEs, non-autonomous short retrotransposons, are widespread in mammalian genomes. Their transcripts are generated by RNA polymerase III (pol III). Transcripts of certain SINEs can be polyadenylated, which requires polyadenylation and pol III termination signals in their sequences. Our sequence analysis divided Can SINEs in canids into four subfamilies, older a1 and a2 and younger b1 and b2. Can_b2 and to a lesser extent Can_b1 remained retrotranspositionally active, while the amplification of Can_a1 and Can_a2 ceased long ago. An extraordinarily high Can amplification was revealed in different dog breeds. Functional polyadenylation signals were analyzed in Can subfamilies, particularly in fractions of recently amplified, i.e., active copies. The transcription of various Can constructs transfected into HeLa cells proposed AATAAA and (TC)n as functional polyadenylation signals. Our analysis indicates that older Can subfamilies (a1, a2, and b1) with an active transcription terminator were amplified by the T+ mechanism (with polyadenylation of pol III transcripts). In the currently active Can_b2 subfamily, the amplification mechanisms with (T+) and without the polyadenylation of pol III transcripts (T−) irregularly alternate. The active transcription terminator tends to shorten, which renders it nonfunctional and favors a switch to the T− retrotransposition. The activity of a truncated terminator is occasionally restored by its elongation, which rehabilitates the T+ retrotransposition for a particular SINE copy.
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14
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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15
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Berrino E, Miglio U, Bellomo SE, Debernardi C, Bragoni A, Petrelli A, Cascardi E, Giordano S, Montemurro F, Marchiò C, Venesio T, Sapino A. The Tumor-Specific Expression of L1 Retrotransposons Independently Correlates with Time to Relapse in Hormone-Negative Breast Cancer Patients. Cells 2022; 11:cells11121944. [PMID: 35741073 PMCID: PMC9221920 DOI: 10.3390/cells11121944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Long-Interspersed Nuclear Element (L1) retrotransposons are silenced in healthy tissues but unrepressed in cancer. Even if L1 reactivation has been associated with reduced overall survival in breast cancer (BC) patients, a comprehensive correlation with clinicopathological features is still missing. METHODS Using quantitative, reverse-transcription PCR, we assessed L1 mRNA expression in 12 BC cells, 210 BC patients and in 47 normal mammary tissues. L1 expression was then correlated with molecular and clinicopathological data. RESULTS We identified a tumor-exclusive expression of L1s, absent in normal mammary cells and tissues. A positive correlation between L1 expression and tumor dedifferentiation, lymph-node involvement and increased immune infiltration was detected. Molecular subtyping highlighted an enrichment of L1s in basal-like cells and cancers. By exploring disease-free survival, we identified L1 overexpression as an independent biomarker for patients with a high risk of recurrence in hormone-receptor-negative BCs. CONCLUSIONS Overall, L1 reactivation identified BCs with aggressive features and patients with a worse clinical fate.
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Affiliation(s)
- Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Umberto Miglio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Oncology, University of Turin, 10124 Turin, Italy
| | - Carla Debernardi
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Alberto Bragoni
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Annalisa Petrelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Eliano Cascardi
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Silvia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Oncology, University of Turin, 10124 Turin, Italy
| | - Filippo Montemurro
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Tiziana Venesio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Correspondence: ; Tel.: +39-011-9933547; Fax: +39-011-9933480
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
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16
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Switzer CH, Cho HJ, Eykyn TR, Lavender P, Eaton P. NOS2 and S-nitrosothiol signaling induces DNA hypomethylation and LINE-1 retrotransposon expression. Proc Natl Acad Sci U S A 2022; 119:e2200022119. [PMID: 35584114 PMCID: PMC9173756 DOI: 10.1073/pnas.2200022119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022] Open
Abstract
Inducible nitric oxide synthase (NOS2) produces high local concentrations of nitric oxide (NO), and its expression is associated with inflammation, cellular stress signals, and cellular transformation. Additionally, NOS2 expression results in aggressive cancer cell phenotypes and is correlated with poor outcomes in patients with breast cancer. DNA hypomethylation, especially of noncoding repeat elements, is an early event in carcinogenesis and is a common feature of cancer cells. In addition to altered gene expression, DNA hypomethylation results in genomic instability via retrotransposon activation. Here, we show that NOS2 expression and associated NO signaling results in substantial DNA hypomethylation in human cell lines by inducing the degradation of DNA (cytosine-5)–methyltransferase 1 (DNMT1) protein. Similarly, NOS2 expression levels were correlated with decreased DNA methylation in human breast tumors. NOS2 expression and NO signaling also resulted in long interspersed noncoding element 1 (LINE-1) retrotransposon hypomethylation, expression, and DNA damage. DNMT1 degradation was mediated by an NO/p38-MAPK/lysine acetyltransferase 5–dependent mechanism. Furthermore, we show that this mechanism is required for NO-mediated epithelial transformation. Therefore, we conclude that NOS2 and NO signaling results in DNA damage and malignant cellular transformation via an epigenetic mechanism.
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Affiliation(s)
- Christopher H. Switzer
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Hyun-Ju Cho
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Thomas R. Eykyn
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, SE1 7EH, United Kingdom
| | - Paul Lavender
- AsthmaUK Centre in Allergic Mechanisms of Asthma, School of Immunology and Microbial Science, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
| | - Philip Eaton
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
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17
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Martin MD, Brown DN, Ramos KS. Computational modeling of RNase, antisense ORF0 RNA, and intracellular compartmentation and their impact on the life cycle of the line retrotransposon. Comput Struct Biotechnol J 2021; 19:5667-5677. [PMID: 34765087 PMCID: PMC8554170 DOI: 10.1016/j.csbj.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/10/2021] [Accepted: 10/01/2021] [Indexed: 11/08/2022] Open
Abstract
Nearly half of the human genome is occupied by repetitive sequences of ancient virus-like genetic elements. The largest class, comprising 17% of the genome, belong to the type 1 Long INterspersed Elements (LINE-1) and are the only class capable of autonomous propagation in the genome. When epigenetic silencing mechanisms of LINE-1 fail, the proteins encoded by LINE-1 engage in reverse transcription to make new copies of their own or other DNAs that are pasted back into the genome. To elucidate how LINE-1 is dysregulated as a result of carcinogen exposure, we developed a computational model of key elements in the LINE-1 lifecycle, namely, the role of cytosolic ribonuclease (RNase), RNA interference (RNAi) by the antisense ORF0 RNA, and sequestration of LINE-1 products into stress granules and multivesicular structures. The model showed that when carcinogen exposure is represented as either a sudden increase in LINE-1 mRNA count, or as an increase in mRNA transcription rate, the retrotransposon copy number exhibits a distinct threshold behavior above which LINE-1 enters a positive feedback loop that allows the cDNA copy number to grow exponentially. We also found that most of the LINE-1 RNA was degraded via the RNAase pathway and that neither ORF0 RNAi, nor the sequestration of LINE-1 products into granules and multivesicular structures, played a significant role in regulating the retrotransposon’s life cycle. Several aspects of the prediction agree with experimental results and indicate that the model has significant potential to inform future experiments related to LINE-1 activation.
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Affiliation(s)
| | - David N Brown
- Western Kentucky University, 1906 College Heights Blvd, Bowling Green, Kentucky 42101, United States
| | - Kenneth S Ramos
- Center for Genomic and Precision Medicine, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
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18
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Alekseeva L, Mironova N. Role of Cell-Free DNA and Deoxyribonucleases in Tumor Progression. Int J Mol Sci 2021; 22:12246. [PMID: 34830126 PMCID: PMC8625144 DOI: 10.3390/ijms222212246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.
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Affiliation(s)
| | - Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia;
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19
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Human Recombinant DNase I (Pulmozyme ®) Inhibits Lung Metastases in Murine Metastatic B16 Melanoma Model That Correlates with Restoration of the DNase Activity and the Decrease SINE/LINE and c-Myc Fragments in Blood Cell-Free DNA. Int J Mol Sci 2021; 22:ijms222112074. [PMID: 34769514 PMCID: PMC8585023 DOI: 10.3390/ijms222112074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022] Open
Abstract
Tumor-associated cell-free DNAs (cfDNA) play an important role in the promotion of metastases. Previous studies proved the high antimetastatic potential of bovine pancreatic DNase I and identified short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs)and fragments of oncogenes in cfDNA as the main molecular targets of enzyme in the bloodstream. Here, recombinant human DNase I (commercial name Pulmozyme®), which is used for the treatment of cystic fibrosis in humans, was repurposed for the inhibition of lung metastases in the B16 melanoma model in mice. We found that Pulmozyme® strongly reduced migration and induced apoptosis of B16 cells in vitro and effectively inhibited metastases in lungs and liver in vivo. Pulmozyme® was shown to be two times more effective when administered intranasally (i.n.) than bovine DNase I, but intramuscular (i.m.) administration forced it to exhibit as high an antimetastatic activity as bovine DNase I. Both DNases administered to mice either i.m. or i.n. enhanced the DNase activity of blood serum to the level of healthy animals, significantly decreased cfDNA concentrations, efficiently degraded SINE and LINE repeats and c-Myc fragments in the bloodstream and induced apoptosis and disintegration of neutrophil extracellular traps in metastatic foci; as a result, this manifested as the inhibition of metastases spread. Thus, Pulmozyme®, which is already an approved drug, can be recommended for use in the treatment of lung metastases.
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20
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Abstract
![]()
Sirtuin 6 (SIRT6)
is an NAD+-dependent protein deacylase
and mono-ADP-ribosyltransferase of the sirtuin family with a wide
substrate specificity. In vitro and in vivo studies have indicated that SIRT6 overexpression or activation has
beneficial effects for cellular processes such as DNA repair, metabolic
regulation, and aging. On the other hand, SIRT6 has contrasting roles
in cancer, acting either as a tumor suppressor or promoter in a context-specific
manner. Given its central role in cellular homeostasis, SIRT6 has
emerged as a promising target for the development of small-molecule
activators and inhibitors possessing a therapeutic potential in diseases
ranging from cancer to age-related disorders. Moreover, specific modulators
allow the molecular details of SIRT6 activity to be scrutinized and
further validate the enzyme as a pharmacological target. In this Perspective,
we summarize the current knowledge about SIRT6 pharmacology and medicinal
chemistry and describe the features of the activators and inhibitors
identified so far.
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Affiliation(s)
- Francesco Fiorentino
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Antonello Mai
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, P.le A Moro 5, 00185 Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, P.le A Moro 5, 00185 Rome, Italy
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21
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Takeda H, Jenkins NA, Copeland NG. Identification of cancer driver genes using Sleeping Beauty transposon mutagenesis. Cancer Sci 2021; 112:2089-2096. [PMID: 33783919 PMCID: PMC8177796 DOI: 10.1111/cas.14901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
Cancer genome sequencing studies have identified driver genes for a variety of different cancers and helped to understand the genetic landscape of human cancer. It is still challenging, however, to identify cancer driver genes with confidence simply from genetic data alone. In vivo forward genetic screens using Sleeping Beauty (SB) transposon mutagenesis provides another powerful genetic tool for identifying candidate cancer driver genes in wild-type and sensitized mouse tumors. By comparing cancer driver genes identified in human and mouse tumors, cancer driver genes can be identified with additional confidence based upon comparative oncogenomics. This review describes how SB mutagenesis works in mice and focuses on studies that have identified cancer driver genes in the mouse gastrointestinal tract.
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Affiliation(s)
- Haruna Takeda
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Nancy A Jenkins
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Neal G Copeland
- Genetics Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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22
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Ukadike KC, Mustelin T. Implications of Endogenous Retroelements in the Etiopathogenesis of Systemic Lupus Erythematosus. J Clin Med 2021; 10:856. [PMID: 33669709 PMCID: PMC7922054 DOI: 10.3390/jcm10040856] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. While its etiology remains elusive, current understanding suggests a multifactorial process with contributions by genetic, immunologic, hormonal, and environmental factors. A hypothesis that combines several of these factors proposes that genomic elements, the L1 retrotransposons, are instrumental in SLE pathogenesis. L1 retroelements are transcriptionally activated in SLE and produce two proteins, ORF1p and ORF2p, which are immunogenic and can drive type I interferon (IFN) production by producing DNA species that activate cytosolic DNA sensors. In addition, these two proteins reside in RNA-rich macromolecular assemblies that also contain well-known SLE autoantigens like Ro60. We surmise that cells expressing L1 will exhibit all the hallmarks of cells infected by a virus, resulting in a cellular and humoral immune response similar to those in chronic viral infections. However, unlike exogenous viruses, L1 retroelements cannot be eliminated from the host genome. Hence, dysregulated L1 will cause a chronic, but perhaps episodic, challenge for the immune system. The clinical and immunological features of SLE can be at least partly explained by this model. Here we review the support for, and the gaps in, this hypothesis of SLE and its potential for new diagnostic, prognostic, and therapeutic options in SLE.
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Affiliation(s)
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington School of Medicine, 750 Republican Street, Seattle, WA 98109, USA;
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23
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Pappalardo AM, Ferrito V, Biscotti MA, Canapa A, Capriglione T. Transposable Elements and Stress in Vertebrates: An Overview. Int J Mol Sci 2021; 22:1970. [PMID: 33671215 PMCID: PMC7922186 DOI: 10.3390/ijms22041970] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/17/2022] Open
Abstract
Since their identification as genomic regulatory elements, Transposable Elements (TEs) were considered, at first, molecular parasites and later as an important source of genetic diversity and regulatory innovations. In vertebrates in particular, TEs have been recognized as playing an important role in major evolutionary transitions and biodiversity. Moreover, in the last decade, a significant number of papers has been published highlighting a correlation between TE activity and exposition to environmental stresses and dietary factors. In this review we present an overview of the impact of TEs in vertebrate genomes, report the silencing mechanisms adopted by host genomes to regulate TE activity, and finally we explore the effects of environmental and dietary factor exposures on TE activity in mammals, which is the most studied group among vertebrates. The studies here reported evidence that several factors can induce changes in the epigenetic status of TEs and silencing mechanisms leading to their activation with consequent effects on the host genome. The study of TE can represent a future challenge for research for developing effective markers able to detect precocious epigenetic changes and prevent human diseases.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Maria Assunta Biscotti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Teresa Capriglione
- Department of Biology, University of Naples "Federico II", Via Cinthia 21-Ed7, 80126 Naples, Italy
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24
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Misawa K, Yamada S, Mima M, Nakagawa T, Kurokawa T, Imai A, Mochizuki D, Shinmura D, Yamada T, Kita J, Ishikawa R, Yamaguchi Y, Misawa Y, Kanazawa T, Kawasaki H, Mineta H. Long interspersed nuclear element 1 hypomethylation has novel prognostic value and potential utility in liquid biopsy for oral cavity cancer. Biomark Res 2020; 8:53. [PMID: 33110605 PMCID: PMC7585304 DOI: 10.1186/s40364-020-00235-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Background New biomarkers are urgently needed to improve personalized treatment approaches for head and neck squamous cell carcinoma (HNSCC). Global DNA hypomethylation has wide-ranging functions in multistep carcinogenesis, and the hypomethylation of long interspersed nucleotide element-1 (LINE-1) is related to increased retrotransposon activity and induced genome instability. However, little information is available regarding LINE-1 hypomethylation and its prognostic implications in HNSCC. Methods In this study, we analyzed LINE-1 hypomethylation levels in a well-characterized dataset of 317 primary HNSCC tissues and 225 matched pairs of normal mucosa tissues, along with five oral cavity cancer (OCC) circulating tumor DNA (ctDNA) samples using quantitative real-time methylation and unmethylation PCR. The analysis was performed according to various clinical characteristics and prognostic implications. Results The results demonstrated that LINE-1 hypomethylation levels were significantly higher in the HNSCC tissues than in corresponding normal tissues from the same individuals (P < 0.001). Univariate analysis revealed that high levels of LINE-1 hypomethylation were correlated with poor disease-free survival (DFS; log-rank test, P = 0.038), whereas multivariate analysis demonstrated that they were significant independent prognostic factor for DFS (hazard ratio: 2.10, 95% confidence interval: 1.02–4.36; P = 0.045). Moreover, samples with high LINE-1 hypomethylation levels exhibited the greatest decrease in 5-hydroxymethylcytosine (5-hmC) levels and increase in tumor-suppressor gene methylation index (P = 0.006 and P < 0.001, respectively). Further, ctDNA studies also showed that LINE-1 hypomethylation had high predictive ability in OCC. Conclusions LINE-1 hypomethylation is associated with a higher risk of early OCC relapse, and is hence, a potential predictive biomarker for OCC. Furthermore, 5-hmC levels also exhibited predictive potential in OCC, based on their inverse correlation with LINE-1 hypomethylation levels. LINE-1 hypomethylation analysis, therefore, has applications in determining patient prognosis and real-time surveillance of disease recurrence, and could serve as an alternative method for OCC screening. Supplementary information Supplementary information accompanies this paper at 10.1186/s40364-020-00235-y.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Satoshi Yamada
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Masato Mima
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Takuya Nakagawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoya Kurokawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Imai
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Daiki Mochizuki
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Daichi Shinmura
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Taiki Yamada
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Junya Kita
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Ryuji Ishikawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Yuki Yamaguchi
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Yuki Misawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Takeharu Kanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi Japan
| | - Hideya Kawasaki
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Mineta
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
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Shademan M, Zare K, Zahedi M, Mosannen Mozaffari H, Bagheri Hosseini H, Ghaffarzadegan K, Goshayeshi L, Dehghani H. Promoter methylation, transcription, and retrotransposition of LINE-1 in colorectal adenomas and adenocarcinomas. Cancer Cell Int 2020; 20:426. [PMID: 32905102 PMCID: PMC7466817 DOI: 10.1186/s12935-020-01511-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The methylation of the CpG islands of the LINE-1 promoter is a tight control mechanism on the function of mobile elements. However, simultaneous quantification of promoter methylation and transcription of LINE-1 has not been performed in progressive stages of colorectal cancer. In addition, the insertion of mobile elements in the genome of advanced adenoma stage, a precancerous stage before colorectal carcinoma has not been emphasized. In this study, we quantify promoter methylation and transcripts of LINE-1 in three stages of colorectal non-advanced adenoma, advanced adenoma, and adenocarcinoma. In addition, we analyze the insertion of LINE-1, Alu, and SVA elements in the genome of patient tumors with colorectal advanced adenomas. METHODS LINE-1 hypomethylation status was evaluated by absolute quantitative analysis of methylated alleles (AQAMA) assay. To quantify the level of transcripts for LINE-1, quantitative RT-PCR was performed. To find mobile element insertions, the advanced adenoma tissue samples were subjected to whole genome sequencing and MELT analysis. RESULTS We found that the LINE-1 promoter methylation in advanced adenoma and adenocarcinoma was significantly lower than that in non-advanced adenomas. Accordingly, the copy number of LINE-1 transcripts in advanced adenoma was significantly higher than that in non-advanced adenomas, and in adenocarcinomas was significantly higher than that in the advanced adenomas. Whole-genome sequencing analysis of colorectal advanced adenomas revealed that at this stage polymorphic insertions of LINE-1, Alu, and SVA comprise approximately 16%, 51%, and 74% of total insertions, respectively. CONCLUSIONS Our correlative analysis showing a decreased methylation of LINE-1 promoter accompanied by the higher level of LINE-1 transcription, and polymorphic genomic insertions in advanced adenoma, suggests that the early and advanced polyp stages may host very important pathogenic processes concluding to cancer.
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Affiliation(s)
- Milad Shademan
- Graduate Program in Physiology, Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Khadijeh Zare
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, 91779-48974 Iran
| | - Morteza Zahedi
- Graduate Program in Physiology, Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hooman Mosannen Mozaffari
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Gastroenterology and Hepatology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Bagheri Hosseini
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Gastroenterology and Hepatology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kamran Ghaffarzadegan
- Pathology Department, Education and Research Department, Razavi Hospital, Mashhad, Iran
| | - Ladan Goshayeshi
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hesam Dehghani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, 91779-48974 Iran
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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Zhang X, Zhang R, Yu J. New Understanding of the Relevant Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation. Front Cell Dev Biol 2020; 8:657. [PMID: 32850797 PMCID: PMC7426637 DOI: 10.3389/fcell.2020.00657] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
Long interspersed nuclear element-1 (LINE-1) retrotransposition is a major hallmark of cancer accompanied by global chromosomal instability, genomic instability, and genetic heterogeneity and has become one indicator for the occurrence, development, and poor prognosis of many diseases. LINE-1 also modulates the immune system and affects the immune microenvironment in a variety of ways. Aberrant expression of LINE-1 retrotransposon can provide strong stimuli for an innate immune response, activate the immune system, and induce autoimmunity and inflammation. Therefore, inhibition the activity of LINE-1 has become a potential treatment strategy for various diseases. In this review, we discussed the components and regulatory mechanisms involved with LINE-1, its correlations with disease and immunity, and multiple inhibitors of LINE-1, providing a new understanding of LINE-1.
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Affiliation(s)
- Xiao Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Rui Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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Park MK, Lee JC, Lee JW, Kang S, Kim J, Park MH, Hwang SJ, Lee M. Effects of fermented rice bran on DEN-induced oxidative stress in mice: GSTP1, LINE-1 methylation, and telomere length ratio. J Food Biochem 2020; 44:e13274. [PMID: 32468620 DOI: 10.1111/jfbc.13274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/01/2020] [Accepted: 04/18/2020] [Indexed: 12/12/2022]
Abstract
N-diethylnitrosamine (DEN), a well-known carcinogen, not only induces excessive reactive oxygen species but also suppresses DNA methylation. This study investigated the effect of fermented rice bran (FRB) treatment on DEN-induced oxidative stress through DNA methylation and telomere length analysis. To evaluate the potential protective role of FRB in oxidative stress, two different doses of FRB, DEN, and their combination were administered to mice that were preadapted or not to FRB. Glutathione-S-transferase P1 (GSTP1) methylation levels significantly decreased at 2 and 24 hr after FRB and DEN co-administration in mice with and without pre-adaptation. Moreover, GSTP1 mRNA was upregulated under DEN-induced oxidative stress. Furthermore, changes in long interspersed nuclear element-1 methylation were observed from the viewpoint of genomic instability. In addition, FRB preadapted mice displayed a lower telomere length ratio than the non-adapted mice, suggesting that FRB adaptation offers advantages over the non-adapted conditions in terms of inflammation suppression. PRACTICAL APPLICATIONS: DEN induces excessive ROS, which is associated with oxidative stress on DNA and other cellular components, resulting in inflammation. This study shows that FRB may alleviate DEN-triggered oxidative stress, based on changes in GSTP1, LINE-1 methylation, and telomere length ratios, thereby, revealing the potential of dietary intervention during inflammation. Furthermore, this study furthers the current understanding of DNA methylation mechanisms underlying the antioxidant and anti-inflammatory effects of functional food components. These results indicate that dietary inclusion of FRB may help decrease oxidative DNA damage and its associated inflammation at early stages of a disease.
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Affiliation(s)
- Min-Koo Park
- Nutrigenetics Institute, Bio-Innovation Park, Erom, Inc., Uiwang, Republic of Korea
| | - Jeong-Chan Lee
- Nutrigenetics Institute, Bio-Innovation Park, Erom, Inc., Uiwang, Republic of Korea
| | - Ji-Won Lee
- Nutrigenetics Institute, Bio-Innovation Park, Erom, Inc., Uiwang, Republic of Korea
| | - Sujin Kang
- Bio R&D Division, Bio-Innovation Park, Erom, Inc., Chuncheon, Republic of Korea
| | - JoongHark Kim
- Bio R&D Division, Bio-Innovation Park, Erom, Inc., Chuncheon, Republic of Korea
| | - Mi Houn Park
- Bio R&D Division, Bio-Innovation Park, Erom, Inc., Chuncheon, Republic of Korea
| | - Sung-Joo Hwang
- Integrated Medicine Institute, Loving Care Hospital, Sampyeong, Republic of Korea
| | - MinJae Lee
- College of Veterinary Medicine, Kangwon National University, Chuncheon, Republic of Korea
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Cavalcante MG, Nagamachi CY, Pieczarka JC, Noronha RCR. Evolutionary insights in Amazonian turtles (Testudines, Podocnemididae): co-location of 5S rDNA and U2 snRNA and wide distribution of Tc1/Mariner. Biol Open 2020; 9:bio049817. [PMID: 32229487 PMCID: PMC7197720 DOI: 10.1242/bio.049817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/18/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic genomes exhibit substantial accumulation of repetitive DNA sequences. These sequences can participate in chromosomal reorganization events and undergo molecular cooption to interfere with the function and evolution of genomes. In turtles, repetitive DNA sequences appear to be accumulated at probable break points and may participate in events such as non-homologous recombination and chromosomal rearrangements. In this study, repeated sequences of 5S rDNA, U2 snRNA and Tc1/Mariner transposons were amplified from the genomes of the turtles, Podocnemis expansa and Podocnemis unifilis, and mapped by fluorescence in situ hybridization. Our data confirm the 2n=28 chromosomes for these species (the second lowest 2n in the order Testudines). We observe high conservation of the co-located 5S rDNA and U2 snRNA genes on a small chromosome pair (pair 13), and surmise that this represents the ancestral condition. Our analysis reveals a wide distribution of the Tc1/Mariner transposons and we discuss how the mobility of these transposons can act on karyotypic reorganization events (contributing to the 2n decrease of those species). Our data add new information for the order Testudines and provide important insights into the dynamics and organization of these sequences in the chelonian genomes.
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Affiliation(s)
- Manoella Gemaque Cavalcante
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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Sharp CN, Korte EA, Hosseinejad K, Pitman J, Lavasanifar A, Eichenberger DJ, Sephton S, Cash E, Jortani SA. ELISA-based detection of Open Reading Frame protein 1 in patients at risk of developing lung cancer. Clin Chim Acta 2020; 507:1-6. [PMID: 32275987 DOI: 10.1016/j.cca.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Early detection of lung cancer significantly improves survival outcomes. Thus, lung cancer screening for high-risk individuals using low-dose CT scan (LDCT) is recommended. LDCT has several limitations, and often requires invasive follow up. Previously, we have developed an ELISA for measurement of Open Reading Frame 1 protein (ORF1p) in serum. We assessed whether ORF1p can be used as a risk assessment biomarker for patients at high risk for developing lung cancer. PATIENTS Patients with risk factors for lung cancer were enrolled in our study with consent under IRB approval. A total of 122 patients were included. The lung cancer cohort consisted of 38 patients with varying stages of cancer undergoing treatment. METHODS ORF1p quantification was performed using our ELISA assay on serum samples. RESULTS ORF1p was significantly increased in the serum of patients with identified lung nodules compared to those without nodules (P = 0.0007). ORF1p was also significantly increased in patients who were recommended for follow up (P = 0.0004). When comparing the at-risk cohort to patients with lung cancer, there was not a significant difference in ORF1p levels. CONCLUSION ORF1p can be used to identify patients at high risk of developing lung cancer and may provide an effective, non-invasive risk assessment marker to complement LDCT screening.
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Affiliation(s)
- Cierra N Sharp
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Erik A Korte
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Keivan Hosseinejad
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Jennifer Pitman
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States
| | - Afsaneh Lavasanifar
- Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | | | - Sandra Sephton
- Department of Psychological and Brain Sciences, University of Louisville, 322A Life Sciences Building, Louisville, KY 40292, United States
| | - Elizabeth Cash
- Department of Otolaryngology-Head and Neck Surgery and Communicative Disorders, University of Louisville School of Medicine, 401 E Chestnut St # 170, Louisville, KY 40202, United States
| | - Saeed A Jortani
- Department of Pathology and Laboratory Medicine, University of Louisville, 511 South Floyd Street, Louisville, KY 40202, United States.
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Cavalcante MG, Souza LF, Vicari MR, de Bastos CEM, de Sousa JV, Nagamachi CY, Pieczarka JC, Martins C, Noronha RCR. Molecular cytogenetics characterization of Rhinoclemmys punctularia (Testudines, Geoemydidae) and description of a Gypsy-H3 association in its genome. Gene 2020; 738:144477. [PMID: 32061764 DOI: 10.1016/j.gene.2020.144477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/01/2020] [Accepted: 02/11/2020] [Indexed: 01/24/2023]
Abstract
The wide variation found in the size of eukaryotic genomes is largely related to the accumulation of repetitive sequences. Studies show that these sequences can go through an evolutionary process (molecular co-optation) and acquire new genomic functions. Cytogenetic studies reveal a wide karyotypic variation between chelonians (order Testudines) (2n = 26-68), attributed mainly to the number of microchromosomes. The study of repetitive DNAs has the potential to provide data on the dynamics of these sequences, and how they influence the organization of the genome. Here, we reveal the first in situ mapping data of 45S rDNA, histone H3 genes, and telomeric sequences, for a species of the genus Rhinoclemmys, R. punctularia. The karyotype described here for R. punctularia is different from previous reports for the diploid complement of this species, with differences probably attributable to centric fissions and pericentric inversions or centromere repositioning. The 45S rDNA are on a single chromosome pair (like in other turtles), telomeric sequences are in terminal position on all the chromosomes, and histone H3 is dispersed in low copy number, with clusters in pericentromeric regions of three chromosome pairs. We report on the presence of a Gypsy retrotransposon insert located within H3 histone of R. punctularia, and the H3 region sequenced contained the open reading frame of the histone sequence. Comparative modeling revealed a functional pattern for the protein, thus suggesting that the Gypsy element might have been recruited for new functions in the genome of this species.
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Affiliation(s)
- Manoella Gemaque Cavalcante
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Luciano Farias Souza
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Carlos Eduardo Matos de Bastos
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.
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Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
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McKerrow W, Fenyö D. L1EM: a tool for accurate locus specific LINE-1 RNA quantification. Bioinformatics 2019; 36:1167-1173. [PMID: 31584629 PMCID: PMC8215917 DOI: 10.1093/bioinformatics/btz724] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/31/2019] [Accepted: 09/25/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION LINE-1 elements are retrotransposons that are capable of copying their sequence to new genomic loci. LINE-1 derepression is associated with a number of disease states, and has the potential to cause significant cellular damage. Because LINE-1 elements are repetitive, it is difficult to quantify LINE-1 RNA at specific loci and to separate transcripts with protein coding capability from other sources of LINE-1 RNA. RESULTS We provide a tool, L1EM that uses the expectation maximization algorithm to quantify LINE-1 RNA at each genomic locus, separating transcripts that are capable of generating retrotransposition from those that are not. We show the accuracy of L1EM on simulated data and against long read sequencing from HEK cells. AVAILABILITY AND IMPLEMENTATION L1EM is written in python. The source code along with the necessary annotations are available at https://github.com/FenyoLab/L1EM and distributed under GPLv3. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - David Fenyö
- To whom correspondence should be addressed. or
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33
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Zhang R, Zhang F, Sun Z, Liu P, Zhang X, Ye Y, Cai B, Walsh MJ, Ren X, Hao X, Zhang W, Yu J. LINE-1 Retrotransposition Promotes the Development and Progression of Lung Squamous Cell Carcinoma by Disrupting the Tumor-Suppressor Gene FGGY. Cancer Res 2019; 79:4453-4465. [PMID: 31289132 DOI: 10.1158/0008-5472.can-19-0076] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/07/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022]
Abstract
Somatic long interspersed element-1 (LINE-1) retrotransposition is a genomic process that relates to gene disruption and tumor occurrence. However, the expression and function of LINE-1 retrotransposition in lung squamous cell carcinoma (LUSC) remain unclear. We analyzed the transcriptomes of LUSC samples in The Cancer Genome Atlas and observed LINE-1 retrotransposition in 90% of tumor samples. Thirteen LINE-1 retrotranspositions of high occurrence were identified and further validated from an independent Chinese LUSC cohort. Among them, LINE-1-FGGY (L1-FGGY) was identified as the most frequent LINE-1 retrotransposition in the Chinese cohort and significantly correlated with poor clinical outcome. L1-FGGY occurred with smoke-induced hypomethylation of the LINE-1 promoter and contributed to the development of local immune evasion and dysfunctional metabolism. Overexpression of L1-FGGY or knockdown of FGGY promoted cell proliferation and invasion in vitro, facilitated tumorigenesis in vivo, and dysregulated cell energy metabolism and cytokine/chemotaxin transcription. Importantly, specific reverse transcription inhibitors, nevirapine and efavirenz, dramatically countered L1-FGGY abundance, inhibited tumor growth, recovered metabolism dysfunction, and improved the local immune evasion. In conclusion, hypomethylation-induced L1-FGGY expression is a frequent genomic event that promotes the development and progression of LUSC and represents a promising predictive biomarker and therapeutic target in LUSC. SIGNIFICANCE: LINE-1-FGGY is a prognosis predictive biomarker and potential therapeutic target to overcome local immune evasion in lung squamous cell carcinoma.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/surgery
- Cell Line, Tumor
- Cohort Studies
- Female
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Humans
- Lipid Metabolism/genetics
- Long Interspersed Nucleotide Elements/genetics
- Lung Neoplasms/genetics
- Lung Neoplasms/mortality
- Lung Neoplasms/pathology
- Lung Neoplasms/surgery
- Male
- Mice, SCID
- Middle Aged
- Promoter Regions, Genetic
- Proteins/genetics
- Smoking/genetics
- Tumor Escape
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Rui Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Fan Zhang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zeguo Sun
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pengpeng Liu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xiao Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yingnan Ye
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Beiqi Cai
- Department of Imaging, Nanjing Bayi Hospital, Nanjing, China
| | - Martin J Walsh
- Departments of Pharmacological Sciences, Genetics and Genomic Sciences and the Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Xiubao Ren
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Immunology, Biotherapy Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Xishan Hao
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Immunology, Biotherapy Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Weijia Zhang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
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Abstract
Over the last decade, several theoretical models have been put forth to describe how animals respond to adverse environments and how this response changes under different physiological demands across life history stages. These models capture the context- and condition-dependent nature of stress responses. Yet, application of the models has been limited thus far in part because each model addresses different aspects of the problems facing the field of stress biology. Thus, there is a need for a unifying theoretical model that incorporates changes in physiological demand with life history stages and age, intricate relationships among physiological systems, and biphasic nature of stress responses. Here, I propose a new integrative framework, the Damage-Fitness Model. In this model, regulators, such as DNA repair mechanisms and glucocorticoids, work together as anti-damage mechanisms to minimize damage at both the cellular and organismal level. When the anti-damage regulators are insufficient or inappropriate, persistent damage accumulates. Previous studies indicate that these damage directly impact reproductive performance, disease risk, and survival. The types of regulators, the threshold at which they are initiated, and the magnitude of the responses are shaped by developmental and current environments. This model unites existing theoretical models by shifting our focus from physiological responses to downstream consequences of the stress responses, circumventing context specificity. Discussions include (1) how the proposed model relates to existing models, (2) steps to test the new model, and (3) how this model can be used to better assess the health of individuals and a population. Lay summary The field of stress physiology faces a challenge of characterizing dynamic cellular, physiological, and behavioral responses when animals encounter a stressor. This paper proposes a new theoretical model which links stress avoidance, damage repair and accumulation, and fitness components.
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Affiliation(s)
- Haruka Wada
- a Department of Biological Sciences, Auburn University , Auburn , AL , USA
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35
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Kalayasiri R, Kraijak K, Mutirangura A, Maes M. Paranoid schizophrenia and methamphetamine-induced paranoia are both characterized by a similar LINE-1 partial methylation profile, which is more pronounced in paranoid schizophrenia. Schizophr Res 2019; 208:221-227. [PMID: 30826260 DOI: 10.1016/j.schres.2019.02.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/03/2019] [Accepted: 02/20/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND There is evidence that schizophrenia is a neuro-immune disorder. Genes linked to intragenic LINE-1 methylation show a strong association with immune-associated disorders including psychosis. The aim of this study was to examine LINE-1 methylation patterns in paranoid schizophrenia and methamphetamine-induced paranoia, a model for schizophrenia. METHODS This study recruited 31 patients with paranoid schizophrenia, 94 with methamphetamine-induced paranoia (MIP) and 163 normal controls. LINE-1 methylation patterns were assayed in peripheral blood mononuclear cells and a combined bisulphite restriction analysis and COBRA were used to estimate LINE1 methylation (mC) and CpG dinucleotide methylation patterns, namely 2 methylated (mCmC) and 2 unmethylated (uCuC) CpGs and the partially methylated loci mCuC (5'm with 3'u) and uCmC (5'u with 3'm). RESULTS Patients with paranoid schizophrenia show highly significant changes in LINE-1 partial methylation patterns, namely a higher percentage of mCuC and lower percentage of uCmC as compared with controls and MIP patients, while the latter show a higher percentage of mCuC but lower percentage of uCmC as compared with controls. Higher mCuC significantly predicts paranoid schizophrenia with a sensitivity of 51.6%, specificity of 97.5% and an area under the ROC curve of 0.895. CONCLUSIONS The results indicate that a common dysfunction in LINE-1 partial methylation may underpin both paranoid schizophrenia and MIP and that this methylation pattern is significantly more expressed in paranoid schizophrenia than MIP. Reciprocal links between impairments in LINE-1 methylation and neuro-immune and neuro-oxidative pathways may underpin the pathophysiology of both MIP and paranoid schizophrenia.
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Affiliation(s)
- Rasmon Kalayasiri
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Psychiatry, King Chulalongkorn Memorial Hospital, Bangkok, Thailand; Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Korakot Kraijak
- Master of Science Program in Medical Science, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; IMPACT Strategic Research Center, Barwon Health, Geelong, Australia; Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria.
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36
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Long interspersed nuclear element-1 mobilization as a target in cancer diagnostics, prognostics and therapeutics. Clin Chim Acta 2019; 493:52-62. [DOI: 10.1016/j.cca.2019.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/11/2019] [Accepted: 02/14/2019] [Indexed: 12/31/2022]
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Profiling of LINE-1-Related Genes in Hepatocellular Carcinoma. Int J Mol Sci 2019; 20:ijms20030645. [PMID: 30717368 PMCID: PMC6387036 DOI: 10.3390/ijms20030645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/26/2019] [Accepted: 01/29/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a prime public health concern that accounts for most of the primary liver malignancies in humans. The most common etiological factor of HCC is hepatitis B virus (HBV). Despite recent advances in treatment strategies, there has been little success in improving the survival of HCC patients. To develop a novel therapeutic approach, evaluation of a working hypothesis based on different viewpoints might be important. Long interspersed element 1 (L1) retrotransposons have been suggested to play a role in HCC. However, the molecular machineries that can modulate L1 biology in HBV-related HCC have not been well-evaluated. Here, we summarize the profiles of expression and/or activation status of L1-related genes in HBV-related HCC, and HBV- and HCC-related genes that may impact L1-mediated tumorigenesis. L1 restriction factors appear to be suppressed by HBV infection. Since some of the L1 restriction factors also limit HBV, these factors may be exhausted in HBV-infected cells, which causes de-suppression of L1. Several HBV- and HCC-related genes that interact with L1 can affect oncogenic processes. Thus, L1 may be a novel prime therapeutic target for HBV-related HCC. Studies in this area will provide insights into HCC and other types of cancers.
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Tsang M, Gantchev J, Netchiporouk E, Moreau L, Ghazawi FM, Glassman S, Sasseville D, Litvinov IV. A study of meiomitosis and novel pathways of genomic instability in cutaneous T-cell lymphomas (CTCL). Oncotarget 2018; 9:37647-37661. [PMID: 30701021 PMCID: PMC6340880 DOI: 10.18632/oncotarget.26479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Genomic instability is a hallmark of cancer and an enabling factor for genetic alterations that drive cancer development and progression. The clashing of mitosis and aberrantly expressed meiosis machineries, which may contribute to genomic instability, has been coined cancer “meiomitosis”. LINE-1 retrotransposition, a process active in germ cells, acts outside of the meiotic machinery to create DNA double strand breaks (DNA DSBs) and has played an important role in the evolution of the human genome. We have previously demonstrated that in CTCL several cancer testis/meiotic genes are expressed. Furthermore, this cancer exhibits extensive and ongoing chromosomal/microsatellite instability. In this study we analyzed immortalized patient-derived cells and primary CTCL patient samples using RT-PCR, western blotting and confocal microscopy and found that proteins critically involved in meiosis and LINE-1 retrotransposition are expressed and are associated with chromosomal instability and DNA DSB formation. Using cell cycle synchronization, we show G1/S phase-transition-specific expression of meiosis proteins. Using the Alu retrotransposition assay, we demonstrate the functional activity of LINE-1 retrotransposon in CTCL. Histone acetyltransferase inhibition results in downregulation of the ectopic germ cell programs and concomitant decrease in DNA DSBs foci formation. Notably, LINE-1 and meiosis genes were expressed across a panel of other solid tumor cell lines. Taken together, our results indicate that malignant cells in culture undergo “cancer meiomitosis” rather than the classic mitosis division. The ectopic expression of meiosis genes and reactivation of LINE-1 may be contributing to genomic instability and represent novel targets for immunotherapy in this and other cancers.
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Affiliation(s)
- Matthew Tsang
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada
| | - Jennifer Gantchev
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Elena Netchiporouk
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Linda Moreau
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Feras M Ghazawi
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada
| | - Steven Glassman
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada
| | - Denis Sasseville
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Ivan V Litvinov
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada.,Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
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39
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Methamphetamine (MA) Use Induces Specific Changes in LINE-1 Partial Methylation Patterns, Which Are Associated with MA-Induced Paranoia: a Multivariate and Neuronal Network Study. Mol Neurobiol 2018; 56:4258-4272. [PMID: 30302724 DOI: 10.1007/s12035-018-1371-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/27/2018] [Indexed: 12/29/2022]
Abstract
The use of psychoactive substances, including methamphetamine (MA) may cause changes in DNA methylation. The aim of this study was to examine the effects of MA use on long interspersed element-1 (LINE-1) methylation patterns in association with MA-induced paranoia. This study recruited 123 normal controls and 974 MA users, 302 with and 672 without MA-induced paranoia. The Semi-Structured Assessment for Drug Dependence and Alcoholism was used to assess demographic and substance use variables. Patterns of LINE-1 methylation were assessed in peripheral blood mononuclear cells and a combined bisulfite restriction analysis (COBRA) was used to estimate overall LINE-1 methylation (mC) while COBRA classified LINE-alleles into four patterns based on the methylation status of two CpG dinucleotides on each strand from 5' to 3', namely two methylated (mCmC) and two unmethylated (uCuC) CpGs and two types of partially methylated loci (mCuC that is 5'm with 3'u and uCmC that is 5'u with 3'm CpGs). MA users showed higher % mCuC and % mCuC + uCmC levels than controls. Use of solvents and opioids, but not cannabis and alcohol dependence, significantly lowered % uCmC levels, while current smoking significantly increased % uCuC levels. MA-induced paranoia was strongly associated with changes in LINE-1 partial methylation patterns (lowered % uCmC), heavy MA use, lower age at onset of MA use, and alcohol dependence. Women who took contraceptives showed significantly lower LINE-1 % mC and % mCmC and higher % uCuC levels than women without contraceptive use and men. The results show that MA-induced changes in LINE-1 partial methylation patterns are associated with MA-induced paranoia and could explain in part the pathophysiology of this type of psychosis. It is argued that MA-induced neuro-oxidative pathways may have altered LINE-1 partial methylation patterns, which in turn may regulate neuro-oxidative and immune pathways, which may increase risk to develop MA-induced paranoia.
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40
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Ishak CA, Classon M, De Carvalho DD. Deregulation of Retroelements as an Emerging Therapeutic Opportunity in Cancer. Trends Cancer 2018; 4:583-597. [DOI: 10.1016/j.trecan.2018.05.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 12/26/2022]
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41
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Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL. Horizontal transfer of BovB and L1 retrotransposons in eukaryotes. Genome Biol 2018; 19:85. [PMID: 29983116 PMCID: PMC6036668 DOI: 10.1186/s13059-018-1456-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/23/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events. RESULTS Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms. CONCLUSIONS We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.
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Affiliation(s)
- Atma M Ivancevic
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Neurogenetics Research Program, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - R Daniel Kortschak
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Terry Bertozzi
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - David L Adelson
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
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42
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Boyne DJ, King WD, Brenner DR, McIntyre JB, Courneya KS, Friedenreich CM. Aerobic exercise and DNA methylation in postmenopausal women: An ancillary analysis of the Alberta Physical Activity and Breast Cancer Prevention (ALPHA) Trial. PLoS One 2018; 13:e0198641. [PMID: 29953441 PMCID: PMC6023230 DOI: 10.1371/journal.pone.0198641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/22/2018] [Indexed: 12/17/2022] Open
Abstract
Physical activity is associated with a lower risk of breast, colon, and endometrial cancer. Epigenetic mechanisms such as changes in DNA methylation may help to explain these protective effects. We assessed the impact of a one year aerobic exercise intervention on DNA methylation biomarkers believed to play a role in carcinogenesis. The Alberta Physical Activity and Breast Cancer Prevention (ALPHA) Trial was a two-armed randomized controlled trial in 320 healthy, inactive, postmenopausal women with no history of cancer. In an ancillary analysis, frozen blood samples (n = 256) were reassessed for levels of DNA methylation within LINE-1 and Alu repeats as well as within the promoter regions of APC, BRCA1, RASSF1, and hTERT genes. Differences between the exercise and control arm at 12-months, after adjusting for baseline values, were estimated within an intent-to-treat and per-protocol analysis using linear regression. No significant differences in DNA methylation between the exercise and control arms were observed. In an exploratory analysis, we found that the prospective change in estimated VO2max was negatively associated with RASSF1 methylation in a dose-response manner (p-trend = 0.04). A year-long aerobic exercise intervention does not affect LINE-1, Alu, APC, BRCA1, RASSF1, or hTERT methylation in healthy, inactive, postmenopausal women. Changes in DNA methylation within these genomic regions may not mediate the association between physical activity and cancer in healthy postmenopausal women. Additional research is needed to validate our findings with RASSF1 methylation. Trial Registration: ClinicalTrials.gov NCT00522262.
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Affiliation(s)
- Devon J. Boyne
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Will D. King
- Department of Public Health Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Darren R. Brenner
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - John B. McIntyre
- Translational Laboratory, Tom Baker Cancer Centre, Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kerry S. Courneya
- Faculty of Physical Education and Recreation, University of Alberta, Edmonton, Alberta, Canada
| | - Christine M. Friedenreich
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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43
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Gogna P, O'Sullivan DE, King WD. The effect of inflammation-related lifestyle exposures and interactions with gene variants on long interspersed nuclear element-1 DNA methylation. Epigenomics 2018; 10:785-796. [PMID: 29888958 DOI: 10.2217/epi-2017-0164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To examine the relationship between inflammation-related lifestyle factors and long interspersed nuclear element-1 (LINE-1) DNA methylation, and test for interaction by gene variants involved in one-carbon metabolism. PATIENTS & METHODS The study population consisted of 280 individuals undergoing colonoscopy screening. Multivariable linear regression was employed to examine associations of physical activity, BMI and NSAID use with LINE-1 DNA methylation and interactions with MTR and MTHFR gene variants. RESULTS The highest quartile of physical activity compared with the lowest was associated with higher LINE-1 DNA methylation (p = 0.005). Long-term NSAID use and a normal BMI were associated with increased LINE-1 DNA methylation among individuals with the variant MTR allele (p = 0.02; p = 0.03). CONCLUSION This study provides evidence that inflammation-related exposures may influence LINE-1 DNA methylation.
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Affiliation(s)
- Priyanka Gogna
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Dylan E O'Sullivan
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Will D King
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
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44
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Tang ML, Xiao P, Zou JZ, Cao DD, Li YY, Chang HB. [Effect of LINE1-ORF1p overexpression on the proliferation of nephroblastoma WT_CLS1 cells]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2018; 20:501-507. [PMID: 29972127 PMCID: PMC7389950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/07/2018] [Indexed: 08/01/2024]
Abstract
OBJECTIVE To prepare the LINE1-ORF1p polyclonal antibody, and to study the effect of LINE1-ORF1p on the proliferation of nephroblastoma WT_CLS1 cells. METHODS A genetic engineering method was used to achieve prokaryotic expression of LINE1-ORF1p, and rabbits were immunized with LINE1-ORF1p to prepare polyclonal antibody. Indirect ELISA was used to evaluate antibody titer, and Western blot and immunohistochemistry were used to evaluate the specific ability of antibody to recognize LINE1-ORF1p. The eukaryotic expression vector pEGFP-N1-LINE1-ORF1 was constructed and used to transfect WT_CLS1 cells. Western blot and qRT-PCR were used to measure the protein and mRNA expression of LINE1-ORF1, respectively, and cell proliferation assay and colony-forming assay were used to evaluate the effect of LINE1-ORF1p on the proliferation of WT_CLS1 cells and the formation of tumor cell clone. RESULTS The LINE1-ORF1p antibody prepared had a titer of >1:16 000 and could specifically recognize LINE1-ORF1p in cells and tumor tissue. WT_CLS1 cells transfected with pEGFP-N1-LINE1-ORF1 had significant increases in the mRNA and protein expression of LINE1-ORF1 and significantly enhanced cell proliferation ability and colony formation ability (P<0.05). CONCLUSIONS LINE1-ORF1p can promote the growth of nephroblastoma cells and the formation of tumor cell clone, and may be involved in the pathogenesis of nephroblastoma.
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Affiliation(s)
- Mei-Ling Tang
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, Beijing 100020, China.
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45
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Tang ML, Xiao P, Zou JZ, Cao DD, Li YY, Chang HB. [Effect of LINE1-ORF1p overexpression on the proliferation of nephroblastoma WT_CLS1 cells]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2018; 20:501-507. [PMID: 29972127 PMCID: PMC7389950 DOI: 10.7499/j.issn.1008-8830.2018.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To prepare the LINE1-ORF1p polyclonal antibody, and to study the effect of LINE1-ORF1p on the proliferation of nephroblastoma WT_CLS1 cells. METHODS A genetic engineering method was used to achieve prokaryotic expression of LINE1-ORF1p, and rabbits were immunized with LINE1-ORF1p to prepare polyclonal antibody. Indirect ELISA was used to evaluate antibody titer, and Western blot and immunohistochemistry were used to evaluate the specific ability of antibody to recognize LINE1-ORF1p. The eukaryotic expression vector pEGFP-N1-LINE1-ORF1 was constructed and used to transfect WT_CLS1 cells. Western blot and qRT-PCR were used to measure the protein and mRNA expression of LINE1-ORF1, respectively, and cell proliferation assay and colony-forming assay were used to evaluate the effect of LINE1-ORF1p on the proliferation of WT_CLS1 cells and the formation of tumor cell clone. RESULTS The LINE1-ORF1p antibody prepared had a titer of >1:16 000 and could specifically recognize LINE1-ORF1p in cells and tumor tissue. WT_CLS1 cells transfected with pEGFP-N1-LINE1-ORF1 had significant increases in the mRNA and protein expression of LINE1-ORF1 and significantly enhanced cell proliferation ability and colony formation ability (P<0.05). CONCLUSIONS LINE1-ORF1p can promote the growth of nephroblastoma cells and the formation of tumor cell clone, and may be involved in the pathogenesis of nephroblastoma.
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Affiliation(s)
- Mei-Ling Tang
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, Beijing 100020, China.
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Giudice A, Crispo A, Grimaldi M, Polo A, Bimonte S, Capunzo M, Amore A, D'Arena G, Cerino P, Budillon A, Botti G, Costantini S, Montella M. The Effect of Light Exposure at Night (LAN) on Carcinogenesis via Decreased Nocturnal Melatonin Synthesis. Molecules 2018; 23:E1308. [PMID: 29844288 PMCID: PMC6100442 DOI: 10.3390/molecules23061308] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
In mammals, a master clock is located within the suprachiasmatic nucleus (SCN) of the hypothalamus, a region that receives input from the retina that is transmitted by the retinohypothalamic tract. The SCN controls the nocturnal synthesis of melatonin by the pineal gland that can influence the activity of the clock's genes and be involved in the inhibition of cancer development. On the other hand, in the literature, some papers highlight that artificial light exposure at night (LAN)-induced circadian disruptions promote cancer. In the present review, we summarize the potential mechanisms by which LAN-evoked disruption of the nocturnal increase in melatonin synthesis counteracts its preventive action on human cancer development and progression. In detail, we discuss: (i) the Warburg effect related to tumor metabolism modification; (ii) genomic instability associated with L1 activity; and (iii) regulation of immunity, including regulatory T cell (Treg) regulation and activity. A better understanding of these processes could significantly contribute to new treatment and prevention strategies against hormone-related cancer types.
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Affiliation(s)
- Aldo Giudice
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Anna Crispo
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Maria Grimaldi
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Andrea Polo
- Experimental Pharmacology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Sabrina Bimonte
- Division of Anesthesia and Pain Medicine, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Mario Capunzo
- Department of Medicine Surgery and Dentistry, University of Salerno, Baronissi, 84081 Salerno, Italy.
| | - Alfonso Amore
- Abdominal Surgical Oncology and Hepatobiliary Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Giovanni D'Arena
- Department of Hematology and Stem Cell Transplantation Unit, IRCCS, Cancer Referral Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno (IZSM), 80055 Portici, Napoli, Italy.
| | - Alfredo Budillon
- Experimental Pharmacology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Gerardo Botti
- Pathology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Susan Costantini
- Experimental Pharmacology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
| | - Maurizio Montella
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
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Dennin RH. Overlooked: Extrachromosomal DNA and Their Possible Impact on Whole Genome Sequencing. Malays J Med Sci 2018; 25:20-26. [PMID: 30918452 PMCID: PMC6422590 DOI: 10.21315/mjms2018.25.2.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 01/05/2018] [Indexed: 02/08/2023] Open
Abstract
Extrachromosomal (ec) DNA in eukaryotic cells has been known for decades. The structures described range from linear double stranded (ds) DNA to circular dsDNA, distinct from mitochondrial (mt) DNA. The sizes of circular forms are described from some hundred base pairs (bp) up to more than 150 kbp. The number of molecules per cell ranges from several hundred to a thousand. Semi-quantitative determinations of circular dsDNA show proportions as high as several percentages of the total DNA per cell. These ecDNA fractions harbor sequences that are known to be present in chromosomal DNA (chrDNA) too. Sequencing projects on, for example the human genome, have to take into account the ecDNA sequences which are simultaneously ascertained; corrections cannot be performed retrospectively. Concerning the results of sequencings derived from extracted whole DNA: if the ecDNA fractions contained therein are not taken into account, erroneous conclusions at the chromosomal level may result.
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Affiliation(s)
- Reinhard H Dennin
- Department of Infectious Diseases and Microbiology, University of Luebeck, UKSH, Campus Luebeck, D-23538 Luebeck, Germany
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Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla. Proc Natl Acad Sci U S A 2018; 115:E4227-E4235. [PMID: 29669918 DOI: 10.1073/pnas.1717227115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The LTR retrotransposon Steamer is a selfish endogenous element in the soft-shell clam genome that was first detected because of its dramatic amplification in bivalve transmissible neoplasia afflicting the species. We amplified and sequenced related retrotransposons from the genomic DNA of many other bivalve species, finding evidence of horizontal transfer of retrotransposons from the genome of one species to another. First, the phylogenetic tree of the Steamer-like elements from 19 bivalve species is markedly discordant with host phylogeny, suggesting frequent cross-species transfer throughout bivalve evolution. Second, sequences nearly identical to Steamer were identified in the genomes of Atlantic razor clams and Baltic clams, indicating recent transfer. Finally, a search of the National Center for Biotechnology Information sequence database revealed that Steamer-like elements are present in the genomes of completely unrelated organisms, including zebrafish, sea urchin, acorn worms, and coral. Phylogenetic incongruity, a patchy distribution, and a higher similarity than would be expected by vertical inheritance all provide evidence for multiple long-distance cross-phyla horizontal transfer events. These data suggest that over both short- and long-term evolutionary timescales, Steamer-like retrotransposons, much like retroviruses, can move between organisms and integrate new copies into new host genomes.
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Selective elimination of long INterspersed element-1 expressing tumour cells by targeted expression of the HSV-TK suicide gene. Oncotarget 2018; 8:38239-38250. [PMID: 28415677 PMCID: PMC5503529 DOI: 10.18632/oncotarget.16013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/02/2017] [Indexed: 12/31/2022] Open
Abstract
In gene therapy, effective and selective suicide gene expression is crucial. We exploited the endogenous Long INterspersed Element-1 (L1) machinery often reactivated in human cancers to integrate the Herpes Simplex Virus Thymidine Kinase (HSV-TK) suicide gene selectively into the genome of cancer cells. We developed a plasmid-based system directing HSV-TK expression only when reverse transcribed and integrated in the host genome via the endogenous L1 ORF1/2 proteins and an Alu element. Delivery of these new constructs into cells followed by Ganciclovir (GCV) treatment selectively induced mortality of L1 ORF1/2 protein expressing cancer cells, but had no effect on primary cells that do not express L1 ORF1/2. This novel strategy for selective targeting of tumour cells provides high tolerability as the HSV-TK gene cannot be expressed without reverse transcription and integration, and high selectivity as these processes take place only in cancer cells expressing high levels of functional L1 ORF1/2.
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Senescent human hematopoietic progenitors show elevated expression of transposable elements and inflammatory genes. Exp Hematol 2018; 62:33-38.e6. [PMID: 29549053 DOI: 10.1016/j.exphem.2018.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/26/2018] [Accepted: 03/04/2018] [Indexed: 12/21/2022]
Abstract
Genomic transposable elements (TEs) constitute the majority of the genome. Expression of TEs is known to activate the double-stranded RNA recognition pathway ("viral mimicry"), leading to the activation of interferon-stimulated genes, inflammation, and immune-mediated cell death. Recently, we showed that the expression of TEs is suppressed along with immune pathways in leukemic stem cells (LSCs) in acute myeloid leukemia, suggesting a potential mechanism for immune escape of LSCs. This indicated that, during oncogenesis, where there is escape from senescence, expression of TEs is suppressed. Senescence is known to activate the interferon response and inflammatory cytokines, known as the senescence-associated secretory phenotype (SASP). We characterized the transcriptome of senescent and active human hematopoietic stem and progenitor cells (HSPCs) in vivo and showed co-occurrence of overexpression of TEs, SASP genes, and gene pathways of inflammation in senescence. The percentage of circulating senescent HSPCs (s-HSPCs) did not increase with age, indicating active clearance. Induction of senescence in human HSPCs in vitro showed increased expression of TE and SASP genes. SASP is known to mediate clearance of senescent cells and active clearance of senescent cells has been shown to increase organismal fitness. We speculate that the expression of TEs in s-HSPCs could contribute to orderly clearance of the cells via activation of immune pathways, warranting further mechanistic studies. This is the first study to characterize the transcriptome of human s-HSPCs in vivo, revealing activated expression of TEs and inflammatory genes.
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