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Gutman EG, Salvio AL, Fernandes RA, Duarte LA, Raposo-Vedovi JV, Alcaraz HF, Teixeira MA, Passos GF, de Medeiros KQM, Hammerle MB, Pires KL, Vasconcelos CCF, Leon LAA, Figueiredo CP, Alves-Leon SV. Long COVID: plasma levels of neurofilament light chain in mild COVID-19 patients with neurocognitive symptoms. Mol Psychiatry 2024; 29:3106-3116. [PMID: 38678084 PMCID: PMC11449780 DOI: 10.1038/s41380-024-02554-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/29/2024]
Abstract
It is well known the potential of severe acute respiratory coronavirus type 2 (SARS-CoV-2) infection to induce post-acute sequelae, a condition called Long COVID. This syndrome includes several symptoms, but the central nervous system (CNS) main one is neurocognitive dysfunction. Recently it has been demonstrated the relevance of plasma levels of neurofilament light chain (pNfL), as a biomarker of early involvement of the CNS in COVID-19. The aim of this study was to investigate the relationship between pNfL in patients with post-acute neurocognitive symptoms and the potential of NfL as a prognostic biomarker in these cases. A group of 63 long COVID patients ranging from 18 to 59 years-old were evaluated, submitted to a neurocognitive battery assessment, and subdivided in different groups, according to results. Plasma samples were collected during the long COVID assessment and used for measurement of pNfL with the Single molecule array (SIMOA) assays. Levels of pNfL were significantly higher in long COVID patients with neurocognitive symptoms when compared to HC (p = 0.0031). Long COVID patients with cognitive impairment and fatigue symptoms presented higher pNfL levels when compared to long COVID patients without these symptoms, individually and combined (p = 0.0263, p = 0.0480, and 0.0142, respectively). Correlation analysis showed that levels of cognitive lost and exacerbation of fatigue in the neurocognitive evaluation had a significative correlation with higher pNfL levels (p = 0.0219 and 0.0255, respectively). Previous reports suggested that pNfL levels are related with higher risk of severity and predict lethality of COVID-19. Our findings demonstrate that SARS-CoV-2 infection seems to have a long-term impact on the brain, even in patients who presented mild acute disease. NfL measurements might be useful to identify CNS involvement in long COVID associated with neurocognitive symptoms and to identify who will need continuous monitoring and treatment support.
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Affiliation(s)
- Elisa Gouvea Gutman
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil
- Clinical Medicine post-graduation program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Andreza Lemos Salvio
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil
| | - Renan Amphilophio Fernandes
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil
| | - Larissa Araujo Duarte
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil
- Clinical Medicine post-graduation program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Jessica Vasques Raposo-Vedovi
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil
| | - Helena França Alcaraz
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil
| | - Milene Ataíde Teixeira
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil
| | | | | | - Mariana Beiral Hammerle
- Division of Neurology, Gaffrée and Guinle University Hospital, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, Brazil
| | - Karina Lebeis Pires
- Division of Neurology, Gaffrée and Guinle University Hospital, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, Brazil
| | | | | | | | - Soniza Vieira Alves-Leon
- Translational Neuroscience Laboratory (LabNet), Biomedical Institute, Federal University of the State of Rio de Janeiro/UNIRIO, Rio de Janeiro, RJ, ZIP CODE 20211-040, Brazil.
- Department of Neurology, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Zhuang X, Shi X, Zhao H, Shang S, Xu X, Wang X, Zheng X, He J. The expression and clinical significance of syncytin-1 in serum exosomes of hepatocellular carcinoma patients. Open Life Sci 2024; 19:20220930. [PMID: 39310811 PMCID: PMC11416070 DOI: 10.1515/biol-2022-0930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 09/25/2024] Open
Abstract
This study aimed to investigate the expression and clinical significance of syncytin-1 in the serum exosomes of hepatocellular carcinoma (HCC) patients. Serum samples were collected from 61 patients with newly diagnosed HCC and 61 healthy individuals. Exosomes were extracted from serum samples and identified using transmission electron microscopy and Western blot. The relative expression levels of syncytin-1 in exosomes were determined by real-time quantitative PCR. The protein expression levels of alpha-fetoprotein and syncytin-1 in HCC patients were detected using enzyme-linked immunosorbent assay (ELISA). Statistical analysis was performed to evaluate the sensitivity and specificity of serum exosomal syncytin-1 in diagnosing HCC. The relationships between syncytin-1 expression and clinical pathological features were analyzed using receiver operating characteristic curve analysis. The results showed that the expression level of syncytin-1 in the serum of patients with newly diagnosed HCC was significantly higher than that in the normal control group (P < 0.0001). Using pathological diagnosis as the gold standard, the sensitivity and specificity of syncytin-1 for the auxiliary diagnosis of HCC were 91.3% and 75.5%, respectively, which were significantly higher than those of alpha-fetoprotein (P < 0.0001). The relative expression level of serum exosomal syncytin-1 was significantly associated with lymph node metastasis, degree of differentiation, and CNLC staging of HCC patients (P < 0.05). In conclusion, syncytin-1 in serum exosomes has high sensitivity and specificity for diagnosing HCC and can serve as a novel tumor marker for early screening, detection, and staging of HCC.
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Affiliation(s)
- Xuewei Zhuang
- The Third Provincial Hospital Affiliated to Shandong University, 250000, Jinan, Shandong, China
| | - Xiao Shi
- Tai’an Municipal Hospital, 271000, Tai’an, Shandong, China
| | - Hui Zhao
- Tai’an Municipal Hospital, 271000, Tai’an, Shandong, China
| | - Shuai Shang
- Tai’an Municipal Hospital, 271000, Tai’an, Shandong, China
| | - Xinyu Xu
- Tai’an Municipal Hospital, 271000, Tai’an, Shandong, China
| | - Xiaomin Wang
- Dezhou Hospital of Traditional Chinese, 250000, Dezhou, Shandong, China
| | - Xin Zheng
- The Third Provincial Hospital Affiliated to Shandong University, 250000, Jinan, Shandong, China
| | - Jing He
- The Third Provincial Hospital Affiliated to Shandong University, 250000, Jinan, Shandong, China
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3
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Bo M, Manetti R, Biggio ML, Sechi LA. The Humoral Immune Response against Human Endogenous Retroviruses in Celiac Disease: A Case-Control Study. Biomedicines 2024; 12:1811. [PMID: 39200275 PMCID: PMC11351412 DOI: 10.3390/biomedicines12081811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
BACKGROUND Celiac disease (CD) is an immune-mediated disease characterized by disruptions of the small intestine. Factors such as viral and bacterial infections can trigger CD. Recently, the reactivation of Human Endogenous Retroviruses (HERVs) has also been implicated, but little is known about their specific role in patients with celiac disease. METHODS The purpose of this study is to explore the humoral immune response mounted against epitopes derived from the envelope portion of three families of HERVs (HERV-K, HERV-H, and HERV-W) in CD patients. Reactivity against the HERV-K, HERV-H, and HERV-W env-su peptides was tested by indirect ELISAs in plasma of 40 patients with celiac disease and 41 age-matched healthy subjects (HCs). RESULTS HERV-K, HERV-H, and HERV-W env-su peptides triggered different antibody responses in CD patients compared to HCs, with a stronger reactivity (p = 0.0001). CONCLUSIONS Present results show, for the first time, that epitopes of HERV-K, HERV-H, and HERV-W are more recognized in patients with CD. Taking into consideration their proinflammatory and autoimmune features, this might suggest that HERVs may contribute to the development of CD or its exacerbation in genetically predisposed subjects. Finally, to elucidate the interplay between gut inflammation and HERVs during the inflammatory process, further studies are required. Those investigations should focus on the expression levels of HERVs and their relationship with the immune response, specifically examining anti-transglutaminase 2 (TG2) antibody levels under both gluten-free and gluten-containing dietary conditions.
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Affiliation(s)
- Marco Bo
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy;
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, 07100 Sassari, Italy
| | - Roberto Manetti
- Department of Medicine, Surgery and Pharmacology, University of Sassari, 07100 Sassari, Italy; (R.M.)
| | - Maria Luigia Biggio
- Department of Medicine, Surgery and Pharmacology, University of Sassari, 07100 Sassari, Italy; (R.M.)
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy;
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, 07100 Sassari, Italy
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Gong N, Alameh MG, El-Mayta R, Xue L, Weissman D, Mitchell MJ. Enhancing in situ cancer vaccines using delivery technologies. Nat Rev Drug Discov 2024; 23:607-625. [PMID: 38951662 DOI: 10.1038/s41573-024-00974-9] [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] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
In situ cancer vaccination refers to any approach that exploits tumour antigens available at a tumour site to induce tumour-specific adaptive immune responses. These approaches hold great promise for the treatment of many solid tumours, with numerous candidate drugs under preclinical or clinical evaluation and several products already approved. However, there are challenges in the development of effective in situ cancer vaccines. For example, inadequate release of tumour antigens from tumour cells limits antigen uptake by immune cells; insufficient antigen processing by antigen-presenting cells restricts the generation of antigen-specific T cell responses; and the suppressive immune microenvironment of the tumour leads to exhaustion and death of effector cells. Rationally designed delivery technologies such as lipid nanoparticles, hydrogels, scaffolds and polymeric nanoparticles are uniquely suited to overcome these challenges through the targeted delivery of therapeutics to tumour cells, immune cells or the extracellular matrix. Here, we discuss delivery technologies that have the potential to reduce various clinical barriers for in situ cancer vaccines. We also provide our perspective on this emerging field that lies at the interface of cancer vaccine biology and delivery technologies.
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Affiliation(s)
- Ningqiang Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, Center for BioAnalytical Chemistry, Hefei National Research Center for Physical Science at the Microscale, University of Science and Technology of China, Hefei, China
| | - Mohamad-Gabriel Alameh
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | - Rakan El-Mayta
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lulu Xue
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Rich J, Bennaroch M, Notel L, Patalakh P, Alberola J, Issa F, Opolon P, Bawa O, Rondof W, Marchais A, Dessen P, Meurice G, Le-Gall M, Polrot M, Ser-Le Roux K, Mamchaoui K, Droin N, Raslova H, Maire P, Geoerger B, Pirozhkova I. DiPRO1 distinctly reprograms muscle and mesenchymal cancer cells. EMBO Mol Med 2024; 16:1840-1885. [PMID: 39009887 PMCID: PMC11319797 DOI: 10.1038/s44321-024-00097-z] [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: 01/10/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
We have recently identified the uncharacterized ZNF555 protein as a component of a productive complex involved in the morbid function of the 4qA locus in facioscapulohumeral dystrophy. Subsequently named DiPRO1 (Death, Differentiation, and PROliferation related PROtein 1), our study provides substantial evidence of its role in the differentiation and proliferation of human myoblasts. DiPRO1 operates through the regulatory binding regions of SIX1, a master regulator of myogenesis. Its relevance extends to mesenchymal tumors, such as rhabdomyosarcoma (RMS) and Ewing sarcoma, where DiPRO1 acts as a repressor via the epigenetic regulators TIF1B and UHRF1, maintaining methylation of cis-regulatory elements and gene promoters. Loss of DiPRO1 mimics the host defense response to virus, awakening retrotransposable repeats and the ZNF/KZFP gene family. This enables the eradication of cancer cells, reprogramming the cellular decision balance towards inflammation and/or apoptosis by controlling TNF-α via NF-kappaB signaling. Finally, our results highlight the vulnerability of mesenchymal cancer tumors to si/shDiPRO1-based nanomedicines, positioning DiPRO1 as a potential therapeutic target.
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Affiliation(s)
- Jeremy Rich
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Melanie Bennaroch
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Laura Notel
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Polina Patalakh
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Julien Alberola
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Fayez Issa
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Paule Opolon
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Olivia Bawa
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Windy Rondof
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Philippe Dessen
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Guillaume Meurice
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Morgane Le-Gall
- Proteom'IC facility, Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014, Paris, France
| | - Melanie Polrot
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Karine Ser-Le Roux
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013, Paris, France
| | - Nathalie Droin
- Genomic Platform, UMS AMMICA US 23 INSERM UAR 3655 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Hana Raslova
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Pascal Maire
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Iryna Pirozhkova
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France.
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France.
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Saw PE, Liu Q, Wong PP, Song E. Cancer stem cell mimicry for immune evasion and therapeutic resistance. Cell Stem Cell 2024; 31:1101-1112. [PMID: 38925125 DOI: 10.1016/j.stem.2024.06.003] [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: 06/15/2023] [Revised: 03/11/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Cancer stem cells (CSCs) are heterogeneous, possess self-renewal attributes, and orchestrate important crosstalk in tumors. We propose that the CSC state represents "mimicry" by cancer cells that leads to phenotypic plasticity. CSC mimicry is suggested as CSCs can impersonate immune cells, vasculo-endothelia, or lymphangiogenic cells to support cancer growth. CSCs facilitate both paracrine and juxtracrine signaling to prime tumor-associated immune and stromal cells to adopt pro-tumoral phenotypes, driving therapeutic resistance. Here, we outline the ingenuity of CSCs' mimicry in their quest to evade immune detection, which leads to immunotherapeutic resistance, and highlight CSC-mimicry-targeted therapeutic strategies for robust immunotherapy.
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Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan, China
| | - Qiang Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping-Pui Wong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan, China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Zenith Institute of Medical Sciences, Guangzhou 510120, China.
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7
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Wang TW, Nakanishi M. Immune surveillance of senescence: potential application to age-related diseases. Trends Cell Biol 2024:S0962-8924(24)00121-1. [PMID: 39025762 DOI: 10.1016/j.tcb.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024]
Abstract
Several lines of evidence suggest that the age-dependent accumulation of senescent cells leads to chronic tissue microinflammation, which in turn contributes to age-related pathologies. In general, senescent cells can be eliminated by the host's innate and adaptive immune surveillance system, including macrophages, NK cells, and T cells. Impaired immune surveillance leads to the accumulation of senescent cells and accelerates the aging process. Recently, senescent cells, like cancer cells, have been shown to express certain types of immune checkpoint proteins as well as non-classical immune-tolerant MHC variants, leading to immune escape from surveillance systems. Thus, immune checkpoint blockade (ICB) may be a promising strategy to enhance immune surveillance of senescence, leading to the amelioration of some age-related diseases and tissue dysfunction.
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Affiliation(s)
- Teh-Wei Wang
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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8
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Honda S, Hatamura M, Kunimoto Y, Ikeda S, Minami N. Chimeric PRMT6 protein produced by an endogenous retrovirus promoter regulates cell fate decision in mouse preimplantation embryos†. Biol Reprod 2024; 110:698-710. [PMID: 38196172 DOI: 10.1093/biolre/ioae002] [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: 05/29/2023] [Revised: 10/11/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2024] Open
Abstract
Murine endogenous retrovirus with leucine tRNA primer, also known as MERVL, is expressed during zygotic genome activation in mammalian embryos. Here we show that protein arginine N-methyltransferase 6 (Prmt6) forms a chimeric transcript with MT2B2, one of the long terminal repeat sequences of murine endogenous retrovirus with leucine tRNA primer, and is translated into an elongated chimeric protein (PRMT6MT2B2) whose function differs from that of the canonical PRMT6 protein (PRMT6CAN) in mouse preimplantation embryos. Overexpression of PRMT6CAN in fibroblast cells increased asymmetric dimethylation of the third arginine residue of both histone H2A (H2AR3me2a) and histone H4 (H4R3me2a), while overexpression of PRMT6MT2B2 increased only H2AR3me2a. In addition, overexpression of PRMT6MT2B2 in one blastomere of mouse two-cell embryos promoted cell proliferation and differentiation of the blastomere into epiblast cells at the blastocyst stage, while overexpression of PRMT6CAN repressed cell proliferation. This is the first report of the translation of a chimeric protein (PRMT6MT2B2) in mouse preimplantation embryos. Our results suggest that analyzing chimeric transcripts with murine endogenous retrovirus with leucine tRNA primer will provide insight into the relationship between zygotic genome activation and subsequent intra- and extra-cellular lineage determination.
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Affiliation(s)
- Shinnosuke Honda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Maho Hatamura
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yuri Kunimoto
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shuntaro Ikeda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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9
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Soleimani-Jelodar R, Arashkia A, Shoja Z, Akhavan S, Yarandi F, Sharifian K, Farahmand M, Nili F, Jalilvand S. The expression analysis of human endogenous retrovirus-K Env, Np9, and Rec transcripts in cervical cancer. J Med Virol 2024; 96:e29501. [PMID: 38445563 DOI: 10.1002/jmv.29501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/27/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
While infection with high-risk human papillomavirus (HPV) types is necessary for cervical cancer (CC) development, it is not enough, and other risk factors are required. Several studies have reported the activation of HERV-K in different cancers; however, the investigation of HERV-K expression levels in CC is scarce. In this study, it was hypothesized that activation of HERV-K could play an essential role in CC development. In this order, the expression levels of HERV-K Env, Np9, and Rec transcripts were investigated on 147 normal to CC uterine cervical tissues using quantitative real-time PCR. The significantly higher levels of HERV-K Env and Np9 transcripts were found in patients with cervical intraepithelial neoplasia (CIN) II-III and CC groups compared to those in the normal/CIN I group. Expression of Rec transcript was also higher only in the CC group than normal/CIN I group. Among CC patients, meaningfully higher levels of HERV-K Env and Np9 transcripts were found in patients with squamous cell carcinoma rather than in adenocarcinoma. When only the HPV 16 positive samples were investigated, it was found that the mean difference in Env and Np9 mRNA levels was meaningfully higher among precancer lesions and the cancer group in comparison with the normal group. However, the Rec mRNA level showed no significant differences. The association between the expression of HERV-K genes was investigated, and a significant positive correlation of Env expression with Np9 transcript was found only in the group with precancer lesions (R = 0.6, p = 0.0037). Moreover, a significant positive correlation was found between Rec and Np9 transcripts in patients with normal cervix tissues (R = 0.26, p = 0.033). However, no correlations were observed between the expression of Env and Rec in the three groups. In conclusion, our results showed that HERV-K transcripts, especially Env and Np9, upregulated during cervical lesion progression. These findings highlight the potential use of HERV-K Env and Np9 as biomarkers for CC diagnosis and prognosis. Further investigation is needed to determine the clinical utility of these markers and whether targeting HERV-K oncogenes could be a viable therapeutic strategy for CC.
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Affiliation(s)
- Rahim Soleimani-Jelodar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Arashkia
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Setareh Akhavan
- Department of Gynecology Oncology, Imam Khomeini Hospital Complex, Valiasr Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Yarandi
- Department of Obstetrics and Gynecology, Yas Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kimia Sharifian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farahmand
- Research Center for Emergency and Disaster Society of the Islamic Republic of Iran, Tehran, Iran
| | - Fatemeh Nili
- Department of Pathology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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10
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Ramirez P, Sun W, Kazempour Dehkordi S, Zare H, Fongang B, Bieniek KF, Frost B. Nanopore-based DNA long-read sequencing analysis of the aged human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark loci," are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements ("jumping genes") as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer's disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer's disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer's disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer's disease neuropathology.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri
| | - Shiva Kazempour Dehkordi
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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11
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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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12
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Tavakolian S, Faghihloo E. The prevalence of varicella zoster virus, herpes simplex virus type 2, and human papillomavirus in breast cancerous tissues and their adjacent ones in Iran. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2023; 28:65. [PMID: 38024515 PMCID: PMC10668219 DOI: 10.4103/jrms.jrms_475_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 02/25/2023] [Accepted: 07/10/2023] [Indexed: 12/01/2023]
Abstract
Background Breast cancer is the second type of cancer in the world. Some internal and external risk factors, especially infection diseases, can progress breast cancer. As the relation between varicella zoster virus (VZV), human papillomavirus (HPV), herpes simplex virus type 2 (HSV-2), and breast cancer has not been understood, it was attempting to find the effect of these viruses and breast cancer in this study. Materials and Methods We collected 40 breast cancer and 50 healthy adjacent tissues from Taleghani and Imam Hossein Hospital, Tehran, Iran, in 3 years starting in 2017. After extracting DNA from breast tissues, multiplex polymerase chain reaction (PCR), nested PCR, and PCR were done to analyze the prevalence of HSV-2, VZV, and HPV. Results Our results showed that HPV may be one of the important causes of breast cancer. Nested PCR illustrated nine breast cancerous tissues (mean age: 43) and three healthy adjacent ones (mean age: 41) were infected by HPV. Phylogenetic analysis illustrated that all of the infected HPV cancerous and healthy tissues were HPV 18 (except two healthy samples infected with HPV 6). Nevertheless, there were not any infected tissues by HSV-2 and VZV. Conclusion It seems that HPV virus type 18 can have high prevalence in breast cancerous tissues in comparison with healthy adjacent ones, and it is likely to have an effect on breast cancer progression. However, the opposite trend is true for HSV-2 and VZV as we did not find any differences between different kinds of breast tissues.
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Affiliation(s)
- Shaian Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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13
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Sfera A, Rahman L, Zapata-Martín Del Campo CM, Kozlakidis Z. Long COVID as a Tauopathy: Of "Brain Fog" and "Fusogen Storms". Int J Mol Sci 2023; 24:12648. [PMID: 37628830 PMCID: PMC10454863 DOI: 10.3390/ijms241612648] [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: 07/13/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Long COVID, also called post-acute sequelae of SARS-CoV-2, is characterized by a multitude of lingering symptoms, including impaired cognition, that can last for many months. This symptom, often called "brain fog", affects the life quality of numerous individuals, increasing medical complications as well as healthcare expenditures. The etiopathogenesis of SARS-CoV-2-induced cognitive deficit is unclear, but the most likely cause is chronic inflammation maintained by a viral remnant thriving in select body reservoirs. These viral sanctuaries are likely comprised of fused, senescent cells, including microglia and astrocytes, that the pathogen can convert into neurotoxic phenotypes. Moreover, as the enteric nervous system contains neurons and glia, the virus likely lingers in the gastrointestinal tract as well, accounting for the intestinal symptoms of long COVID. Fusogens are proteins that can overcome the repulsive forces between cell membranes, allowing the virus to coalesce with host cells and enter the cytoplasm. In the intracellular compartment, the pathogen hijacks the actin cytoskeleton, fusing host cells with each other and engendering pathological syncytia. Cell-cell fusion enables the virus to infect the healthy neighboring cells. We surmise that syncytia formation drives cognitive impairment by facilitating the "seeding" of hyperphosphorylated Tau, documented in COVID-19. In our previous work, we hypothesized that the SARS-CoV-2 virus induces premature endothelial senescence, increasing the permeability of the intestinal and blood-brain barrier. This enables the migration of gastrointestinal tract microbes and/or their components into the host circulation, eventually reaching the brain where they may induce cognitive dysfunction. For example, translocated lipopolysaccharides or microbial DNA can induce Tau hyperphosphorylation, likely accounting for memory problems. In this perspective article, we examine the pathogenetic mechanisms and potential biomarkers of long COVID, including microbial cell-free DNA, interleukin 22, and phosphorylated Tau, as well as the beneficial effect of transcutaneous vagal nerve stimulation.
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Affiliation(s)
- Adonis Sfera
- Paton State Hospital, 3102 Highland Ave, Patton, CA 92369, USA
- School of Behavioral Health, Loma Linda University, 11139 Anderson St., Loma Linda, CA 92350, USA
- Department of Psychiatry, University of California, Riverside 900 University Ave, Riverside, CA 92521, USA
| | - Leah Rahman
- Department of Neuroscience, University of Oregon, 222 Huestis Hall, Eugene, OR 97401, USA
| | | | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France
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14
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Sibarov DA, Tsytsarev V, Volnova A, Vaganova AN, Alves J, Rojas L, Sanabria P, Ignashchenkova A, Savage ED, Inyushin M. Arc protein, a remnant of ancient retrovirus, forms virus-like particles, which are abundantly generated by neurons during epileptic seizures, and affects epileptic susceptibility in rodent models. Front Neurol 2023; 14:1201104. [PMID: 37483450 PMCID: PMC10361770 DOI: 10.3389/fneur.2023.1201104] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/02/2023] [Indexed: 07/25/2023] Open
Abstract
A product of the immediate early gene Arc (Activity-regulated cytoskeleton-associated protein or Arc protein) of retroviral ancestry resides in the genome of all tetrapods for millions of years and is expressed endogenously in neurons. It is a well-known protein, very important for synaptic plasticity and memory consolidation. Activity-dependent Arc expression concentrated in glutamatergic synapses affects the long-time synaptic strength of those excitatory synapses. Because it modulates excitatory-inhibitory balance in a neuronal network, the Arc gene itself was found to be related to the pathogenesis of epilepsy. General Arc knockout rodent models develop a susceptibility to epileptic seizures. Because of activity dependence, synaptic Arc protein synthesis also is affected by seizures. Interestingly, it was found that Arc protein in synapses of active neurons self-assemble in capsids of retrovirus-like particles, which can transfer genetic information between neurons, at least across neuronal synaptic boutons. Released Arc particles can be accumulated in astrocytes after seizures. It is still not known how capsid assembling and transmission timescale is affected by seizures. This scientific field is relatively novel and is experiencing swift transformation as it grapples with difficult concepts in light of evolving experimental findings. We summarize the emergent literature on the subject and also discuss the specific rodent models for studying Arc effects in epilepsy. We summarized both to clarify the possible role of Arc-related pseudo-viral particles in epileptic disorders, which may be helpful to researchers interested in this growing area of investigation.
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Affiliation(s)
- Dmitry A. Sibarov
- Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vassiliy Tsytsarev
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Anna Volnova
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anastasia N. Vaganova
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Janaina Alves
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | - Legier Rojas
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | - Priscila Sanabria
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | | | | | - Mikhail Inyushin
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
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15
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Lee KH, Hwang HJ, Im YJ, Nam AR, Lee JW, Cho JY. New oncogenic functions of LINE1 retroelement as a ceRNA for tumor suppressive microRNA miR-126 on ENPP5. PLoS One 2023; 18:e0286814. [PMID: 37352273 PMCID: PMC10289412 DOI: 10.1371/journal.pone.0286814] [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: 01/30/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
Retroelements (REs) had been considered 'Junk' until the encyclopedia of DNA elements (ENCODE) project demonstrated that most genome is functional. Although the function of retroelements has been reported in diverse cancers including human breast cancer (HBC) and subtypes, only a few studies have suggested the putative functions of REs via their random genome integration. A canine mammary tumor (CMT) has been highlighted due to the similarities in molecular and pathophysiology with HBC. This study investigated the putative roles of REs common in both HBC and CMT. The human LINE and HERV-K sequences harbor many miRNAs responsive elements (MREs) for tumor-suppressive miRNA such as let-7. We also observed that various MREs are exist in the ERV and LINE highly expressed in the transcriptome data of CMT as well as HBC sets. MREs against miR-126 were highly expressed in both HBC and CMT while the levels of miR-126 were down-regulated. Oppositely, the expression of miR-126 target genes was significantly up-regulated in the cancers. Moreover, cancer patients with an increased level of miR-126 showed better overall survival. The expression of ENPP5, a putative miR-126 target gene, was downregulated by miR-126 mimic. Importantly, overexpression of LINE fragment significantly suppressed miR-126 function on the target gene expression. We propose the functional role of REs expression in tumorigenesis as competing endogenous RNAs (ceRNA) against tumor-suppressive miRNAs. This study provided pieces of evidence that LINE expression, even partial and fragmented, have a regulatory function in ENPP5 gene expression via the competition with miR-126.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Hyeon-Ji Hwang
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Yeo-Jin Im
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - A-Reum Nam
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
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16
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Jain V, Baraniya D, El-Hadedy DE, Chen T, Slifker M, Alakwaa F, Cai KQ, Chitrala KN, Fundakowski C, Al-Hebshi NN. Integrative Metatranscriptomic Analysis Reveals Disease-specific Microbiome-host Interactions in Oral Squamous Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:807-820. [PMID: 37377901 PMCID: PMC10166004 DOI: 10.1158/2767-9764.crc-22-0349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/05/2023] [Accepted: 04/13/2023] [Indexed: 06/29/2023]
Abstract
Studies on the microbiome of oral squamous cell carcinoma (OSCC) have been limited to 16S rRNA gene sequencing. Here, laser microdissection coupled with brute-force, deep metatranscriptome sequencing was employed to simultaneously characterize the microbiome and host transcriptomes and predict their interaction in OSCC. The analysis involved 20 HPV16/18-negative OSCC tumor/adjacent normal tissue pairs (TT and ANT) along with deep tongue scrapings from 20 matched healthy controls (HC). Standard bioinformatic tools coupled with in-house algorithms were used to map, analyze, and integrate microbial and host data. Host transcriptome analysis identified enrichment of known cancer-related gene sets, not only in TT versus ANT and HC, but also in the ANT versus HC contrast, consistent with field cancerization. Microbial analysis identified a low abundance yet transcriptionally active, unique multi-kingdom microbiome in OSCC tissues predominated by bacteria and bacteriophages. HC showed a different taxonomic profile yet shared major microbial enzyme classes and pathways with TT/ANT, consistent with functional redundancy. Key taxa enriched in TT/ANT compared with HC were Cutibacterium acnes, Malassezia restricta, Human Herpes Virus 6B, and bacteriophage Yuavirus. Functionally, hyaluronate lyase was overexpressed by C. acnes in TT/ANT. Microbiome-host data integration revealed that OSCC-enriched taxa were associated with upregulation of proliferation-related pathways. In a preliminary in vitro validation experiment, infection of SCC25 oral cancer cells with C. acnes resulted in upregulation of MYC expression. The study provides a new insight into potential mechanisms by which the microbiome can contribute to oral carcinogenesis, which can be validated in future experimental studies. Significance Studies have shown that a distinct microbiome is associated with OSCC, but how the microbiome functions within the tumor interacts with the host cells remains unclear. By simultaneously characterizing the microbial and host transcriptomes in OSCC and control tissues, the study provides novel insights into microbiome-host interactions in OSCC which can be validated in future mechanistic studies.
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Affiliation(s)
- Vinay Jain
- Oral Microbiome Research Laboratory, Department of Oral Health Sciences, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, Pennsylvania
- Low level Radiation Research Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Divyashri Baraniya
- Oral Microbiome Research Laboratory, Department of Oral Health Sciences, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, Pennsylvania
| | - Doaa E. El-Hadedy
- Oral Microbiome Research Laboratory, Department of Oral Health Sciences, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, Pennsylvania
| | - Tsute Chen
- Department of Microbiology, Forsyth Institute, Cambridge, Massachusetts
| | - Michael Slifker
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Fadhl Alakwaa
- Department of Internal Medicine, Nephrology Division, University of Michigan, Ann Arbor, Michigan
| | - Kathy Q. Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kumaraswamy N. Chitrala
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | | | - Nezar N. Al-Hebshi
- Oral Microbiome Research Laboratory, Department of Oral Health Sciences, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, Pennsylvania
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania
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17
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A Systems Biology Approach on the Regulatory Footprint of Human Endogenous Retroviruses (HERVs). Diseases 2022; 10:diseases10040098. [PMID: 36412592 PMCID: PMC9680359 DOI: 10.3390/diseases10040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. ENCODE Project has offered a wealth of epigenetic data based on omics technologies. I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. On the one side, HERVs are in 1 out of 9 cCREs (>100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. On the other side, promoter-associated HERV cCREs are present adjacent to (in a 200 bp window) the transcription start sites of 256 human genes. Regulatory network production, followed by centrality analysis led to the discovery of 90 core genes containing HERV-associated promoters. Pathway analysis on the core network genes and their immediate neighbors revealed a regulatory footprint that, among others, is associated with inflammation, chemokine signaling and response to viral infection. Collectively, these results support the concept that the expansion of regulatory sequences derived from HERVs is critical for epigenetic innovation that may have wired together genes into novel transcriptional networks with critical roles in cellular physiology and pathology.
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18
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Transcriptome Analysis of Human Endogenous Retroviruses at Locus-Specific Resolution in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14184433. [PMID: 36139593 PMCID: PMC9497127 DOI: 10.3390/cancers14184433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/28/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lung cancer is the second most commonly diagnosed cancer and the leading cause of cancer deaths worldwide. Among its subtypes, lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are the most common, accounting for more than 85% of lung cancer diagnoses. Despite the incredible efforts and recent advances in lung cancer treatments, patients affected by this condition still have a poor prognosis. Therefore, novel diagnostic biomarkers are needed. Recently, a class of transposable elements called human endogenous retroviruses (HERVs) has been found to be implicated in cancer development and later employed as novel biomarkers for several tumor types. In this study, we first ever characterized the expression of HERVs at genomic locus-specific resolution in both LUAD and LUSC cohorts available in The Cancer Genome Atlas (TCGA). Precisely, (i) we profiled the expression of HERVs in TCGA-LUAD and TCGA-LUSC cohorts; (ii) we identified the dysregulated HERVs in both lung cancer subtypes; (iii) we evaluated the impact of the dysregulated HERVs on signaling pathways using neural network-based predictions; and (iv) we assessed their association with overall survival (OS) and relapse-free survival (RFS). In conclusion, we believe this study may help elucidate another layer of dysregulation that occurs in lung cancer involving HERVs, paving the way for identifying novel lung cancer biomarkers.
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19
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Ilse V, Scholz R, Wermann M, Naumann M, Staege MS, Roßner S, Cynis H. Immunogenicity of the Envelope Surface Unit of Human Endogenous Retrovirus K18 in Mice. Int J Mol Sci 2022; 23:ijms23158330. [PMID: 35955468 PMCID: PMC9369184 DOI: 10.3390/ijms23158330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
The triggers for the development of multiple sclerosis (MS) have not been fully understood to date. One hypothesis proposes a viral etiology. Interestingly, viral proteins from human endogenous retroviruses (HERVs) may play a role in the pathogenesis of MS. Allelic variants of the HERV-K18 env gene represent a genetic risk factor for MS, and the envelope protein is considered to be an Epstein–Barr virus-trans-activated superantigen. To further specify a possible role for HERV-K18 in MS, the present study examined the immunogenicity of the purified surface unit (SU). HERV-K18(SU) induced envelope-specific plasma IgG in immunized mice and triggered proliferation of T cells isolated from these mice. It did not trigger phenotypic changes in a mouse model of experimental autoimmune encephalomyelitis. Further studies are needed to investigate the underlying mechanisms of HERV-K18 interaction with immune system regulators in more detail.
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Affiliation(s)
- Victoria Ilse
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Rebekka Scholz
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Michael Wermann
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Marcel Naumann
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany;
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstraße 19, 04103 Leipzig, Germany;
| | - Holger Cynis
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
- Correspondence: ; Tel.: +49-345-13142835; Fax: +49-345-13142801
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20
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Li J, Lin J, Lin JR, Farris M, Robbins L, Andrada L, Grohol B, Nong S, Liu Y. Dolutegravir Inhibits Proliferation and Motility of BT-20 Tumor Cells Through Inhibition of Human Endogenous Retrovirus Type K. Cureus 2022; 14:e26525. [PMID: 35936147 PMCID: PMC9345775 DOI: 10.7759/cureus.26525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/03/2022] [Indexed: 11/25/2022] Open
Abstract
Increasing evidence points to the role of endogenous retroviruses (ERVs) in driving cancer cell proliferation. The purpose of this study was to explore the possibility of repurposing antiretroviral agents to inhibit ERVs as a new approach to cancer treatment. We found that an integrase strand-transfer inhibitor, dolutegravir (DTG), effectively inhibited the proliferation of multiple cancer cell lines and its antiproliferative potency was positively correlated with the expression levels of the human endogenous retrovirus type K (HERV-K). DTG inhibited the expression of HERV-K in multiple human cancer cell lines and the mouse mammary tumor virus (MMTV) in the murine 4T1 mammary cancer cell line. We chose the fast-growing BT-20 cell line as a model to study the in vitro antiproliferative mechanisms of DTG. BT-20 cells overexpressing both HERV-K env and pol genes became more resistant to DTG than cells transduced with vector alone. Knockdown of HERV-K also increased DTG resistance of BT-20 cells. The antiproliferative effect of DTG correlated with enhanced expression of E-cadherin and reduction in cell motility and invasiveness. Surprisingly, DTG stimulated expression of the env gene of MMTV in vivo and promoted metastasis of 4T1 tumor cells to the lungs. Taken together, our data support the role of ERVs in tumor development and encourage the further search for antiretroviral agents to treat malignancies in which ERVs are active.
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21
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Gurova K. Can aggressive cancers be identified by the "aggressiveness" of their chromatin? Bioessays 2022; 44:e2100212. [PMID: 35452144 DOI: 10.1002/bies.202100212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022]
Abstract
Phenotypic plasticity is a crucial feature of aggressive cancer, providing the means for cancer progression. Stochastic changes in tumor cell transcriptional programs increase the chances of survival under any condition. I hypothesize that unstable chromatin permits stochastic transitions between transcriptional programs in aggressive cancers and supports non-genetic heterogeneity of tumor cells as a basis for their adaptability. I present a mechanistic model for unstable chromatin which includes destabilized nucleosomes, mobile chromatin fibers and random enhancer-promoter contacts, resulting in stochastic transcription. I suggest potential markers for "unsettled" chromatin in tumors associated with poor prognosis. Although many of the characteristics of unstable chromatin have been described, they were mostly used to explain changes in the transcription of individual genes. I discuss approaches to evaluate the role of unstable chromatin in non-genetic tumor cell heterogeneity and suggest using the degree of chromatin instability and transcriptional noise in tumor cells to predict cancer aggressiveness.
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Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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22
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Targeting the gut and tumor microbiota in cancer. Nat Med 2022; 28:690-703. [PMID: 35440726 DOI: 10.1038/s41591-022-01779-2] [Citation(s) in RCA: 193] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
Abstract
Microorganisms within the gut and other niches may contribute to carcinogenesis, as well as shaping cancer immunosurveillance and response to immunotherapy. Our understanding of the complex relationship between different host-intrinsic microorganisms, as well as the multifaceted mechanisms by which they influence health and disease, has grown tremendously-hastening development of novel therapeutic strategies that target the microbiota to improve treatment outcomes in cancer. Accordingly, the evaluation of a patient's microbial composition and function and its subsequent targeted modulation represent key elements of future multidisciplinary and precision-medicine approaches. In this Review, we outline the current state of research toward harnessing the microbiome to better prevent and treat cancer.
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23
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Lamont RJ, Fitzsimonds ZR, Wang H, Gao S. Role of Porphyromonas gingivalis in oral and orodigestive squamous cell carcinoma. Periodontol 2000 2022; 89:154-165. [PMID: 35244980 DOI: 10.1111/prd.12425] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oral and esophageal squamous cell carcinomas harbor a diverse microbiome that differs compositionally from precancerous and healthy tissues. Though causality is yet to be definitively established, emerging trends implicate periodontal pathogens such as Porphyromonas gingivalis as associated with the cancerous state. Moreover, infection with P. gingivalis correlates with a poor prognosis, and P. gingivalis is oncopathogenic in animal models. Mechanistically, properties of P. gingivalis that have been established in vitro and could promote tumor development include induction of a dysbiotic inflammatory microenvironment, inhibition of apoptosis, increased cell proliferation, enhanced angiogenesis, activation of epithelial-to-mesenchymal transition, and production of carcinogenic metabolites. The microbial community context is also relevant to oncopathogenicity, and consortia of P. gingivalis and Fusobacterium nucleatum are synergistically pathogenic in oral cancer models in vivo. In contrast, oral streptococci, such as Streptococcus gordonii, can antagonize protumorigenic epithelial cell phenotypes induced by P. gingivalis, indicating functionally specialized roles for bacteria in oncogenic communities. Consistent with the notion of the bacterial community constituting the etiologic unit, metatranscriptomic data indicate that functional, rather than compositional, properties of the tumor-associated communities have more relevance to cancer development. A consistent association of P. gingivalis with oral and orodigestive carcinoma could have diagnostic potential for early detection of these conditions that have a high incidence and low survival rates.
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Affiliation(s)
- Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Zackary R Fitzsimonds
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Huizhi Wang
- Department of Oral and Craniofacial Molecular Biology, VCU School of Dentistry, Richmond, Virginia, USA
| | - Shegan Gao
- Henan Key Laboratory of Cancer Epigenetics, Cancer Institute, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
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24
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Zhang H, Ma H, Yang X, Fan L, Tian S, Niu R, Yan M, Zheng M, Zhang S. Cell Fusion-Related Proteins and Signaling Pathways, and Their Roles in the Development and Progression of Cancer. Front Cell Dev Biol 2022; 9:809668. [PMID: 35178400 PMCID: PMC8846309 DOI: 10.3389/fcell.2021.809668] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/22/2021] [Indexed: 12/16/2022] Open
Abstract
Cell fusion is involved in many physiological and pathological processes, including gamete binding, and cancer development. The basic processes of cell fusion include membrane fusion, cytoplasmic mixing, and nuclear fusion. Cell fusion is regulated by different proteins and signaling pathways. Syncytin-1, syncytin-2, glial cell missing 1, galectin-1 and other proteins (annexins, myomaker, myomerger etc.) involved in cell fusion via the cyclic adenosine-dependent protein kinase A, mitogen-activated protein kinase, wingless/integrase-1, and c-Jun N-terminal kinase signaling pathways. In the progression of malignant tumors, cell fusion is essential during the organ-specific metastasis, epithelial-mesenchymal transformation, the formation of cancer stem cells (CSCs), cancer angiogenesis and cancer immunity. In addition, diploid cells can be induced to form polyploid giant cancer cells (PGCCs) via cell fusion under many kinds of stimuli, including cobalt chloride, chemotherapy, radiotherapy, and traditional Chinese medicine. PGCCs have CSC-like properties, and the daughter cells derived from PGCCs have a mesenchymal phenotype and exhibit strong migration, invasion, and proliferation abilities. Therefore, exploring the molecular mechanisms of cell fusion can enable us better understand the development of malignant tumors. In this review, the basic process of cell fusion and its significance in cancer is discussed.
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Affiliation(s)
- Hao Zhang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hong Ma
- Tianjin Union Medical Center, Nankai University, Tianjin, China
| | - Xiaohui Yang
- Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Linlin Fan
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shifeng Tian
- Graduate School, Tianjin Medical University, Tianjin, China
| | - Rui Niu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Man Yan
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Minying Zheng
- Tianjin Union Medical Center, Nankai University, Tianjin, China
| | - Shiwu Zhang
- Tianjin Union Medical Center, Nankai University, Tianjin, China
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25
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Wei Y, Wei H, Wei Y, Tan A, Chen X, Liao X, Xie B, Wei X, Li L, Liu Z, Dai S, Khan A, Pang X, Hassan NMA, Xiong K, Zhang K, Leng J, Lv J, Hu Y. Screening and Identification of Human Endogenous Retrovirus-K mRNAs for Breast Cancer Through Integrative Analysis of Multiple Datasets. Front Oncol 2022; 12:820883. [PMID: 35265522 PMCID: PMC8900282 DOI: 10.3389/fonc.2022.820883] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Human endogenous retroviruses (HERVs) make up 8% of the human genome. HERVs are biologically active elements related to multiple diseases. HERV-K, a subfamily of HERVs, has been associated with certain types of cancer and suggested as an immunologic target in some tumors. The expression levels of HERV-K in breast cancer (BCa) have been studied as biomarkers and immunologic therapeutic targets. However, HERV-K has multiple copies in the human genome, and few studies determined the transcriptional profile of HERV-K copies across the human genome for BCa. Methods Ninety-one HERV-K indexes with entire proviral sequences were used as the reference database. Nine raw sequencing datasets with 243 BCa and 137 control samples were mapped to this database by Salmon software. The differential proviral expression across several groups was analyzed by DESeq2 software. Results First, the clustering of each dataset demonstrated that these 91 HERV-K proviruses could well cluster the BCa and control samples when the normal controls were normal cells or healthy donor tissues. Second, several common HERV-K proviruses that are closely related with BCa risk were significantly differentially expressed (padj < 0.05 and absolute log2FC > 1.5) in the tissues and cell lines. Additionally, almost all the HERV-K proviruses had higher expression in BCa tissue than in healthy donor tissue. Notably, we first found the expression of 17p13.1 provirus that located with TP53 should regulate TP53 expression in ER+ and HER2+ BCa. Conclusion The expression profiling of these 91 HERV-K proviruses can be used as biomarkers to distinguish individuals with BCa and healthy controls. Some proviruses, especially 17p13.1, were strongly associated with BCa risk. The results suggest that HERV-K expression profiles may be appropriate biomarkers and targets for BCa.
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Affiliation(s)
- Yongzhong Wei
- Guangxi Clinical Center for AIDS Prevention and Treatment, Chest Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
| | - Huilin Wei
- Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Yinfeng Wei
- Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Aihua Tan
- Department of Chemotherapy, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Xiuyong Chen
- Guangxi Clinical Center for AIDS Prevention and Treatment, Chest Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
| | - Xiuquan Liao
- Guangxi Clinical Center for AIDS Prevention and Treatment, Chest Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
| | - Bo Xie
- Guangxi Medical University School of Information and Management, Nanning, China
| | - Xihua Wei
- Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Lanxiang Li
- Basic Medical College of Guangxi Medical University, Nanning, China
| | - Zengjing Liu
- Guangxi Medical University School of Information and Management, Nanning, China
| | - Shengkang Dai
- Cancer Hospital, Guangxi Medical University, Nanning, China
| | - Adil Khan
- Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Xianwu Pang
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, China
| | - Nada M. A. Hassan
- Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Kai Xiong
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, China
| | - Kai Zhang
- Guangxi Clinical Center for AIDS Prevention and Treatment, Chest Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
| | - Jing Leng
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases With Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, China
| | - Jiannan Lv
- Guangxi Clinical Center for AIDS Prevention and Treatment, Chest Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
- *Correspondence: Yanling Hu, ; Jiannan Lv,
| | - Yanling Hu
- Institute of Life Sciences, Guangxi Medical University, Nanning, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- *Correspondence: Yanling Hu, ; Jiannan Lv,
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26
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Gerber JP, Russ J, Chandrasekar V, Offermann N, Lee HM, Spear S, Guzzi N, Maida S, Pattabiraman S, Zhang R, Kayvanjoo AH, Datta P, Kasturiarachchi J, Sposito T, Izotova N, Händler K, Adams PD, Marafioti T, Enver T, Wenzel J, Beyer M, Mass E, Bellodi C, Schultze JL, Capasso M, Nimmo R, Salomoni P. Aberrant chromatin landscape following loss of the H3.3 chaperone Daxx in haematopoietic precursors leads to Pu.1-mediated neutrophilia and inflammation. Nat Cell Biol 2021; 23:1224-1239. [PMID: 34876685 PMCID: PMC8683376 DOI: 10.1038/s41556-021-00774-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/14/2021] [Indexed: 12/25/2022]
Abstract
Defective silencing of retrotransposable elements has been linked to inflammageing, cancer and autoimmune diseases. However, the underlying mechanisms are only partially understood. Here we implicate the histone H3.3 chaperone Daxx, a retrotransposable element repressor inactivated in myeloid leukaemia and other neoplasms, in protection from inflammatory disease. Loss of Daxx alters the chromatin landscape, H3.3 distribution and histone marks of haematopoietic progenitors, leading to engagement of a Pu.1-dependent transcriptional programme for myelopoiesis at the expense of B-cell differentiation. This causes neutrophilia and inflammation, predisposing mice to develop an autoinflammatory skin disease. While these molecular and phenotypic perturbations are in part reverted in animals lacking both Pu.1 and Daxx, haematopoietic progenitors in these mice show unique chromatin and transcriptome alterations, suggesting an interaction between these two pathways. Overall, our findings implicate retrotransposable element silencing in haematopoiesis and suggest a cross-talk between the H3.3 loading machinery and the pioneer transcription factor Pu.1.
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Grants
- P01 AG031862 NIA NIH HHS
- C416/A25145 Cancer Research UK
- C16420/A18066 Cancer Research UK
- MC_U132670601 Medical Research Council
- C33499/A20265 Cancer Research UK
- Deutsches Zentrum für Neurodegenerative Erkrankungen (German Center for Neurodegenerative Diseases)
- Worldwide Cancer Research
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- EC | EC Seventh Framework Programm | FP7 People: Marie-Curie Actions (FP7-PEOPLE - Specific Programme People Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster Immunosensation2
- Aging and Metabolic Programming (AMPro) Consortium from Helmholtz
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster Immunosensation2ImmunoSensation2
- Cancer Research UK (CRUK)
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster ImmunoSensation2
- EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: Ideas Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Wilhelm Sander-Stiftung (Wilhelm Sander Foundation)
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048, Excellence Cluster ImmunoSensation2 Aging and Metabolic Programming (AMPro) Consortium from Helmholtz
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Affiliation(s)
- Julia P Gerber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jenny Russ
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Nina Offermann
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Hang-Mao Lee
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sarah Spear
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Simona Maida
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Ruoyu Zhang
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Amir H Kayvanjoo
- Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Preeta Datta
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | | | - Teresa Sposito
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Natalia Izotova
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
| | - Teresa Marafioti
- Department of Cancer Biology, UCL Cancer Institute, London, UK
- Department of Pathology, University College London, London, UK
| | - Tariq Enver
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jörg Wenzel
- Department of Dermatology and Allergy, University Medical Center, Bonn, Germany
| | - Marc Beyer
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Elvira Mass
- Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Melania Capasso
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rachael Nimmo
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- Department of Cancer Biology, UCL Cancer Institute, London, UK.
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Helmy M, Selvarajoo K. Systems Biology to Understand and Regulate Human Retroviral Proinflammatory Response. Front Immunol 2021; 12:736349. [PMID: 34867957 PMCID: PMC8635014 DOI: 10.3389/fimmu.2021.736349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/21/2021] [Indexed: 01/13/2023] Open
Abstract
The majority of human genome are non-coding genes. Recent research have revealed that about half of these genome sequences make up of transposable elements (TEs). A branch of these belong to the endogenous retroviruses (ERVs), which are germline viral infection that occurred over millions of years ago. They are generally harmless as evolutionary mutations have made them unable to produce viral agents and are mostly epigenetically silenced. Nevertheless, ERVs are able to express by still unknown mechanisms and recent evidences have shown links between ERVs and major proinflammatory diseases and cancers. The major challenge is to elucidate a detailed mechanistic understanding between them, so that novel therapeutic approaches can be explored. Here, we provide a brief overview of TEs, human ERVs and their links to microbiome, innate immune response, proinflammatory diseases and cancer. Finally, we recommend the employment of systems biology approaches for future HERV research.
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Affiliation(s)
- Mohamed Helmy
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON, Canada
| | - Kumar Selvarajoo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Synthetic Biology Translational Research Program & SynCTI, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Kent Ridge, Singapore
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28
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Tavakolian S, Goudarzi H, Moridi A, Faghihloo E. Analysing the HERV-K env, np9, rec and gag expression in cervical tissues. New Microbes New Infect 2021; 44:100936. [PMID: 34621524 PMCID: PMC8484807 DOI: 10.1016/j.nmni.2021.100936] [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] [Indexed: 10/26/2022] Open
Abstract
Cervical cancer is considered to be the fourth common cancer. It is assumed that numerous risk factors, especially infectious ones, can have a detrimental effect on cervical cancer. In this study, we evaluated the expression of Herv-K env, np9, rec and gag in cervical tissues. After RNA extraction and cDNA sensitizing of 12 cervical cancer tissues and CIN3, 51 CIN1,2 and 18 normal ones, Herv-K env, np9, rec and gag were assessed using quantitative real-time PCR analysis. There was a decrease in the level of HERV-K env expression in cervical cancer and CIN 1-3 in compression with normal tissues. Cervical cancer and CIN3 indicated the most increase in expression. Meanwhile, we observed an increase in gag and rec expression in CIN 1,2; although cervical cancer and CIN 3 had a decrease in rec and gag expression, we did not report any changes in np expression. In conclusion, given the relationship between HERV-associated genes and cervical cancer, our study suggests that these genes can be useful for cancer diagnosis. However, further investigations are needed to provide a better perspective about the effectiveness of these genes in the diagnostic strategies of gastrointestinal cancer. These results are just an observation that could open a wider investigation to test the correlation between the expression of these genes and cervical cancer.
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Affiliation(s)
- S Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - H Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Moridi
- Clinical Research Development Center, Mahdiyeh Educational Hospital, Shahid Beheshti University Of Medical Sciences, Tehran, Iran
| | - E Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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29
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Marongiu L, Allgayer H. Viruses in colorectal cancer. Mol Oncol 2021; 16:1423-1450. [PMID: 34514694 PMCID: PMC8978519 DOI: 10.1002/1878-0261.13100] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/15/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Increasing evidence suggests that microorganisms might represent at least highly interesting cofactors in colorectal cancer (CRC) oncogenesis and progression. Still, associated mechanisms, specifically in colonocytes and their microenvironmental interactions, are still poorly understood. Although, currently, at least seven viruses are being recognized as human carcinogens, only three of these – Epstein–Barr virus (EBV), human papillomavirus (HPV) and John Cunningham virus (JCV) – have been described, with varying levels of evidence, in CRC. In addition, cytomegalovirus (CMV) has been associated with CRC in some publications, albeit not being a fully acknowledged oncovirus. Moreover, recent microbiome studies set increasing grounds for new hypotheses on bacteriophages as interesting additional modulators in CRC carcinogenesis and progression. The present Review summarizes how particular groups of viruses, including bacteriophages, affect cells and the cellular and microbial microenvironment, thereby putatively contributing to foster CRC. This could be achieved, for example, by promoting several processes – such as DNA damage, chromosomal instability, or molecular aspects of cell proliferation, CRC progression and metastasis – not necessarily by direct infection of epithelial cells only, but also by interaction with the microenvironment of infected cells. In this context, there are striking common features of EBV, CMV, HPV and JCV that are able to promote oncogenesis, in terms of establishing latent infections and affecting p53‐/pRb‐driven, epithelial–mesenchymal transition (EMT)‐/EGFR‐associated and especially Wnt/β‐catenin‐driven pathways. We speculate that, at least in part, such viral impacts on particular pathways might be reflected in lasting (e.g. mutational or further genomic) fingerprints of viruses in cells. Also, the complex interplay between several species within the intestinal microbiome, involving a direct or indirect impact on colorectal and microenvironmental cells but also between, for example, phages and bacterial and viral pathogens, and further novel species certainly might, in part, explain ongoing difficulties to establish unequivocal monocausal links between specific viral infections and CRC.
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Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
| | - Heike Allgayer
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
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30
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Kasperek A, Béguin A, Bawa O, De Azevedo K, Job B, Massard C, Scoazec JY, Heidmann T, Heidmann O. Therapeutic potential of the human endogenous retroviral envelope protein HEMO: a pan-cancer analysis. Mol Oncol 2021; 16:1451-1473. [PMID: 34318590 PMCID: PMC8978518 DOI: 10.1002/1878-0261.13069] [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: 03/24/2021] [Revised: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 12/02/2022] Open
Abstract
Human endogenous retroviruses represent approximately 8% of our genome. Most of these sequences are defective except for a few genes such as the ancestral retroviral HEMO envelope gene (Human Endogenous MER34 ORF), recently characterized by our group. In this study, we characterized transcriptional activation of HEMO in primary tumors from The Cancer Genome Atlas (TCGA) and in metastatic tumors from a Gustave Roussy cohort. Pan‐cancer detection of the HEMO protein in a series of patient samples validated these results. Differential gene expression analysis in various TCGA datasets revealed a link between HEMO expression and activation of Wnt/β‐catenin signaling, in particular in endometrial cancer. Studies on cell models led us to propose that the Wnt/β‐catenin pathway could act as an upstream regulator of this retroviral endogenous sequence in tumor condition. Characterization of transcriptomic profiles of both HEMOLow and HEMOHigh tumors suggested that activation of HEMO is negatively associated with immune response signatures. Taken together, these results highlight that HEMO, as an endogenous retroviral envelope protein specifically expressed in tumors, represents a promising tumor biomarker and therapeutic target.
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Affiliation(s)
- Amélie Kasperek
- CNRS UMR 9196, Laboratory of Physiology and Pathology of Infectious and Endogenous Retroviruses, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
| | - Anthony Béguin
- CNRS UMR 9196, Laboratory of Physiology and Pathology of Infectious and Endogenous Retroviruses, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
| | - Olivia Bawa
- PETRA platform, AMMICa, CNRS-UMS 3655 and INSERM-US23, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
| | - Kévin De Azevedo
- CNRS UMR 9196, Laboratory of Physiology and Pathology of Infectious and Endogenous Retroviruses, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
| | - Bastien Job
- Bioinformatic Core Facility, AMMICa, CNRS-UMS 3655 and INSERM-US23, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
| | - Christophe Massard
- Drug Development Department (DITEP), Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
| | - Jean-Yves Scoazec
- PETRA platform, AMMICa, CNRS-UMS 3655 and INSERM-US23, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France.,University Paris-Saclay, Faculty of Medicine, Le Kremlin Bicêtre, 94270, France.,Department of Pathology, Gustave Roussy, Villejuif, 94805, France
| | - Thierry Heidmann
- CNRS UMR 9196, Laboratory of Physiology and Pathology of Infectious and Endogenous Retroviruses, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
| | - Odile Heidmann
- CNRS UMR 9196, Laboratory of Physiology and Pathology of Infectious and Endogenous Retroviruses, Gustave Roussy, University Paris-Saclay, Villejuif, 94805, France
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Hossain SM, Lynch-Sutherland CF, Chatterjee A, Macaulay EC, Eccles MR. Can Immune Suppression and Epigenome Regulation in Placenta Offer Novel Insights into Cancer Immune Evasion and Immunotherapy Resistance? EPIGENOMES 2021; 5:16. [PMID: 34968365 PMCID: PMC8594685 DOI: 10.3390/epigenomes5030016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/18/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer is the second leading cause of mortality and morbidity in the developed world. Cancer progression involves genetic and epigenetic alterations, accompanied by aggressive changes, such as increased immune evasion, onset of metastasis, and drug resistance. Similar to cancer, DNA hypomethylation, immune suppression, and invasive cell behaviours are also observed in the human placenta. Mechanisms that lead to the acquisition of invasive behaviour, immune evasion, and drug and immunotherapy resistance are presently under intense investigations to improve patient outcomes. Here, we review current knowledge regarding the similarities between immune suppression and epigenome regulation, including the expression of repetitive elements (REs), endogenous retroviruses (ERVs) and transposable elements (TEs) in cells of the placenta and in cancer, which are associated with changes in immune regulation and invasiveness. We explore whether immune suppression and epigenome regulation in placenta offers novel insights into immunotherapy resistance in cancer, and we also discuss the implications and the knowledge gaps relevant to these findings, which are rapidly being accrued in these quite disparate research fields. Finally, we discuss potential linkages between TE, ERV and RE activation and expression, regarding mechanisms of immune regulation in placenta and cancer. A greater understanding of the role of immune suppression and associated epigenome regulation in placenta could help to elucidate some comparable mechanisms operating in cancer, and identify potential new therapeutic targets for treating cancer.
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Affiliation(s)
- Sultana Mehbuba Hossain
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (S.M.H.); (C.F.L.-S.); (A.C.); (E.C.M.)
| | - Chiemi F. Lynch-Sutherland
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (S.M.H.); (C.F.L.-S.); (A.C.); (E.C.M.)
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (S.M.H.); (C.F.L.-S.); (A.C.); (E.C.M.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Erin C. Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (S.M.H.); (C.F.L.-S.); (A.C.); (E.C.M.)
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (S.M.H.); (C.F.L.-S.); (A.C.); (E.C.M.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
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32
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Human Endogenous Retrovirus Reactivation: Implications for Cancer Immunotherapy. Cancers (Basel) 2021; 13:cancers13091999. [PMID: 33919186 PMCID: PMC8122352 DOI: 10.3390/cancers13091999] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/08/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) derive from ancestral exogenous retroviruses whose genetic material has been integrated in our germline DNA. Several lines of evidence indicate that cancer immunotherapy may benefit from HERV reactivation, which can be induced either by drugs or by cellular changes occurring in tumor cells. Indeed, several studies indicate that HERV proviral DNA can be transcribed either to double-stranded RNA (dsRNA) that is sensed as a "danger signal" by pattern recognition receptors (PRRs), leading to a viral mimicry state, or to mRNA that is translated into proteins that may contribute to the landscape of tumor-specific antigens (TSAs). Alternatively, HERV reactivation is associated with the expression of long noncoding RNAs (lncRNAs). In this review, we will highlight recent findings on HERV reactivation in cancer and its implications for cancer immunotherapy.
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Keegan RM, Talbot LR, Chang YH, Metzger MJ, Dubnau J. Intercellular viral spread and intracellular transposition of Drosophila gypsy. PLoS Genet 2021; 17:e1009535. [PMID: 33886543 PMCID: PMC8096092 DOI: 10.1371/journal.pgen.1009535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 05/04/2021] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
It has become increasingly clear that retrotransposons (RTEs) are more widely expressed in somatic tissues than previously appreciated. RTE expression has been implicated in a myriad of biological processes ranging from normal development and aging, to age related diseases such as cancer and neurodegeneration. Long Terminal Repeat (LTR)-RTEs are evolutionary ancestors to, and share many features with, exogenous retroviruses. In fact, many organisms contain endogenous retroviruses (ERVs) derived from exogenous retroviruses that integrated into the germ line. These ERVs are inherited in Mendelian fashion like RTEs, and some retain the ability to transmit between cells like viruses, while others develop the ability to act as RTEs. The process of evolutionary transition between LTR-RTE and retroviruses is thought to involve multiple steps by which the element loses or gains the ability to transmit copies between cells versus the ability to replicate intracellularly. But, typically, these two modes of transmission are incompatible because they require assembly in different sub-cellular compartments. Like murine IAP/IAP-E elements, the gypsy family of retroelements in arthropods appear to sit along this evolutionary transition. Indeed, there is some evidence that gypsy may exhibit retroviral properties. Given that gypsy elements have been found to actively mobilize in neurons and glial cells during normal aging and in models of neurodegeneration, this raises the question of whether gypsy replication in somatic cells occurs via intracellular retrotransposition, intercellular viral spread, or some combination of the two. These modes of replication in somatic tissues would have quite different biological implications. Here, we demonstrate that Drosophila gypsy is capable of both cell-associated and cell-free viral transmission between cultured S2 cells of somatic origin. Further, we demonstrate that the ability of gypsy to move between cells is dependent upon a functional copy of its viral envelope protein. This argues that the gypsy element has transitioned from an RTE into a functional endogenous retrovirus with the acquisition of its envelope gene. On the other hand, we also find that intracellular retrotransposition of the same genomic copy of gypsy can occur in the absence of the Env protein. Thus, gypsy exhibits both intracellular retrotransposition and intercellular viral transmission as modes of replicating its genome.
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Affiliation(s)
- Richard M. Keegan
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Lillian R. Talbot
- Medical Scientist Training Program, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
| | - Michael J. Metzger
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Josh Dubnau
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
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34
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Glinsky GV. Genomics-Guided Drawing of Molecular and Pathophysiological Components of Malignant Regulatory Signatures Reveals a Pivotal Role in Human Diseases of Stem Cell-Associated Retroviral Sequences and Functionally-Active hESC Enhancers. Front Oncol 2021; 11:638363. [PMID: 33869024 PMCID: PMC8044830 DOI: 10.3389/fonc.2021.638363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/10/2021] [Indexed: 12/31/2022] Open
Abstract
Repetitive DNA sequences (repeats) colonized two-third of human genome and a majority of repeats comprised of transposable genetic elements (TE). Evolutionary distinct categories of TE represent nucleic acid sequences that are repeatedly copied from and pasted into chromosomes at multiple genomic locations and acquired a multitude of regulatory functions. Here, genomics-guided maps of stemness regulatory signatures were drawn to dissect the contribution of TE to clinical manifestations of malignant phenotypes of human cancers. From patients’ and physicians’ perspectives, the clinical definition of a tumor’s malignant phenotype could be restricted to the early diagnosis of sub-types of malignancies with the increased risk of existing therapy failure and high likelihood of death from cancer. It is the viewpoint from which the understanding of stemness and malignant regulatory signatures is considered in this contribution. Genomics-guided analyses of experimental and clinical observations revealed the pivotal role of human stem cell-associated retroviral sequences (SCARS) in the origin and pathophysiology of clinically-lethal malignancies. SCARS were defined as the evolutionary- and biologically-related family of genomic regulatory sequences, the principal physiological function of which is to create and maintain the stemness phenotype during human preimplantation embryogenesis. For cell differentiation to occur, SCARS expression must be silenced and SCARS activity remains repressed in most terminally-differentiated human cells which are destined to perform specialized functions in the human body. Epigenetic reprogramming, de-repression, and sustained activity of SCARS results in various differentiation-defective phenotypes. One of the most prominent tissue- and organ-specific clinical manifestations of sustained SCARS activities is diagnosed as a pathological condition defined by a consensus of morphological, molecular, and genetic examinations as the malignant growth. Here, contemporary evidence are acquired, analyzed, and reported defining both novel diagnostic tools and druggable molecular targets readily amenable for diagnosis and efficient therapeutic management of clinically-lethal malignancies. These diagnostic and therapeutic approaches are based on monitoring of high-fidelity molecular signals of continuing SCARS activities in conjunction with genomic regulatory networks of thousands’ functionally-active embryonic enhancers affecting down-stream phenotype-altering genetic loci. Collectively, reported herein observations support a model of SCARS-activation triggered singular source code facilitating the intracellular propagation and intercellular (systemic) dissemination of disease states in the human body.
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Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States.,Department of Functional & Translational Genomics, OncoSCAR, Inc., Portland, OR, United States
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35
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Golkaram M, Salmans ML, Kaplan S, Vijayaraghavan R, Martins M, Khan N, Garbutt C, Wise A, Yao J, Casimiro S, Abreu C, Macedo D, Costa AL, Alvim C, Mansinho A, Filipe P, Marques da Costa P, Fernandes A, Borralho P, Ferreira C, Aldeia F, Malaquias J, Godsey J, So A, Pawlowski T, Costa L, Zhang S, Liu L. HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome. NPJ Genom Med 2021; 6:13. [PMID: 33589643 PMCID: PMC7884730 DOI: 10.1038/s41525-021-00177-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/12/2021] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal malignancies. The extreme heterogeneity in survival rate is driving the need for new prognostic biomarkers. Human endogenous retroviruses (hERVs) have been suggested to influence tumor progression, oncogenesis and elicit an immune response. We examined multiple next-generation sequencing (NGS)-derived biomarkers in 114 CRC patients with paired whole-exome and whole-transcriptome sequencing (WES and WTS, respectively). First, we demonstrate that the median expression of hERVs can serve as a potential biomarker for prognosis, relapse, and resistance to chemotherapy in stage II and III CRC. We show that hERV expression and CD8+ tumor-infiltrating T-lymphocytes (TILs) synergistically stratify overall and relapse-free survival (OS and RFS): the median OS of the CD8-/hERV+ subgroup was 29.8 months compared with 37.5 months for other subgroups (HR = 4.4, log-rank P < 0.001). Combing NGS-based biomarkers (hERV/CD8 status) with clinicopathological factors provided a better prediction of patient survival compared to clinicopathological factors alone. Moreover, we explored the association between genomic and transcriptomic features of tumors with high hERV expression and establish this subtype as distinct from previously described consensus molecular subtypes of CRC. Overall, our results underscore a previously unknown role for hERVs in leading to a more aggressive subtype of CRC.
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Affiliation(s)
| | | | | | | | - Marta Martins
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | | | | | | | - Sandra Casimiro
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Catarina Abreu
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Daniela Macedo
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Ana Lúcia Costa
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Cecília Alvim
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - André Mansinho
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Pedro Filipe
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Pedro Marques da Costa
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal.,Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Afonso Fernandes
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Borralho
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Cristina Ferreira
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Fernando Aldeia
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - João Malaquias
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | | | - Alex So
- Illumina Inc., San Diego, CA, USA
| | | | - Luis Costa
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal.
| | | | - Li Liu
- Illumina Inc., San Diego, CA, USA.
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36
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Grabski DF, Ratan A, Gray LR, Bekiranov S, Rekosh D, Hammarskjold ML, Rasmussen SK. Upregulation of human endogenous retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers. J Pediatr Surg 2021; 56:286-292. [PMID: 32682541 DOI: 10.1016/j.jpedsurg.2020.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/28/2020] [Accepted: 05/18/2020] [Indexed: 12/28/2022]
Abstract
PURPOSE Hepatoblastoma is the most common liver malignancy in children. In order to advance therapy against hepatoblastoma, novel immunologic targets and biomarkers are needed. Our purpose in this investigation is to examine hepatoblastoma transcriptomes for the expression of a class of genomic elements known as Human Endogenous Retrovirus (HERVs). HERVs are abundant in the human genome and are biologically active elements that have been associated with multiple malignancies and proposed as immunologic targets in a subset of tumors. A sub-family of HERVs, HERV-K(HML-2) (HERV-K), have been shown to be tightly regulated in fetal development, making investigation of these elements in pediatric tumors paramount. METHODS We first created a HERVK-FASTA file utilizing 91 previously described HML-2 proviruses. We then concatenated the file onto the GRCh38.95 cDNA library from Ensembl. We used this reference database to evaluate existing RNA-seq data from 10 hepatoblastoma tumors and 3 normal liver controls (GEO accession ID: GSE8977575). Quantification and differential proviral expression analysis between hepatoblastoma and normal liver controls was performed using the pseudo-alignment program Salmon and DESeq2, respectively. RESULTS HERV-K mRNA was expressed in hepatoblastoma from multiple proviral loci. All expressed HERV-K proviral loci were upregulated in hepatoblastoma compared to normal liver controls. Five HERV-K proviruses (1q21.3, 3q27.2, 7q22.2, 12q24.33 and 17p13.1) were significantly differentially expressed (p-adjusted value <0.05, |log2 fold change| > 1.5) across conditions. The provirus at 17p13.1 had an approximately 300-fold increased expression in hepatoblastoma as compared to normal liver. This was in part due to the near absence of HERV-K mRNA at the 17p13.1 locus in fully differentiated liver samples. CONCLUSIONS Our investigation demonstrates that HERV-K is expressed from multiple loci in hepatoblastoma and that the expression is increased for several proviruses compared to normal liver controls. Our results suggest that HERV-K mRNA expression may be useful as a biomarker in hepatoblastoma, given the large differential expression profiles in hepatoblastoma, with very low mRNA levels in liver control samples.
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Affiliation(s)
- David F Grabski
- Department of Surgery, University of Virginia School of Medicine, Charlottesville, Virginia; Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - Aakrosh Ratan
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Laurie R Gray
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia; Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia; Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia; Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Sara K Rasmussen
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia; Seattle Children's Hospital, Division of Transplantation, University of Washington Department of Surgery, 4800 Sand Point Way, Seattle, WA 98105.
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37
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Natoli M, Gallon J, Lu H, Amgheib A, Pinato DJ, Mauri FA, Marafioti T, Akarca AU, Ullmo I, Ip J, Aboagye EO, Brown R, Karadimitris A, Ghaem-Maghami S. Transcriptional analysis of multiple ovarian cancer cohorts reveals prognostic and immunomodulatory consequences of ERV expression. J Immunother Cancer 2021; 9:jitc-2020-001519. [PMID: 33436485 PMCID: PMC7805370 DOI: 10.1136/jitc-2020-001519] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Endogenous retroviruses (ERVs) play a role in a variety of biological processes, including embryogenesis and cancer. DNA methyltransferase inhibitors (DNMTi)-induced ERV expression triggers interferon responses in ovarian cancer cells via the viral sensing machinery. Baseline expression of ERVs also occurs in cancer cells, though this process is poorly understood and previously unexplored in epithelial ovarian cancer (EOC). Here, the prognostic and immunomodulatory consequences of baseline ERV expression was assessed in EOC. METHODS ERV expression was assessed using EOC transcriptional data from The Cancer Genome Atlas (TCGA) and from an independent cohort (Hammersmith Hospital, HH), as well as from untreated or DNMTi-treated EOC cell lines. Least absolute shrinkage and selection operator (LASSO) logistic regression defined an ERV expression score to predict patient prognosis. Immunohistochemistry (IHC) was conducted on the HH cohort. Combination of DNMTi treatment with γδ T cells was tested in vitro, using EOC cell lines and patient-derived tumor cells. RESULTS ERV expression was found to define clinically relevant subsets of EOC patients. An ERV prognostic score was successfully generated in TCGA and validated in the independent cohort. In EOC patients from this cohort, a high ERV score was associated with better survival (log-rank p=0.0009) and correlated with infiltration of CD8+PD1+T cells (r=0.46, p=0.0001). In the TCGA dataset, a higher ERV score was found in BRCA1/2 mutant tumors, compared to wild type (p=0.015), while a lower ERV score was found in CCNE1 amplified tumors, compared to wild type (p=0.019). In vitro, baseline ERV expression dictates the level of ERV induction in response to DNMTi. Manipulation of an ERV expression threshold by DNMTi resulted in improved EOC cell killing by cytotoxic immune cells. CONCLUSIONS These findings uncover the potential for baseline ERV expression to robustly inform EOC patient prognosis, influence tumor immune infiltration and affect antitumor immunity.
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Affiliation(s)
- Marina Natoli
- Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - John Gallon
- Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Haonan Lu
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Ala Amgheib
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - David J Pinato
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Francesco A Mauri
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Teresa Marafioti
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Ayse U Akarca
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Ines Ullmo
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jacey Ip
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Eric O Aboagye
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Robert Brown
- Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Pathology, Institute of Cancer Research, London, UK
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38
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Nakagawa S, Kawashima M, Miyatake Y, Kudo K, Kotaki R, Ando K, Kotani A. Expression of ERV3-1 in leukocytes of acute myelogenous leukemia patients. Gene 2020; 773:145363. [PMID: 33338509 DOI: 10.1016/j.gene.2020.145363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/28/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
Acute myelogenous leukemia (AML) is one of the major hematological malignancies. In the human genome, several have been found to originate from retroviruses, and some of which are involved in the progression of various cancers. Hence, to investigate whether retroviral-like genes are associated with AML development, we conducted a transcriptome sequencing analysis of 12 retroviral-like genes of 150 AML patients and 32 healthy donor samples, of which RNA sequencing data were obtained from public databases. We found high expression of ERV3-1, an envelope gene of endogenous retrovirus group 3 member 1, in all AML patients examined in this study. In particular, blood and bone marrow cells of the myeloid lineage in AML patients, exhibited higher expression of ERV3-1 than those of the monocytic AML lineage. We also examined the protein expression of ERV3-1 by immunohistochemical analysis and found expression of the ERV3-1 protein in all 12 myeloid-phenotype patients and 7 out of 12 monocytic-phenotype patients, with a particular concentration observed at the membrane of some leukemic cells. Transcriptome analysis further suggested that upregulated ERV3-1 expression may be associated with chromosome 8 trisomy as anomaly was found to be more common among the high expression group than the low expression group. However, this finding was not corroborated by the immunohistochemical data. This discrepancy may have been caused, in part, by the small number of samples analyzed in this study. Although the precise associated molecular mechanisms remain unclear, our results suggest that ERV3-1 may be involved in AML development.
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Affiliation(s)
- So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan; Division of Genome Sciences, Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan.
| | - Masaharu Kawashima
- Division of Clinical Oncology and Hematology, The Jikei University School of Medicine, Minato-ku, Tokyo 105-8471, Japan; Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan
| | - Yuji Miyatake
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Advanced Medical Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Kai Kudo
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Advanced Medical Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Ryutaro Kotaki
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan
| | - Kiyoshi Ando
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Ai Kotani
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Advanced Medical Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
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Dolci M, Favero C, Toumi W, Favi E, Tarantini L, Signorini L, Basile G, Bollati V, D'Alessandro S, Bagnoli P, Ferrante P, Delbue S. Human Endogenous Retroviruses Long Terminal Repeat Methylation, Transcription, and Protein Expression in Human Colon Cancer. Front Oncol 2020; 10:569015. [PMID: 33194657 PMCID: PMC7653092 DOI: 10.3389/fonc.2020.569015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022] Open
Abstract
Colon cancer is the fourth most common malignancy in both incidence and mortality in developed countries. Infectious agents are among the risk factors for colon cancer. Variations in human endogenous retrovirus (HERV) transcript and protein levels are associated with several types of cancers, but few studies address HERV expression in colon cancer. Fifty-eight patients with advanced-stage colon cancer were enrolled in this study. HERV-H, -K (HML-2), -P LTRs, Alu, and LINE-1 methylation levels and transcription of HERV-H, -K (HML-2), and -P env and HERV-K pol genes in normal adjacent and tumor tissues were investigated by pyrosequencing and RT-qPCR, respectively. Expression of the HERV-K (HML-2) Pol and Env proteins in selected tissues was examined by Western blotting. Associations between HERV transcript expression and methylation levels and between clinical characteristics and HERV expression were evaluated. Compared to adjacent normal tissues, LINE-1 was hypomethylated in tumor tissues (p < 0.05), whereas Alu, HERV-K (HML-2), and -H LTRs showed a decreasing trend in tumor tissue compared to normal tissue, though without a significant difference. The transcription levels of HERV env and pol genes were similar. However, the HERV-K (HML-2) Pol protein was more highly expressed (p < 0.01) in surrounding normal tissues, but the HERV-K (HML-2) Env protein was only expressed in tumor tissues. Although HERV LTR methylation and gene expression did not show significant differences between tumor and normal tissues, HERV protein expression differed greatly. Pol protein expression in normal cells may induce reverse transcription and subsequent integration into the host genome, likely favoring cell transformation; in contrast, the Env protein in tumor tissue may contribute to cancer progression through cell-to-cell fusion.
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Affiliation(s)
- Maria Dolci
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Chiara Favero
- EPIGET-Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Wafa Toumi
- Laboratory Services, Viral and Molecular Tumor Diagnostics Unit, Habib Thameur Hospital, Tunis, Tunisia
| | - Evaldo Favi
- Renal Transplantation, Fondazione Scientific Institute for Research, Hospitalization and Health Care Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Letizia Tarantini
- EPIGET-Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Giuseppe Basile
- Orthopedic Department, San Siro Clinical Institute, Milan, Italy
| | - Valentina Bollati
- EPIGET-Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Sarah D'Alessandro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Pietro Bagnoli
- Surgical Department, Istituto Clinico Città Studi, Milan, Italy
| | - Pasquale Ferrante
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
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40
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Cao W, Kang R, Xiang Y, Hong J. Human Endogenous Retroviruses in Clear Cell Renal Cell Carcinoma: Biological Functions and Clinical Values. Onco Targets Ther 2020; 13:7877-7885. [PMID: 32821127 PMCID: PMC7423347 DOI: 10.2147/ott.s259534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/13/2020] [Indexed: 01/05/2023] Open
Abstract
Human endogenous retroviruses (HERVs) form an important part of the human genome, commonly losing their coding ability and exhibiting only rare expression in healthy tissues to promote the stability of the genome. However, overexpression of HERVs has been observed in various malignant tumors, including clear cell renal cell carcinoma (ccRCC), and may be closely correlated with tumorigenesis and progression. HERVs may activate the interferon (IFN) signaling pathway by a viral mimicry process to enhance antitumor immune responses. There is increasing interest in the diagnostic and prognostic value of HERVs in cancers, and they may be candidate targets for tumor immunotherapy. The review will introduce the biological functions of HERVs in ccRCC and their clinical value, especially in regard to immunotherapy.
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Affiliation(s)
- Wenjun Cao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Ran Kang
- Department of Urology, The First Affiliated Hospital of University of South China, Hengyang, Hunan, People's Republic of China
| | - Yining Xiang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jidong Hong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
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41
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Lee HE, Park SJ, Huh JW, Imai H, Kim HS. Enhancer Function of MicroRNA-3681 Derived from Long Terminal Repeats Represses the Activity of Variable Number Tandem Repeats in the 3' UTR of SHISA7. Mol Cells 2020; 43:607-618. [PMID: 32655015 PMCID: PMC7398795 DOI: 10.14348/molcells.2020.0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 01/03/2023] Open
Abstract
microRNAs (miRNAs) are non-coding RNA molecules involved in the regulation of gene expression. miRNAs inhibit gene expression by binding to the 3' untranslated region (UTR) of their target gene. miRNAs can originate from transposable elements (TEs), which comprise approximately half of the eukaryotic genome and one type of TE, called the long terminal repeat (LTR) is found in class of retrotransposons. Amongst the miRNAs derived from LTR, hsa-miR-3681 was chosen and analyzed using bioinformatics tools and experimental analysis. Studies on hsa-miR-3681 have been scarce and this study provides the relative expression analysis of hsa-miR-3681-5p from humans, chimpanzees, crab-eating monkeys, and mice. Luciferase assay for hsa-miR-3681-5p and its target gene SHISA7 supports our hypothesis that the number of miRNA binding sites affects target gene expression. Especially, the variable number tandem repeat (VNTR) and hsa-miR-3681-5p share the binding sites in the 3' UTR of SHISA7, which leads the enhancer function of hsa-miR-3681-5p to inhibit the activity of VNTR. In conclusion, hsa-miR-3681-5p acts as a super-enhancer and the enhancer function of hsa-miR-3681-5p acts as a repressor of VNTR activity in the 3' UTR of SHISA7.
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Affiliation(s)
- Hee-Eun Lee
- Department of Integrated Biological Science, Pusan National University, Busan 4624, Korea
- Institute of Systems Biology, Pusan National University, Busan 4641, Korea
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon 3113, Korea
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama 484-806, Japan
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 4641, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 4241, Korea
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42
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Regulation of stem cell function and neuronal differentiation by HERV-K via mTOR pathway. Proc Natl Acad Sci U S A 2020; 117:17842-17853. [PMID: 32669437 DOI: 10.1073/pnas.2002427117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Stem cells are capable of unlimited proliferation but can be induced to form brain cells. Factors that specifically regulate human development are poorly understood. We found that human stem cells expressed high levels of the envelope protein of an endogenized human-specific retrovirus (HERV-K, HML-2) from loci in chromosomes 12 and 19. The envelope protein was expressed on the cell membrane of the stem cells and was critical in maintaining the stemness via interactions with CD98HC, leading to triggering of human-specific signaling pathways involving mammalian target of rapamycin (mTOR) and lysophosphatidylcholine acyltransferase (LPCAT1)-mediated epigenetic changes. Down-regulation or epigenetic silencing of HML-2 env resulted in dissociation of the stem cell colonies and enhanced differentiation along neuronal pathways. Thus HML-2 regulation is critical for human embryonic and neurodevelopment, while it's dysregulation may play a role in tumorigenesis and neurodegeneration.
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43
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Human Endogenous Retrovirus K in Cancer: A Potential Biomarker and Immunotherapeutic Target. Viruses 2020; 12:v12070726. [PMID: 32640516 PMCID: PMC7412025 DOI: 10.3390/v12070726] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022] Open
Abstract
In diseases where epigenetic mechanisms are changed, such as cancer, many genes show altered gene expression and inhibited genes become activated. Human endogenous retrovirus type K (HERV-K) expression is usually inhibited in normal cells from healthy adults. In tumor cells, however, HERV-K mRNA expression has been frequently documented to increase. Importantly, HERV-K-derived proteins can act as tumor-specific antigens, a class of neoantigens, and induce immune responses in different types of cancer. In this review, we describe the function of the HERV-K HML-2 subtype in carcinogenesis as biomarkers, and their potential as targets for cancer immunotherapy.
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Chen X, Li D. ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data. Bioinformatics 2020; 35:3913-3922. [PMID: 30895294 DOI: 10.1093/bioinformatics/btz205] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Approximately 8% of the human genome is derived from endogenous retroviruses (ERVs). In recent years, an increasing number of human diseases have been found to be associated with ERVs. However, it remains challenging to accurately detect the full spectrum of polymorphic (unfixed) ERVs using whole-genome sequencing (WGS) data. RESULTS We designed a new tool, ERVcaller, to detect and genotype transposable element (TE) insertions, including ERVs, in the human genome. We evaluated ERVcaller using both simulated and real benchmark WGS datasets. Compared to existing tools, ERVcaller consistently obtained both the highest sensitivity and precision for detecting simulated ERV and other TE insertions derived from real polymorphic TE sequences. For the WGS data from the 1000 Genomes Project, ERVcaller detected the largest number of TE insertions per sample based on consensus TE loci. By analyzing the experimentally verified TE insertions, ERVcaller had 94.0% TE detection sensitivity and 96.6% genotyping accuracy. Polymerase chain reaction and Sanger sequencing in a small sample set verified 86.7% of examined insertion statuses and 100% of examined genotypes. In conclusion, ERVcaller is capable of detecting and genotyping TE insertions using WGS data with both high sensitivity and precision. This tool can be applied broadly to other species. AVAILABILITY AND IMPLEMENTATION http://www.uvm.edu/genomics/software/ERVcaller.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT, USA.,Department of Computer Science, University of Vermont, Burlington, VT, USA
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45
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de Oliveira WF, dos Santos Silva PM, Coelho LCBB, dos Santos Correia MT. Biomarkers, Biosensors and Biomedicine. Curr Med Chem 2020; 27:3519-3533. [DOI: 10.2174/0929867326666190124103125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/31/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023]
Abstract
The discovery of new biomarkers associated with cancer, neurological and cardiovascular
diseases is necessary, since these are common, recurrent diseases considered as leading causes of
death in the human population. Molecular signatures of these disorders that can be identified at the
outset of their pathogenesis leading to prompt and targeted treatment may increase patient survival.
Cancer is a heterogeneous disease that can be expressed differently among individuals; in addition,
treatments may have a differentiated approach according to the type of malignant neoplasm. Thus,
these neoplastic cells can synthesize and release specific molecules depending on the site where
carcinogenesis begins. Moreover, life expectancy is increasing especially in developed countries,
however, cases of neurodegenerative diseases have grown in the older members of the population.
Commonly, some neurological disorders, which can occur physiologically by the process of senescence,
are confused with Alzheimer's Disease (AD). In addition, cardiovascular diseases are the
main cause of death in the world; studies capable of identifying, through molecular probes, the beginning
of development of an atherosclerotic process can lead to early treatment to avoid an acute
myocardial infarction. Accuracy in the detection of these biomarkers can be obtained through biosensors
whose design has been increasingly studied to elaborate inexpensive sensory platforms capable
of precise detection, even at low concentrations, of the molecule to be measured. The aim of
this review is to address biomarkers to be used in diagnoses instead of invasive exams; biosensors
for the specific and sensitive detection of these biological markers are also investigated.
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Affiliation(s)
- Weslley Felix de Oliveira
- Departamento de Bioquimica, Centro de Biociencias, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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Chong C, Müller M, Pak H, Harnett D, Huber F, Grun D, Leleu M, Auger A, Arnaud M, Stevenson BJ, Michaux J, Bilic I, Hirsekorn A, Calviello L, Simó-Riudalbas L, Planet E, Lubiński J, Bryśkiewicz M, Wiznerowicz M, Xenarios I, Zhang L, Trono D, Harari A, Ohler U, Coukos G, Bassani-Sternberg M. Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nat Commun 2020; 11:1293. [PMID: 32157095 PMCID: PMC7064602 DOI: 10.1038/s41467-020-14968-9] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass spectrometry (MS)-based proteogenomics approaches are required to robustly identify these non-canonical peptides. We present an MS-based analytical approach that characterizes the non-canonical tumor HLA peptide repertoire, by incorporating whole exome sequencing, bulk and single-cell transcriptomics, ribosome profiling, and two MS/MS search tools in combination. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLA peptides, including an immunogenic peptide derived from an open reading frame downstream of the melanoma stem cell marker gene ABCB5. These findings hold great promise for the discovery of previously unknown tumor antigens for cancer immunotherapy.
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Affiliation(s)
- Chloe Chong
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Markus Müller
- Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Dermot Harnett
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Florian Huber
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland
| | - Aymeric Auger
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Brian J Stevenson
- Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Ilija Bilic
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Antje Hirsekorn
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Lorenzo Calviello
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Laia Simó-Riudalbas
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. Rybacka 1, 70-204, Szczecin, Poland
- International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland
| | - Marta Bryśkiewicz
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. Rybacka 1, 70-204, Szczecin, Poland
- International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland
- Poznan University of Medical Sciences, Fredry 10, 61-701, Poznań, Poland
| | - Ioannis Xenarios
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Genome Center Health 2030, Chemin de Mines 9, 1202, Genève, Switzerland
- Department of Training and Research, CHUV/UNIL Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
| | - Lin Zhang
- Center for Research on Reproduction and Women's Health, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Uwe Ohler
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany
- Departments of Biology and Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.
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Tavakolian S, Goudarzi H, Lak E, Faghihloo E. The evaluation of HERV-K env, np9, rec, gag expression in normal, polyp and cancerous tissues of gastric and colon. Future Virol 2019. [DOI: 10.2217/fvl-2019-0114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aim: Gastrointestinal cancer is one of the most alarming cancers worldwide. Infections exert an impact on tumor progression in gastrointestinal tissues. The alteration in the expression of human endogenous retrovirus-K ( HERV-K) genes could remarkably induce oncogenic activity. Materials & methods: In 22 gastric and 23 colon cancer patients, the expression level of HERV-K env, rec, gag and np9 were evaluated. Results: While there was a slight increase in the expression of HERV-K env in colon cancer tissues, the expression level of this gene decreased in gastric tissues. Moreover, the expression of both np9 and gag HERV-K were upregulated only in colon cancer. Nevertheless, rec HERV-K was downregulated in gastric cancer tissues. Conclusion: HERV-K-associated genes can be used as a possible biomarker for cancers diagnosis.
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Affiliation(s)
- Shaian Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elena Lak
- Department of gastric & liver, Emam Hossein hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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48
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Tavakolian S, Goudarzi H, Faghihloo E. Evaluating the expression level of HERV-K env, np9, rec and gag in breast tissue. Infect Agent Cancer 2019; 14:42. [PMID: 31798679 PMCID: PMC6884765 DOI: 10.1186/s13027-019-0260-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Breast cancer is one of the most common health problems. It has been suggested that several risk factors, either considered as external or internal, play a critical role in the pathogenesis of breast cancer, which among them, HERV-k, has the most fundamental role. In the present study, we aimed to evaluate the role of HERV-k env, gag, rec, np9 expressions in breast cancer progression. MATERIALS AND METHODS We collected 40 breast cancer tissues and their normal adjacent ones. After extracting the RNA of breast samples, we evaluated the expression of HERV-k env, gag, rec, np9 by using Quantitative real-time PCR (qRT-PCR). RESULTS The resulting data revealed that while there was a meaningful increase in the expression level of HERV-k env, gag and np9 in breast cancer tissues (P ≤ 0.01, 0.05, 0.05, respectively), we failed to find any significant elevation in the expression level of rec mRNA level. CONCLUSION The results of our study suggested that there is a plausible correlation between the mRNA expression level of HERV-K env, gag and np9 and the progression of breast cancer, proposing these markers as promising biomarkers to diagnose breast cancer.
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Affiliation(s)
- Shaian Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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49
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Horak V, Palanova A, Cizkova J, Miltrova V, Vodicka P, Kupcova Skalnikova H. Melanoma-Bearing Libechov Minipig (MeLiM): The Unique Swine Model of Hereditary Metastatic Melanoma. Genes (Basel) 2019; 10:E915. [PMID: 31717496 PMCID: PMC6895830 DOI: 10.3390/genes10110915] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 12/12/2022] Open
Abstract
National cancer databases document that melanoma is the most aggressive and deadly cutaneous malignancy with worldwide increasing incidence in the Caucasian population. Around 10% of melanomas occur in families. Several germline mutations were identified that might help to indicate individuals at risk for preventive interventions and early disease detection. More than 50% of sporadic melanomas carry mutations in Ras/Raf/mitogen-activated protein kinase (MAPK/MEK) pathway, which may represent aims of novel targeted therapies. Despite advances in targeted therapies and immunotherapies, the outcomes in metastatic tumor are still unsatisfactory. Here, we review animal models that help our understanding of melanoma development and treatment, including non-vertebrate, mouse, swine, and other mammal models, with an emphasis on those with spontaneously developing melanoma. Special attention is paid to the melanoma-bearing Libechov minipig (MeLiM). This original swine model of hereditary metastatic melanoma enables studying biological processes underlying melanoma progression, as well as spontaneous regression. Current histological, immunohistochemical, biochemical, genetic, hematological, immunological, and skin microbiome findings in the MeLiM model are summarized, together with development of new therapeutic approaches based on tumor devitalization. The ongoing study of molecular and immunological base of spontaneous regression in MeLiM model has potential to bring new knowledge of clinical importance.
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Affiliation(s)
| | | | | | | | | | - Helena Kupcova Skalnikova
- Czech Academy of Sciences, Institute of Animal Physiology and Genetics, Laboratory of Applied Proteome Analyses and Research Center PIGMOD, 277 21 Libechov, Czech Republic; (V.H.); (A.P.); (J.C.); (V.M.); (P.V.)
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Horváth KB, Boros Á, Kálmán E, Pankovics P, Delwart E, Reuter G. Characterization of an integrated, endogenous mouse mammary tumor virus-like (MMTV) betaretrovirus genome in a black Syrian hamster (Mesocricetus auratus). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 75:103995. [PMID: 31404669 DOI: 10.1016/j.meegid.2019.103995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022]
Abstract
Retroviruses (family Retroviridae) are important agents of humans and animals. This study reports the detection and complete genome characterization of a novel endogenous retrovirus from the black Syrian hamster (Mesocricetus auratus) with a squamous cell skin tumor. The proviral genome, tentatively named black Syrian hamster retrovirus (BSHRV/2013/HUN, MK304634), was 8784 nucleotide in length with typical full-length betaretrovirus genome organization of 5'LTR-gag-pro-pol-env-3'LTR and with a characteristic mouse mammary tumor virus-like (MMTV) betaretrovirus dUTPase domain but without a sag gene. The BSHRV gag (534aa), pro/pol (~1099aa) and env (672aa) proteins had 56%/63%/50% aa identity to the corresponding proteins of MMTV (AF228552). The proviral DNA is detectable in tumor as well as in tumor-free cells by conventional PCR and qPCR but only visible in the tumor cells by in situ hybridization. Low level retroviral RNA expression was found only in the DNase-treated RNA tumor samples using RT/nested PCR. BSHRV/2013/HUN-like betaretrovirus DNA was also identified from a faecal and tissue samples from 1 of the further 3 tested individuals by nested-PCR and qPCR. Further research is needed to investigate the distribution, activity and etiological role of this novel MMTV-like betaretrovirus species in hamster.
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Affiliation(s)
- Katalin B Horváth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Endre Kálmán
- Department of Pathology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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