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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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2
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Shin W, Mun S, Han K. Human Endogenous Retrovirus-K (HML-2)-Related Genetic Variation: Human Genome Diversity and Disease. Genes (Basel) 2023; 14:2150. [PMID: 38136972 PMCID: PMC10742618 DOI: 10.3390/genes14122150] [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: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs) comprise a significant portion of the human genome, making up roughly 8%, a notable comparison to the 2-3% represented by coding sequences. Numerous studies have underscored the critical role and importance of HERVs, highlighting their diverse and extensive influence on the evolution of the human genome and establishing their complex correlation with various diseases. Among HERVs, the HERV-K (HML-2) subfamily has recently attracted significant attention, integrating into the human genome after the divergence between humans and chimpanzees. Its insertion in the human genome has received considerable attention due to its structural and functional characteristics and the time of insertion. Originating from ancient exogenous retroviruses, these elements succeeded in infecting germ cells, enabling vertical transmission and existing as proviruses within the genome. Remarkably, these sequences have retained the capacity to form complete viral sequences, exhibiting activity in transcription and translation. The HERV-K (HML-2) subfamily is the subject of active debate about its potential positive or negative effects on human genome evolution and various pathologies. This review summarizes the variation, regulation, and diseases in human genome evolution arising from the influence of HERV-K (HML-2).
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Affiliation(s)
- Wonseok Shin
- NGS Clinical Laboratory, Division of Cancer Research, Dankook University Hospital, Cheonan 31116, Republic of Korea;
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
| | - Seyoung Mun
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
| | - Kyudong Han
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Republic of Korea
- R&D Center, HuNBiome Co., Ltd., Seoul 08507, Republic of Korea
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Shah AH, Rivas SR, Doucet-O’Hare TT, Govindarajan V, DeMarino C, Wang T, Ampie L, Zhang Y, Banasavadi-Siddegowda YK, Walbridge S, Maric D, Garcia-Montojo M, Suter RK, Lee MH, Zaghloul KA, Steiner J, Elkahloun AG, Chandar J, Seetharam D, Desgraves J, Li W, Johnson K, Ivan ME, Komotar RJ, Gilbert MR, Heiss JD, Nath A. Human endogenous retrovirus K contributes to a stem cell niche in glioblastoma. J Clin Invest 2023; 133:e167929. [PMID: 37395282 PMCID: PMC10313366 DOI: 10.1172/jci167929] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/19/2023] [Indexed: 07/04/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are ancestral viral relics that constitute nearly 8% of the human genome. Although normally silenced, the most recently integrated provirus HERV-K (HML-2) can be reactivated in certain cancers. Here, we report pathological expression of HML-2 in malignant gliomas in both cerebrospinal fluid and tumor tissue that was associated with a cancer stem cell phenotype and poor outcomes. Using single-cell RNA-Seq, we identified glioblastoma cellular populations with elevated HML-2 transcripts in neural progenitor-like cells (NPC-like) that drive cellular plasticity. Using CRISPR interference, we demonstrate that HML-2 critically maintained glioblastoma stemness and tumorigenesis in both glioblastoma neurospheres and intracranial orthotopic murine models. Additionally, we demonstrate that HML-2 critically regulated embryonic stem cell programs in NPC-derived astroglia and altered their 3D cellular morphology by activating the nuclear transcription factor OCT4, which binds to an HML-2-specific long-terminal repeat (LTR5Hs). Moreover, we discovered that some glioblastoma cells formed immature retroviral virions, and inhibiting HML-2 expression with antiretroviral drugs reduced reverse transcriptase activity in the extracellular compartment, tumor viability, and pluripotency. Our results suggest that HML-2 fundamentally contributes to the glioblastoma stem cell niche. Because persistence of glioblastoma stem cells is considered responsible for treatment resistance and recurrence, HML-2 may serve as a unique therapeutic target.
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Affiliation(s)
- Ashish H. Shah
- University of Miami School of Medicine, Department of Neurosurgery, Miami, Florida, USA
| | - Sarah R. Rivas
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Tara T. Doucet-O’Hare
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Vaidya Govindarajan
- University of Miami School of Medicine, Department of Neurosurgery, Miami, Florida, USA
| | - Catherine DeMarino
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Tongguang Wang
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Leonel Ampie
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Yong Zhang
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | | | - Stuart Walbridge
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Dragan Maric
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Marta Garcia-Montojo
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Robert K. Suter
- Georgetown University, Bioinformatics Section, Washington, DC, USA
| | - Myoung-Hwa Lee
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Kareem A. Zaghloul
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Joseph Steiner
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Abdel G. Elkahloun
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Jay Chandar
- University of Miami School of Medicine, Department of Neurosurgery, Miami, Florida, USA
| | - Deepa Seetharam
- University of Miami School of Medicine, Department of Neurosurgery, Miami, Florida, USA
| | - Jelisah Desgraves
- University of Miami School of Medicine, Department of Neurosurgery, Miami, Florida, USA
| | - Wenxue Li
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Kory Johnson
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Michael E. Ivan
- University of Miami School of Medicine, Department of Neurosurgery, Miami, Florida, USA
| | - Ricardo J. Komotar
- University of Miami School of Medicine, Department of Neurosurgery, Miami, Florida, USA
| | - Mark R. Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - John D. Heiss
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Avindra Nath
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
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Romerio F. Origin and functional role of antisense transcription in endogenous and exogenous retroviruses. Retrovirology 2023; 20:6. [PMID: 37194028 DOI: 10.1186/s12977-023-00622-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
Most proteins expressed by endogenous and exogenous retroviruses are encoded in the sense (positive) strand of the genome and are under the control of regulatory elements within the 5' long terminal repeat (LTR). A number of retroviral genomes also encode genes in the antisense (negative) strand and their expression is under the control of negative sense promoters within the 3' LTR. In the case of the Human T-cell Lymphotropic Virus 1 (HTLV-1), the antisense protein HBZ has been shown to play a critical role in the virus lifecycle and in the pathogenic process, while the function of the Human Immunodeficiency Virus 1 (HIV-1) antisense protein ASP remains unknown. However, the expression of 3' LTR-driven antisense transcripts is not always demonstrably associated with the presence of an antisense open reading frame encoding a viral protein. Moreover, even in the case of retroviruses that do express an antisense protein, such as HTLV-1 and the pandemic strains of HIV-1, the 3' LTR-driven antisense transcript shows both protein-coding and noncoding activities. Indeed, the ability to express antisense transcripts appears to be phylogenetically more widespread among endogenous and exogenous retroviruses than the presence of a functional antisense open reading frame within these transcripts. This suggests that retroviral antisense transcripts may have originated as noncoding molecules with regulatory activity that in some cases later acquired protein-coding function. Here, we will review examples of endogenous and exogenous retroviral antisense transcripts, and the ways through which they benefit viral persistence in the host.
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Affiliation(s)
- Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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5
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Russ E, Mikhalkevich N, Iordanskiy S. Expression of Human Endogenous Retrovirus Group K (HERV-K) HML-2 Correlates with Immune Activation of Macrophages and Type I Interferon Response. Microbiol Spectr 2023; 11:e0443822. [PMID: 36861980 PMCID: PMC10100713 DOI: 10.1128/spectrum.04438-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Human endogenous retroviruses (HERVs) comprise about 8.3% of the human genome and are capable of producing RNA molecules that can be sensed by pattern recognition receptors, leading to the activation of innate immune response pathways. The HERV-K (HML-2) subgroup is the youngest HERV clade with the highest degree of coding competence. Its expression is associated with inflammation-related diseases. However, the precise HML-2 loci, stimuli, and signaling pathways involved in these associations are not well understood or defined. To elucidate HML-2 expression on a locus-specific level, we used the retroelement sequencing tools TEcount and Telescope to analyze publicly available transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation (ChIP) sequencing data sets of macrophages treated with a wide range of agonists. We found that macrophage polarization significantly correlates with modulation of the expression of specific HML-2 proviral loci. Further analysis demonstrated that the provirus HERV-K102, located in an intergenic region of locus 1q22, constituted the majority of the HML-2 derived transcripts following pro-inflammatory (M1) polarization and was upregulated explicitly in response to interferon gamma (IFN-γ) signaling. We found that signal transducer and activator of transcription 1 and interferon regulatory factor 1 interact with a solo long terminal repeat (LTR) located upstream of HERV-K102, termed LTR12F, following IFN-γ signaling. Using reporter constructs, we demonstrated that LTR12F is critical for HERV-K102 upregulation by IFN-γ. In THP1-derived macrophages, knockdown of HML-2 or knockout of MAVS, an adaptor of RNA-sensing pathways, significantly downregulated genes containing interferon-stimulated response elements (ISREs) in their promoters, suggesting an intermediate role of HERV-K102 in the switch from IFN-γ signaling to the activation of type I interferon expression and, therefore, in a positive feedback loop to enhance pro-inflammatory signaling. IMPORTANCE The human endogenous retrovirus group K subgroup, HML-2, is known to be elevated in a long list of inflammation-associated diseases. However, a clear mechanism for HML-2 upregulation in response to inflammation has not been defined. In this study, we identify a provirus of the HML-2 subgroup, HERV-K102, which is significantly upregulated and constitutes the majority of the HML-2 derived transcripts in response to pro-inflammatory activation of macrophages. Moreover, we identify the mechanism of HERV-K102 upregulation and demonstrate that HML-2 expression enhances interferon-stimulated response element activation. We also demonstrate that this provirus is elevated in vivo and correlates with interferon gamma signaling activity in cutaneous leishmaniasis patients. This study provides key insights into the HML-2 subgroup and suggests that it may participate in enhancing pro-inflammatory signaling in macrophages and probably other immune cells.
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Affiliation(s)
- Eric Russ
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
- Graduate Program of Cellular and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Natallia Mikhalkevich
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Sergey Iordanskiy
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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6
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Fan TJ, Cui J. Human Endogenous Retroviruses in Diseases. Subcell Biochem 2023; 106:403-439. [PMID: 38159236 DOI: 10.1007/978-3-031-40086-5_15] [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] [Indexed: 01/03/2024]
Abstract
Human endogenous retroviruses (HERVs), which are conserved sequences of ancient retroviruses, are widely distributed in the human genome. Although most HERVs have been rendered inactive by evolution, some have continued to exhibit important cytological functions. HERVs in the human genome perform dual functions: on the one hand, they are involved in important physiological processes such as placental development and immune regulation; on the other hand, their aberrant expression is closely associated with the pathological processes of several diseases, such as cancers, autoimmune diseases, and viral infections. HERVs can also regulate a variety of host cellular functions, including the expression of protein-coding genes and regulatory elements that have evolved from HERVs. Here, we present recent research on the roles of HERVs in viral infections and cancers, including the dysregulation of HERVs in various viral infections, HERV-induced epigenetic modifications of histones (such as methylation and acetylation), and the potential mechanisms of HERV-mediated antiviral immunity. We also describe therapies to improve the efficacy of vaccines and medications either by directly or indirectly targeting HERVs, depending on the HERV.
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Affiliation(s)
- Tian-Jiao Fan
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
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Human Endogenous Retroviruses: Friends and Foes in Urology Clinics. Int Neurourol J 2022; 26:275-287. [PMID: 36599336 PMCID: PMC9816444 DOI: 10.5213/inj.2244284.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are originated from ancient exogenous retroviruses, which infected human germ line cells millions of years ago. HERVs have generally lost their replication and retrotransposition abilities, but adopted physiological roles in human biology. Though mostly inactive, HERVs can be reactivated by internal and external factors such as inflammations and environmental conditions. Their aberrant expression can participate in various human malignancies with complex etiology. This review describes the features and functions of HERVs in urological subjects, such as urological cancers and human reproduction. It provides the current knowledge of the HERVs and useful insights helping practice in urology clinics.
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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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Agoni L. Alternative and aberrant splicing of human endogenous retroviruses in cancer. What about head and neck? —A mini review. Front Oncol 2022; 12:1019085. [PMID: 36338752 PMCID: PMC9631305 DOI: 10.3389/fonc.2022.1019085] [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: 08/14/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are transcribed in many cancer types, including head and neck cancer. Because of accumulating mutations at proviral loci over evolutionary time, HERVs are functionally defective and cannot complete their viral life cycle. Despite that, HERV transcripts, including full-length viral RNAs and viral RNAs spliced as expected at the conventional viral splice sites, can be detected in particular conditions, such as cancer. Interestingly, non-viral–related transcription, including aberrant, non-conventionally spliced RNAs, has been reported as well. The role of HERV transcription in cancer and its contribution to oncogenesis or progression are still debated. Nonetheless, HERVs may constitute a suitable cancer biomarker or a target for therapy. Thus, ongoing research aims both to clarify the basic mechanisms underlying HERV transcription in cancer and to exploit its potential toward clinical application. In this mini-review, we summarize the current knowledge, the most recent findings, and the future perspectives of research on HERV transcription and splicing, with particular focus on head and neck cancer.
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Bendall ML, Francis JH, Shoushtari AN, Nixon DF. Specific human endogenous retroviruses predict metastatic potential in uveal melanoma. JCI Insight 2022; 7:e147172. [PMID: 35349481 PMCID: PMC9090245 DOI: 10.1172/jci.insight.147172] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Uveal melanoma (UM) is a unique disease in that patients with primary UM are well stratified based on their risk of developing metastasis, yet there are limited effective treatments once metastases occur. There is an urgent need to better understand the distinct molecular pathogenesis of UM and the characteristics of patients at high risk for metastasis to identify neoantigenic targets that can be used in immunotherapy and to develop novel therapeutic strategies that may effectively target this lethal transition. An important and overlooked area of molecular pathogenesis and neoantigenic targets in UM comes from human endogenous retroviruses (HERVs). We investigated the HERV expression landscape in primary UM and found that tumors were stratified into 4 HERV-based subsets that provide clear delineation of risk outcome and support subtypes identified by other molecular indicators. Specific HERV loci are associated with the risk of uveal melanoma metastasis and may offer mechanistic insights into this process, including dysregulation of HERVs on chromosomes 3 and 8. A HERV signature composed of 17 loci was sufficient to classify tumors according to subtype with greater than 95% accuracy, including at least 1 intergenic HERV with coding potential (HERVE_Xp11.23) that could represent a potential HERV E target for immunotherapy.
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Affiliation(s)
- Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | - Alexander N. Shoushtari
- Melanoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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11
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Guo Y, Yang C, Liu Y, Li T, Li H, Han J, Jia L, Wang X, Zhang B, Li J, Li L. High Expression of HERV-K (HML-2) Might Stimulate Interferon in COVID-19 Patients. Viruses 2022; 14:996. [PMID: 35632738 PMCID: PMC9143815 DOI: 10.3390/v14050996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 12/15/2022] Open
Abstract
Background. Interferon is a marker of host antiviral immunity, which is disordered in COVID-19 patients. ERV can affect the secretion of interferon through the cGAS-STING pathway. In this study, we explored whether IFN-I and HERV-K (HML-2) were activated in COVID-19 patients and whether there was an interaction between them. Methods. We collected blood samples from COVID-19 patients and healthy controls. We first detected the expression of HERV-K (HML-2) gag, env, and pol genes and IFN-I-related genes between patients and healthy people by qPCR, synchronously detected VERO cells infected with SARS-CoV-2. Then, the chromosome distributions of highly expressed HERV-K (HML-2) gag, env, and pol genes were mapped by the next-generation sequencing results, and GO analysis was performed on the related genes. Results. We found that the HERV-K (HML-2) gag, env, and pol genes were highly expressed in COVID-19 patients and VERO cells infected with SARS-CoV-2. The interferon-related genes IFNB1, ISG15, and IFIT1 were also activated in COVID-19 patients, and GO analysis showed that HERV-K (HML-2) can regulate the secretion of interferon. Conclusions. The high expression of HERV-K (HML-2) might activate the increase of interferon in COVID-19 patients, proving that HERV-K does not only play a negative role in the human body.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.G.); (C.Y.); (Y.L.); (T.L.); (H.L.); (J.H.); (L.J.); (X.W.); (B.Z.); (J.L.)
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12
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Kitsou K, Iliopoulou M, Spoulou V, Lagiou P, Magiorkinis G. Viral Causality of Human Cancer and Potential Roles of Human Endogenous Retroviruses in the Multi-Omics Era: An Evolutionary Epidemiology Review. Front Oncol 2021; 11:687631. [PMID: 34778024 PMCID: PMC8586426 DOI: 10.3389/fonc.2021.687631] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Being responsible for almost 12% of cancers worldwide, viruses are among the oldest known and most prevalent oncogenic agents. The quality of the evidence for the in vivo tumorigenic potential of microorganisms varies, thus accordingly, viruses were classified in 4 evidence-based categories by the International Agency for Research on Cancer in 2009. Since then, our understanding of the role of viruses in cancer has significantly improved, firstly due to the emergence of high throughput sequencing technologies that allowed the “brute-force” recovery of unknown viral genomes. At the same time, multi-omics approaches unravelled novel virus-host interactions in stem-cell biology. We now know that viral elements, either exogenous or endogenous, have multiple sometimes conflicting roles in human pathophysiology and the development of cancer. Here we integrate emerging evidence on viral causality in human cancer from basic mechanisms to clinical studies. We analyze viral tumorigenesis under the scope of deep-in-time human-virus evolutionary relationships and critically comment on the evidence through the eyes of clinical epidemiology, firstly by reviewing recognized oncoviruses and their mechanisms of inducing tumorigenesis, and then by examining the potential role of integrated viruses in our genome in the process of carcinogenesis.
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Affiliation(s)
- Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Iliopoulou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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13
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Mao J, Zhang Q, Cong YS. Human endogenous retroviruses in development and disease. Comput Struct Biotechnol J 2021; 19:5978-5986. [PMID: 34849202 PMCID: PMC8604659 DOI: 10.1016/j.csbj.2021.10.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) represent ∼8% of human genome, deriving from exogenous retroviral infections of germ line cells occurred millions of years ago and being inherited by the offspring in a Mendelian fashion. Most of HERVs are nonprotein-coding because of the accumulation of mutations, insertions, deletions, and/or truncations. It has been long thought that HERVs were "junk DNA". However, it is now known that HERVs are involved in various biological processes through encoding proteins, acting as promoters/enhancers, or lncRNAs to affect human health and disease. In this review, we summarized recent findings about HERVs, with implications in embryonic development, pluripotency, cancer, aging, and neurodegenerative diseases.
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Affiliation(s)
- Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University School of Basic Medical Sciences, Hangzhou, China
| | - Qian Zhang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University School of Basic Medical Sciences, Hangzhou, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University School of Basic Medical Sciences, Hangzhou, China
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14
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Dittmar T, Weiler J, Luo T, Hass R. Cell-Cell Fusion Mediated by Viruses and HERV-Derived Fusogens in Cancer Initiation and Progression. Cancers (Basel) 2021; 13:5363. [PMID: 34771528 PMCID: PMC8582398 DOI: 10.3390/cancers13215363] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/13/2022] Open
Abstract
Cell fusion is a well-known, but still scarcely understood biological phenomenon, which might play a role in cancer initiation, progression and formation of metastases. Although the merging of two (cancer) cells appears simple, the entire process is highly complex, energy-dependent and tightly regulated. Among cell fusion-inducing and -regulating factors, so-called fusogens have been identified as a specific type of proteins that are indispensable for overcoming fusion-associated energetic barriers and final merging of plasma membranes. About 8% of the human genome is of retroviral origin and some well-known fusogens, such as syncytin-1, are expressed by human (cancer) cells. Likewise, enveloped viruses can enable and facilitate cell fusion due to evolutionarily optimized fusogens, and are also capable to induce bi- and multinucleation underlining their fusion capacity. Moreover, multinucleated giant cancer cells have been found in tumors derived from oncogenic viruses. Accordingly, a potential correlation between viruses and fusogens of human endogenous retroviral origin in cancer cell fusion will be summarized in this review.
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Affiliation(s)
- Thomas Dittmar
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58448 Witten, Germany;
| | - Julian Weiler
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58448 Witten, Germany;
| | - Tianjiao Luo
- Biochemistry and Tumor Biology Laboratory, Department of Obstetrics and Gynecology, Hannover Medical School, 30625 Hannover, Germany;
| | - Ralf Hass
- Biochemistry and Tumor Biology Laboratory, Department of Obstetrics and Gynecology, Hannover Medical School, 30625 Hannover, Germany;
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15
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Steiner MC, Marston JL, Iñiguez LP, Bendall ML, Chiappinelli KB, Nixon DF, Crandall KA. Locus-Specific Characterization of Human Endogenous Retrovirus Expression in Prostate, Breast, and Colon Cancers. Cancer Res 2021; 81:3449-3460. [PMID: 33941616 PMCID: PMC8260468 DOI: 10.1158/0008-5472.can-20-3975] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
Human endogenous retroviruses (HERV) have been implicated in a variety of diseases including cancers. Recent research implicates HERVs in epigenetic gene regulation. Here we utilize a recently developed bioinformatics tool for identifying HERV expression at the locus-specific level to identify differential expression of HERVs in matched tumor-normal RNA-sequencing (RNA-seq) data from The Cancer Genome Atlas. Data from 52 prostate cancer, 111 breast cancer, and 24 colon cancer cases were analyzed. Locus-specific analysis identified active HERV elements and differentially expressed HERVs in prostate cancer, breast cancer, and colon cancer. In addition, differentially expressed host genes were identified across prostate, breast, and colon cancer datasets, respectively, including several involved in demethylation and antiviral response pathways, supporting previous findings regarding the pathogenic mechanisms of HERVs. A majority of differentially expressed HERVs intersected protein coding genes or lncRNAs in each dataset, and a subset of differentially expressed HERVs intersected differentially expressed genes in prostate, breast, and colon cancers, providing evidence towards regulatory function. Finally, patterns in HERV expression were identified in multiple cancer types, with 155 HERVs differentially expressed in all three cancer types. This analysis extends previous results identifying HERV transcription in cancer RNA-seq datasets to a locus-specific level, and in doing so provides a foundation for future studies investigating the functional role of HERV in cancers and identifies a number of novel targets for cancer biomarkers and immunotherapy. SIGNIFICANCE: Expressed human endogenous retroviruses are mapped at locus-specific resolution and linked to specific pathways to identify potential biomarkers and therapeutic targets in prostate, breast, and colon cancers.
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Affiliation(s)
- Margaret C Steiner
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, D.C
| | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Luis P Iñiguez
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, D.C
- The GW Cancer Center, The George Washington University, Washington, D.C
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, D.C.
- The GW Cancer Center, The George Washington University, Washington, D.C
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, D.C
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16
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SMARCB1 deletion in atypical teratoid rhabdoid tumors results in human endogenous retrovirus K (HML-2) expression. Sci Rep 2021; 11:12893. [PMID: 34145313 PMCID: PMC8213802 DOI: 10.1038/s41598-021-92223-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Atypical Teratoid Rhabdoid Tumor (AT/RT) is a rare pediatric central nervous system cancer often characterized by deletion or mutation of SMARCB1, a tumor suppressor gene. In this study, we found that SMARCB1 regulates Human Endogenous Retrovirus K (HERV-K, subtype HML-2) expression. HML-2 is a repetitive element scattered throughout the human genome, encoding several intact viral proteins that have been associated with stem cell maintenance and tumorigenesis. We found HML-2 env expression in both the intracellular and extracellular compartments in all AT/RT cell lines (n = 4) and in 95% of AT/RT patient tissues (n = 37) evaluated. SMARCB1 knock-down in neural stem cells (NSCs) led to an upregulation of HML-2 transcription. We found that SMARCB1 binds adjacent to the HML-2 promoter, repressing its transcription via chromatin immunoprecipitation; restoration of SMARCB1 expression in AT/RT cell lines significantly downregulated HML-2 expression. Further, targeted downregulation of HML-2 transcription via CRISPR-dCas9 coupled with suppressor proteins led to cellular dispersion, decreased proliferation, and cell death in vitro. HML-2 knock-down with shRNA, siRNA, and CRISPR-dCas9 significantly decreased Ras expression as measured by qRT-PCR, suggesting that HML-2 modulates MAPK/ERK signaling in AT/RT cells. Overexpression of NRAS was sufficient to restore cellular proliferation, and MYC, a transcription factor downstream of NRAS, was bound to the HERV-K LTR significantly more in the absence of SMARCB1 expression in AT/RT cells. We show a mechanism by which these undifferentiated tumors remain pluripotent, and we demonstrate that their formation is aided by aberrant HML-2 activation, which is dependent on SMARCB1 and its interaction with MYC.
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17
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Padmanabhan Nair V, Liu H, Ciceri G, Jungverdorben J, Frishman G, Tchieu J, Cederquist GY, Rothenaigner I, Schorpp K, Klepper L, Walsh RM, Kim TW, Cornacchia D, Ruepp A, Mayer J, Hadian K, Frishman D, Studer L, Vincendeau M. Activation of HERV-K(HML-2) disrupts cortical patterning and neuronal differentiation by increasing NTRK3. Cell Stem Cell 2021; 28:1566-1581.e8. [PMID: 33951478 DOI: 10.1016/j.stem.2021.04.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 03/05/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022]
Abstract
The biological function and disease association of human endogenous retroviruses (HERVs) are largely elusive. HERV-K(HML-2) has been associated with neurotoxicity, but there is no clear understanding of its role or mechanistic basis. We addressed the physiological functions of HERV-K(HML-2) in neuronal differentiation using CRISPR engineering to activate or repress its expression levels in a human-pluripotent-stem-cell-based system. We found that elevated HERV-K(HML-2) transcription is detrimental for the development and function of cortical neurons. These effects are cell-type-specific, as dopaminergic neurons are unaffected. Moreover, high HERV-K(HML-2) transcription alters cortical layer formation in forebrain organoids. HERV-K(HML-2) transcriptional activation leads to hyperactivation of NTRK3 expression and other neurodegeneration-related genes. Direct activation of NTRK3 phenotypically resembles HERV-K(HML-2) induction, and reducing NTRK3 levels in context of HERV-K(HML-2) induction restores cortical neuron differentiation. Hence, these findings unravel a cell-type-specific role for HERV-K(HML-2) in cortical neuron development.
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Affiliation(s)
| | - Hengyuan Liu
- Department of Genome-Oriented Bioinformatics, Technical University Munich, Munich, Germany
| | - Gabriele Ciceri
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Johannes Jungverdorben
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Goar Frishman
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jason Tchieu
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gustav Y Cederquist
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ina Rothenaigner
- Assay Development and Screening Platform, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kenji Schorpp
- Assay Development and Screening Platform, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lena Klepper
- Institute of Virology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ryan M Walsh
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tae Wan Kim
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniela Cornacchia
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Ruepp
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jens Mayer
- Institute of Human Genetics, University of Saarland, Homburg, Germany
| | - Kamyar Hadian
- Assay Development and Screening Platform, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dmitrij Frishman
- Department of Genome-Oriented Bioinformatics, Technical University Munich, Munich, Germany
| | - Lorenz Studer
- Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Vincendeau
- Institute of Virology, Helmholtz Zentrum München, Neuherberg, Germany; Developmental Biology and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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18
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HERV-K Gag RNA and Protein Levels Are Elevated in Malignant Regions of the Prostate in Males with Prostate Cancer. Viruses 2021; 13:v13030449. [PMID: 33802118 PMCID: PMC7999808 DOI: 10.3390/v13030449] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
Heightened expression of human endogenous retrovirus (HERV) sequences has been associated with a range of malignancies, including prostate cancer, suggesting that they may serve as useful diagnostic or prognostic cancer biomarkers. We analysed the expression of HERV-K (Gag and Env/Np9 regions), HERV-E 4.1 (Pol and Env regions), HERV-H (Pol) and HERV-W (Gag) sequences in prostate cancer cells lines and normal prostate epithelial cells using qRT-PCR. HERV expression was also analysed in matched malignant and benign prostate tissue samples from men with prostate cancer (n = 27, median age 65.2 years (range 47-70)) and compared to prostate cancer-free male controls (n = 11). Prostate cancer epithelial cell lines exhibited a signature of HERV RNA overexpression, with all HERVs analysed, except HERV-E Pol, showing heightened expression in at least two, but more commonly all, cell lines analysed. Analysis of primary prostate material indicated increased expression of HERV-E Pol but decreased expression of HERV-E Env in both malignant and benign regions of the prostate in men with prostate cancer as compared to those without. Expression of HERV-K Gag was significantly higher in malignant regions of the prostate in men with prostate cancer as compared to matched benign regions and prostate cancer-free men (p < 0.001 for both), with 85.2% of prostate cancers donors showing malignancy-associated upregulation of HERV-K Gag RNA. HERV-K Gag protein was detected in 12/18 (66.7%) malignant tissues using immunohistochemistry, but only 1/18 (5.6%) benign tissue sections. Heightened expression of HERV-K Gag RNA and protein appears to be a sensitive and specific biomarker of prostate malignancy in this cohort of men with prostate carcinoma, supporting its potential utility as a non-invasive, adjunct clinical biomarker.
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19
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The Regulation and Functions of Endogenous Retrovirus in Embryo Development and Stem Cell Differentiation. Stem Cells Int 2021; 2021:6660936. [PMID: 33727936 PMCID: PMC7937486 DOI: 10.1155/2021/6660936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
Endogenous retroviruses (ERVs) are repetitive sequences in the genome, belonging to the retrotransposon family. During the course of life, ERVs are associated with multiple aspects of chromatin and transcriptional regulation in development and pathological conditions. In mammalian embryos, ERVs are extensively activated in early embryo development, but with a highly restricted spatial-temporal pattern; and they are drastically silenced during differentiation with exceptions in extraembryonic tissue and germlines. The dynamic activation pattern of ERVs raises questions about how ERVs are regulated in the life cycle and whether they are functionally important to cell fate decision during early embryo and somatic cell development. Therefore, in this review, we focus on the pieces of evidence demonstrating regulations and functions of ERVs during stem cell differentiation, which suggests that ERV activation is not a passive result of cell fate transition but the active epigenetic and transcriptional regulation during mammalian development and stem cell differentiation.
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20
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Salavatiha Z, Soleimani-Jelodar R, Jalilvand S. The role of endogenous retroviruses-K in human cancer. Rev Med Virol 2020; 30:1-13. [PMID: 32734655 DOI: 10.1002/rmv.2142] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022]
Abstract
It is known that human endogenous retroviruses (HERVs) constitute almost 8% of the human genome. Although the expression of HERVs from the human genome is tightly regulated, different exogenous and endogenous factors could trigger HERV activation. Aberrant expression of different HERVs may potentially cause a variety of diseases such as neurological and autoimmune diseases as well as cancer. It is suggested that HERV-K can induce cancer through different mechanisms that are discussed. The interplay between some tumor viruses and HERV-K seems to be a key player in progression of viral-associated cancers because elevated levels of Rec and Np9 proteins are observed in several cancers. The frequent over expression of HERV proteins and some specific antibodies in cancer cells could be considered as suitable prognostic and therapeutic biomarkers in diagnosis and treatment of cancers. The expression of HERV proteins in cancers and development of immune responses against them may also be used as targets for cancer immunotherapy. Further studies are warranted to evaluate the role of HERVs in cancer formation and use of different HERV proteins in developing new diagnostic and therapeutic approaches for cancer treatments.
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Affiliation(s)
- Zahra Salavatiha
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Rahim Soleimani-Jelodar
- Department of Virology, School of Public Health, 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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21
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Xue B, Sechi LA, Kelvin DJ. Human Endogenous Retrovirus K (HML-2) in Health and Disease. Front Microbiol 2020; 11:1690. [PMID: 32765477 PMCID: PMC7380069 DOI: 10.3389/fmicb.2020.01690] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/29/2020] [Indexed: 02/05/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are derived from exogenous retrovirus infections in the evolution of primates and account for about 8% of the human genome. They were considered as silent passengers within our genomes for a long time, however, reactivation of HERVs has been associated with tumors and autoimmune diseases, especially the HERV-K (HML-2) family, the most recent integration groups with the least number of mutations and the most biologically active to encode functional retroviral proteins and produce retrovirus-like particles. Increasing studies are committed to determining the potential role of HERV-K (HML-2) in pathogenicity. Although there is still no evidence for HERV-K (HML-2) as a direct cause of diseases, aberrant expression profiles of the HERV-K (HML-2) transcripts and their regulatory function to their proximal host-genes were identified in different diseases. In this review, we summarized the advances between HERV-K (HML-2) and diseases to provide basis for further studies on the causal relationship between HERV-K (HML-2) and diseases. We recommended more attention to polymorphic integrated HERV-K (HML-2) loci which could be genetic causative factors and be associated with inter-individual differences in tumorigenesis and autoimmune diseases.
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Affiliation(s)
- Bei Xue
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Mediterranean Center for Disease Control, University of Sassari, Sassari, Italy
| | - David J. Kelvin
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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22
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Vergara Bermejo A, Ragonnaud E, Daradoumis J, Holst P. Cancer Associated Endogenous Retroviruses: Ideal Immune Targets for Adenovirus-Based Immunotherapy. Int J Mol Sci 2020; 21:ijms21144843. [PMID: 32650622 PMCID: PMC7402293 DOI: 10.3390/ijms21144843] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022] Open
Abstract
Cancer is a major challenge in our societies, according to the World Health Organization (WHO) about 1/6 deaths were cancer related in 2018 and it is considered the second leading cause of death globally. Immunotherapies have changed the paradigm of oncologic treatment for several cancers where the field had fallen short in providing competent therapies. Despite the improvement, broadly acting and highly effective therapies capable of eliminating or preventing human cancers with insufficient mutated antigens are still missing. Adenoviral vector-based vaccines are a successful tool in the treatment of various diseases including cancer; however, their success has been limited. In this review we discuss the potential of adenovirus as therapeutic tools and the current developments to use them against cancer. More specifically, we examine how to use them to target endogenous retroviruses (ERVs). ERVs, comprising 8% of the human genome, have been detected in several cancers, while they remain silent in healthy tissues. Their low immunogenicity together with their immunosuppressive capacity aid cancer to escape immunosurveillance. In that regard, virus-like-vaccine (VLV) technology, combining adenoviral vectors and virus-like-particles (VLPs), can be ideal to target ERVs and elicit B-cell responses, as well as CD8+ and CD4+ T-cells responses.
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Affiliation(s)
- Amaia Vergara Bermejo
- InProTher, Bioinnovation Institute, Copenhagen Bio Science Park, 2200 Copenhagen, Denmark; (E.R.); (J.D.)
- Correspondence: (A.V.B.); (P.H.)
| | - Emeline Ragonnaud
- InProTher, Bioinnovation Institute, Copenhagen Bio Science Park, 2200 Copenhagen, Denmark; (E.R.); (J.D.)
| | - Joana Daradoumis
- InProTher, Bioinnovation Institute, Copenhagen Bio Science Park, 2200 Copenhagen, Denmark; (E.R.); (J.D.)
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Peter Holst
- InProTher, Bioinnovation Institute, Copenhagen Bio Science Park, 2200 Copenhagen, Denmark; (E.R.); (J.D.)
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: (A.V.B.); (P.H.)
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23
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Ye X, Waite JC, Dhanik A, Gupta N, Zhong M, Adler C, Malahias E, Ni M, Wei Y, Gurer C, Zhang W, Macdonald LE, Murphy AJ, Sleeman MA, Skokos D. Endogenous retroviral proteins provide an immunodominant but not requisite antigen in a murine immunotherapy tumor model. Oncoimmunology 2020; 9:1758602. [PMID: 32923116 PMCID: PMC7458611 DOI: 10.1080/2162402x.2020.1758602] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clinical observations suggest that responses to cancer immunotherapy are correlated with intra-tumoral T cell receptor (TCR) clonality, tumor mutation burden (TMB) and host HLA genotype, highlighting the importance of host T cell recognition of tumor antigens. However, the dynamic interplay between T cell activation state and changes in TCR repertoire in driving the identification of potential immunodominant antigen(s) remains largely unexplored. Here, we performed single-cell RNA-sequencing on CD8+ tumor-infiltrating T cells (TILs) using the murine colorectal tumor model MC38 to identify unique TCR sequences and validate their tumor reactivity. We found that the majority of clonally expanded TILs are tumor-reactive and their TCR repertoire is unique amongst individual MC38 tumor-bearing mice. Our query identified that multiple expanded TCR clones recognized the retroviral epitope p15E as an immunodominant antigen. In addition, we found that the endogenous retroviral genome encoding for p15E is highly expressed in MC38 tumors, but not in normal tissues, due to epigenetic derepression. Further, we demonstrated that the p15E-specific TILs exhibit an activated phenotype and an increase in frequency upon treatment with anti-41BB and anti-PD-1 combination immunotherapy. Importantly, we showed that although p15E-specific TILs are not required to mount a primary anti-tumor response, they contributed to the development of strong immune memory. Overall our results revealed that endogenous retroviral antigens expressed by tumor cells may represent an important and underappreciated category of tumor antigens that could be readily targeted in the clinic.
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Affiliation(s)
- Xuan Ye
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Janelle C Waite
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Ankur Dhanik
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Namita Gupta
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Maggie Zhong
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Christina Adler
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | | | - Min Ni
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Yi Wei
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Cagan Gurer
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Wen Zhang
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Lynn E Macdonald
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Andrew J Murphy
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | | | - Dimitris Skokos
- Cancer Immunology, Regeneron Pharmaceuticals, Tarrytown, NY, USA
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24
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Yin Q, Strong MJ, Zhuang Y, Flemington EK, Kaminski N, de Andrade JA, Lasky JA. Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq. BMC Pulm Med 2020; 20:81. [PMID: 32245461 PMCID: PMC7119082 DOI: 10.1186/s12890-020-1114-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 03/13/2020] [Indexed: 11/23/2022] Open
Abstract
Background Numerous publications suggest an association between herpes virus infection and idiopathic pulmonary fibrosis (IPF). These reports have employed immunohistochemistry, in situ hybridization and/or PCR, which are susceptible to specificity artifacts. Methods We investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide a high degree of both sensitivity and specificity. We quantified viral RNA expression for 740 viruses in 28 IPF patient lung biopsy samples and 20 controls. Key RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, HCV, herpesvirus saimiri and HERV-K). Results We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. Conclusions To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
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Affiliation(s)
- Qinyan Yin
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Michael J Strong
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Yan Zhuang
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Erik K Flemington
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, 300 Cedar Street, Ste S441D, New Haven, CT, 06519, USA
| | - Joao A de Andrade
- Division of Allergy, Pulmonary, Critical Care Medicine, Department of Medicine, Vanderbilt University, 1161 21st Avenue South, B1317 MCN, Nashville, TN, 37232-2650, USA
| | - Joseph A Lasky
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA.
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25
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Ebelt ND, Zuniga E, Johnson BL, Diamond DJ, Manuel ER. 5-Azacytidine Potentiates Anti-tumor Immunity in a Model of Pancreatic Ductal Adenocarcinoma. Front Immunol 2020; 11:538. [PMID: 32296439 PMCID: PMC7136411 DOI: 10.3389/fimmu.2020.00538] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/09/2020] [Indexed: 12/26/2022] Open
Abstract
Tumors evolve a variety of mechanisms to escape immune detection while expressing tumor-promoting molecules that can be immunogenic. Here, we show that transposable elements (TE) and gene encoded, tumor-associated antigens (TAA), which can be both highly immunogenic and tumor-promoting, are significantly upregulated during the transition from pre-malignancy to malignancy in an inducible model of pancreatic ductal adenocarcinoma (PDAC). Coincident with the increased presence of TEs and TAAs was the downregulation of gene transcripts associated with antigen presentation, T cell recruitment and intrinsic anti-viral responses, suggesting a unique strategy employed by PDAC to possibly augment tumorigenesis while escaping detection by the immune system. In vitro treatment of mouse and human PDAC cell lines with the DNA methyltransferase inhibitor 5-azacytidine (Aza) resulted in augmented expression of transcripts for antigen presentation machinery and T cell chemokines. When immunocompetent mice implanted with PDAC were therapeutically treated with Aza, we observed significant tumor regression that was not observed in immunocompromised mice, implicating anti-tumor immunity as the principal mechanism of tumor growth control. Analysis of PDAC tumors, immediately following Aza treatment in immunocompetent mice, revealed a significantly greater infiltration of T cells and various innate immune subsets compared to control treatment, suggesting that Aza treatment enhances tumor immunogenicity. Thus, augmenting antigen presentation and T cell chemokine expression using DNA methyltransferase inhibitors could be leveraged to potentiate adaptive anti-tumor immune responses against PDAC.
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Affiliation(s)
- Nancy D. Ebelt
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Edith Zuniga
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Benjamin L. Johnson
- Department of Hematology and Hematopoietic Stem Cell Transplantation, City of Hope, Duarte, CA, United States
| | - Don J. Diamond
- Department of Hematology and Hematopoietic Stem Cell Transplantation, City of Hope, Duarte, CA, United States
| | - Edwin R. Manuel
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, United States
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26
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Tatkiewicz W, Dickie J, Bedford F, Jones A, Atkin M, Kiernan M, Maze EA, Agit B, Farnham G, Kanapin A, Belshaw R. Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines. Mob DNA 2020; 11:9. [PMID: 32055257 PMCID: PMC7007669 DOI: 10.1186/s13100-020-0204-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The cell-surface attachment protein (Env) of the HERV-K(HML-2) lineage of endogenous retroviruses is a potentially attractive tumour-associated antigen for anti-cancer immunotherapy. The human genome contains around 100 integrated copies (called proviruses or loci) of the HERV-K(HML-2) virus and we argue that it is important for therapy development to know which and how many of these contribute to protein expression, and how this varies across tissues. We measured relative provirus expression in HERV-K(HML-2), using enriched RNA-Seq analysis with both short- and long-read sequencing, in three Mantle Cell Lymphoma cell lines (JVM2, Granta519 and REC1). We also confirmed expression of the Env protein in two of our cell lines using Western blotting, and analysed provirus expression data from all other relevant published studies. RESULTS Firstly, in both our and other reanalysed studies, approximately 10% of the transcripts mapping to HERV-K(HML-2) came from Env-encoding proviruses. Secondly, in one cell line the majority of the protein expression appears to come from one provirus (12q14.1). Thirdly, we find a strong tissue-specific pattern of provirus expression. CONCLUSIONS A possible dependency of Env expression on a single provirus, combined with the earlier observation that this provirus is not present in all individuals and a general pattern of tissue-specific expression among proviruses, has serious implications for future HERV-K(HML-2)-targeted immunotherapy. Further research into HERV-K(HML-2) as a possible tumour-associated antigen in blood cancers requires a more targeted, proteome-based, screening protocol that will consider these polymorphisms within HERV-K(HML-2). We include a plan (and necessary alignments) for such work.
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Affiliation(s)
- Witold Tatkiewicz
- Peninsula Medical School, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - James Dickie
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Franchesca Bedford
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Alexander Jones
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Mark Atkin
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Michele Kiernan
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Emmanuel Atangana Maze
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Bora Agit
- Peninsula Medical School, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Garry Farnham
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Alexander Kanapin
- Department of Oncology, University of Oxford, Oxford, UK
- Current address: Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Robert Belshaw
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
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27
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Karimi A, Esmaili N, Ranjkesh M, Zolfaghari MA. Expression of human endogenous retroviruses in pemphigus vulgaris patients. Mol Biol Rep 2019; 46:6181-6186. [PMID: 31473891 DOI: 10.1007/s11033-019-05053-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/28/2019] [Indexed: 01/09/2023]
Abstract
Pemphigus is a severe, potentially life-threatening autoimmune blistering mucocutaneous disease which establishes with autoreactive IgG antibodies that target cellular adhesions, precisely extracellular domains of keratinocyte proteins. Several genetic and environmental elements are believed to contribute to the pathogenesis of the disease. The extent to which the initiation and progress of this autoimmune blistering disease may be influenced by the expression of human endogenous retroviruses (HERVs) remains to be elucidated. In this study, we evaluated the expression of HERV groups (K, W, and H) in pemphigus vulgaris (PV) patients in comparison to controls. Peripheral blood samples were collected from 24 PV patients and the corresponding age- and sex-matched healthy controls to extract total RNA for evaluation of HERV-K (HML-2), HERV-W, and HERV-H, env gene expression profile by qPCR. The mRNA expression level of HERV-K, HERV-W, and HERV-H were significantly upregulated in PV patients in comparison to healthy controls (P < 0.0001). The difference in expression of studied HERVs groups between men and women was no significant (P > 0.05). Although rituximab taking patients had a decreased expression level of studied HERVs, the results were not significant (P > 0.05). According to our obtained data, HERVs expression could be measured as a possible diagnostic tool for detection of PV and monitoring of the treatment.
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Affiliation(s)
- Abbas Karimi
- Autoimmune Bullous Diseases Research Center, Tehran University of Medical Sciences, Razi Hospital, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Nafiseh Esmaili
- Autoimmune Bullous Diseases Research Center, Tehran University of Medical Sciences, Razi Hospital, Tehran, Iran.
| | - Mohammadreza Ranjkesh
- Department of Dermatology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Ali Zolfaghari
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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28
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Guffanti G, Bartlett A, Klengel T, Klengel C, Hunter R, Glinsky G, Macciardi F. Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex. Mol Biol Evol 2019; 35:2435-2453. [PMID: 30053206 PMCID: PMC6188555 DOI: 10.1093/molbev/msy143] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Expression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates’ evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Andrew Bartlett
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Goettingen, Germany
| | - Claudia Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Richard Hunter
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Gennadi Glinsky
- Translational & Functional Genomics, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA
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29
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Li F, Sabunciyan S, Yolken RH, Lee D, Kim S, Karlsson H. Transcription of human endogenous retroviruses in human brain by RNA-seq analysis. PLoS One 2019; 14:e0207353. [PMID: 30605476 PMCID: PMC6317784 DOI: 10.1371/journal.pone.0207353] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/30/2018] [Indexed: 01/01/2023] Open
Abstract
Background Human endogenous retroviruses (HERV) comprise 8% of the human genome and can be classified into at least 31 families. Increased levels of transcripts from the W and H families of HERV have been observed in association with human diseases, such as multiple sclerosis and schizophrenia. Although HERV transcripts have been detected in many tissues and cell-types based on microarray and PCR studies, the extent of HERV expression in different cell-types and diseases state has been less comprehensively studied. Results We examined overall transcription of HERV, and particularly of HERV-W and HERV-H elements in human postmortem brain samples obtained from individuals with psychiatric diagnoses (n = 111) and healthy controls (n = 51) by analyzing publicly available RNA sequencing datasets. Sequence reads were aligned to prototypical sequences representing HERV, downloaded from Repbase. We reported a consistent expression (0.1~0.2% of mappable reads) of different HERV families across three regions of human brains. Spearman correlations revealed highly correlated expression levels between three brain regionsacross 475 consensus sequences. By mapping sequences that aligned to the consensus sequences of HERV-W and HERV-H families to individual loci on chromosome 7, more than 60 loci from each family were identified, part of which are being transcribed. The ERVWE1, locus located at chr7q21.2, exhibited high levels of transcription across the three datasets. Notably, we demonstrated a trend of increased expression of overall HERV, as well as HERV-W family in samples from both schizophrenia and bipolar disorder patients. Conclusions The current analyses indicate that RNA sequencing is a useful approach for investigating global expression of repetitive elements, such as HERV, in the human genome. HERV-W/H with the tendency of transcription up-regulation in patients suggests potential implication of HERV-W/H in psychiatric diseases.
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MESH Headings
- Bipolar Disorder/genetics
- Bipolar Disorder/virology
- Brain/metabolism
- Brain/virology
- Chromosomes, Human, Pair 7/genetics
- Depression/genetics
- Depression/virology
- Endogenous Retroviruses/genetics
- Gene Expression Regulation, Viral
- Genetic Loci
- Genome, Human
- Humans
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Repetitive Sequences, Nucleic Acid/genetics
- Schizophrenia/genetics
- Schizophrenia/virology
- Sequence Analysis, RNA
- Statistics, Nonparametric
- Transcription, Genetic
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Affiliation(s)
- Fang Li
- The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (FL); (HK)
| | - Sarven Sabunciyan
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Robert H. Yolken
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Doheon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
| | - Sanghyeon Kim
- Stanley Medical Research Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Håkan Karlsson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (FL); (HK)
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30
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Garcia-Montojo M, Doucet-O'Hare T, Henderson L, Nath A. Human endogenous retrovirus-K (HML-2): a comprehensive review. Crit Rev Microbiol 2018; 44:715-738. [PMID: 30318978 DOI: 10.1080/1040841x.2018.1501345] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The human genome contains a large number of retroviral elements acquired over the process of evolution, some of which are specific to primates. However, as many of these are defective or silenced through epigenetic changes, they were historically considered "junk DNA" and their potential role in human physiology or pathological circumstances have been poorly studied. The most recently acquired, human endogenous retrovirus-K (HERV-K), has multiple copies in the human genome and some of them have complete open reading frames that are transcribed and translated, especially in early embryogenesis. Phylogenetically, HERV-K is considered a supergroup of viruses. One of the subtypes, termed HML-2, seems to be the most active and hence, it is the best studied. Aberrant expression of HML-2 in adult tissues has been associated with certain types of cancer and with neurodegenerative diseases. This review discusses the discovery of these viruses, their classification, structure, regulation and potential for replication, physiological roles, and their involvement in disease pathogenesis. Finally, it presents different therapeutic approaches being considered to target these viruses.
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Affiliation(s)
- Marta Garcia-Montojo
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Tara Doucet-O'Hare
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Lisa Henderson
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Avindra Nath
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
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31
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Matteucci C, Balestrieri E, Argaw-Denboba A, Sinibaldi-Vallebona P. Human endogenous retroviruses role in cancer cell stemness. Semin Cancer Biol 2018; 53:17-30. [PMID: 30317035 DOI: 10.1016/j.semcancer.2018.10.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/30/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022]
Abstract
Cancer incidence and mortality, metastasis, drug resistance and recurrence are still the critical issues of oncological diseases. In this scenario, increasing scientific evidences demonstrate that the activation of human endogenous retroviruses (HERVs) is involved in the aggressiveness of tumors such as melanoma, breast, germ cell, renal, ovarian, liver and haematological cancers. In their dynamic regulation, HERVs have also proved to be important determinants of pluripotency in human embryonic stem cells (ESC) and of the reprogramming process of induced pluripotent stem cells (iPSCs). In many types of tumors, essential characteristics of aggressiveness have been associated with the achievement of stemness features, often accompanied with the identification of defined subpopulations, termed cancer stem cells (CSCs), which possess stem cell-like properties and sustain tumorigenesis. Indeed, CSCs show high self-renewal capacity with a peculiar potential in tumor initiation, progression, metastasis, heterogeneity, recurrence, radiotherapy and drug resistance. However, HERVs role in CSCs biology is still not fully elucidated. In this regard, CD133 is a widely recognized marker of CSCs, and our group demonstrated, for the first time, the requirement of HERV-K activation to expand and maintain a CD133+ melanoma cell subpopulation with stemness features in response to microenvironmental modifications. The review will discuss HERVs expression as cancer hallmark, with particular focus on their role in the regulation of cancer stemness features and the potential involvement as targets for therapy.
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Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy.
| | - Emanuela Balestrieri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy
| | - Ayele Argaw-Denboba
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy; European Molecular Biology Laboratory (EMBL), Adriano Buzzati-Traverso Campus, Monterotondo, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy; Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere, 100, 00133, Rome, Italy
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Disruption by SaCas9 Endonuclease of HERV-K env, a Retroviral Gene with Oncogenic and Neuropathogenic Potential, Inhibits Molecules Involved in Cancer and Amyotrophic Lateral Sclerosis. Viruses 2018; 10:v10080412. [PMID: 30087231 PMCID: PMC6115762 DOI: 10.3390/v10080412] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The human endogenous retrovirus (HERV)-K, human mouse mammary tumor virus like-2 (HML-2) subgroup of HERVs is activated in several tumors and has been related to prostate cancer progression and motor neuron diseases. The cellular splicing factor 2/alternative splicing factor (SF2/ASF) is a positive regulator of gene expression, coded by a potent proto-oncogene, amplified, and abnormally expressed in tumors. TAR DNA-binding protein-43 (TDP-43) is a DNA/RNA-binding protein, negative regulator of alternative splicing, known for causing neurodegeneration, and with complex roles in oncogenesis. We used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, with the Cas9 system from Staphylococcus aureus (SaCas9), to disrupt the HERV-K(HML-2)env gene, and evaluated the effects on cultured cells. The tool was tested on human prostate cancer LNCaP cells, whose HERV-Kenv transcription profile is known. It caused HERV-K(HML-2)env disruption (the first reported of a HERV gene), as evaluated by DNA sequencing, and inhibition of env transcripts and proteins. The HERV-K(HML-2)env disruption was found to interfere with important regulators of cell expression and proliferation, involved in manaling, RNA-binding, and alternative splicing, such as epidermal growth factor receptor (EGF-R), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), SF2/ASF, and TDP-43. These novel findings suggest that HERV-K is not an innocent bystander, they reinforce its links to oncogenesis and motor neuron diseases, and they open potential innovative therapeutic options.
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33
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Mayer J, Harz C, Sanchez L, Pereira GC, Maldener E, Heras SR, Ostrow LW, Ravits J, Batra R, Meese E, García-Pérez JL, Goodier JL. Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. Mol Neurodegener 2018; 13:39. [PMID: 30068350 PMCID: PMC6091006 DOI: 10.1186/s13024-018-0275-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder. About 90% of ALS cases are without a known genetic cause. The human endogenous retrovirus multi-copy HERV-K(HML-2) group was recently reported to potentially contribute to neurodegeneration and disease pathogenesis in ALS because of transcriptional upregulation and toxic effects of HML-2 Envelope (Env) protein. Env and other proteins are encoded by some transcriptionally active HML-2 loci. However, more detailed information is required regarding which HML-2 loci are transcribed in ALS, which of their proteins are expressed, and differences between the disease and non-disease states. METHODS For brain and spinal cord tissue samples from ALS patients and controls, we identified transcribed HML-2 loci by generating and mapping HML-2-specific cDNA sequences. We predicted expression of HML-2 env gene-derived proteins based on the observed cDNA sequences. Furthermore, we determined overall HML-2 transcript levels by RT-qPCR and investigated presence of HML-2 Env protein in ALS and control tissue samples by Western blotting. RESULTS We identified 24 different transcribed HML-2 loci. Some of those loci are transcribed at relatively high levels. However, significant differences in HML-2 loci transcriptional activities were not seen when comparing ALS and controls. Likewise, overall HML-2 transcript levels, as determined by RT-qPCR, were not significantly different between ALS and controls. Indeed, we were unable to detect full-length HML-2 Env protein in ALS and control tissue samples despite reasonable sensitivity. Rather our analyses suggest that a number of HML-2 protein variants other than full-length Env may potentially be expressed in ALS patients. CONCLUSIONS Our results expand and refine recent publications on HERV-K(HML-2) and ALS. Some of our results are in conflict with recent findings and call for further specific analyses. Our profiling of HML-2 transcription in ALS opens up the possibility that HML-2 proteins other than canonical full-length Env may have to be considered when studying the role of HML-2 in ALS disease.
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Affiliation(s)
- Jens Mayer
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Christian Harz
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Esther Maldener
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Lyle W. Ostrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 28217 USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA USA
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA USA
| | - Eckart Meese
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
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Turnbull MG, Douville RN. Related Endogenous Retrovirus-K Elements Harbor Distinct Protease Active Site Motifs. Front Microbiol 2018; 9:1577. [PMID: 30072963 PMCID: PMC6058741 DOI: 10.3389/fmicb.2018.01577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023] Open
Abstract
Background: Endogenous retrovirus-K is a group of related genomic elements descending from retroviral infections in human ancestors. HML2 is the clade of these viruses which contains the most intact provirus copies. These elements can be transcribed and translated in healthy and diseased tissues, and some of them produce active retroviral enzymes, such as protease. Retroviral gene products, including protease, contribute to illness in exogenous retroviral infections. There are ongoing efforts to test anti-retroviral regimens against endogenous retroviruses. Herein, we examine the potential activity and diversity of human endogenous retrovirus-K proteases, and their potential for impact on immunity and human disease. Results: Sequences similar to the endogenous retrovirus-K HML2 protease and reverse transcriptase were identified in the human genome, classified by phylogenetic inference and compared to Repbase reference sequences. The topologies of trees inferred from protease and reverse transcriptase sequences were similar and agreed with the classification using reference sequences. Surprisingly, only 62/480 protease sequences identified by BLAST were classified as HML2; the remainder were classified as other HML groups, with the majority (216) classified as HML3. Variation in functionally significant protease motifs was explored, and two major active site variants were identified – the DTGAD variant is common in all groups, but the DTGVD motif appears limited to HML3, HML5, and HML6. Furthermore, distinct RNA expression patterns of protease variants are seen in disease states, such as amyotrophic lateral sclerosis, breast cancer, and prostate cancer. Conclusion: Transcribed ERVK proteases exhibit a diversity which could impact immunity and inhibitor-based treatments, and these facets should be considered when designing therapeutic regimens.
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Affiliation(s)
| | - Renée N Douville
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada.,Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
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35
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Fosso B, Santamaria M, D'Antonio M, Lovero D, Corrado G, Vizza E, Passaro N, Garbuglia AR, Capobianchi MR, Crescenzi M, Valiente G, Pesole G. MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data. Bioinformatics 2018; 33:1730-1732. [PMID: 28130230 PMCID: PMC5447231 DOI: 10.1093/bioinformatics/btx036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 01/19/2017] [Indexed: 11/12/2022] Open
Abstract
Summary Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets. Availability and Implementation https://github.com/bfosso/MetaShot. Contact graziano.pesole@uniba.it. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- B Fosso
- Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - M Santamaria
- Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy
| | | | - D Lovero
- Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - G Corrado
- Department of Oncological Surgery, Gynecologic Oncology Unit, "Regina Elena" National Cancer Institute, Rome, Italy
| | - E Vizza
- Department of Oncological Surgery, Gynecologic Oncology Unit, "Regina Elena" National Cancer Institute, Rome, Italy
| | - N Passaro
- Department of Cell Biology and Neurosciences, Italian National Institute of Health, Rome, Italy
| | - A R Garbuglia
- Lazzaro Spallanzani National Institute for Infectious Diseases, Rome, Italy
| | - M R Capobianchi
- Lazzaro Spallanzani National Institute for Infectious Diseases, Rome, Italy
| | - M Crescenzi
- Department of Cell Biology and Neurosciences, Italian National Institute of Health, Rome, Italy
| | - G Valiente
- Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain
| | - G Pesole
- Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
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36
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Bannert N, Hofmann H, Block A, Hohn O. HERVs New Role in Cancer: From Accused Perpetrators to Cheerful Protectors. Front Microbiol 2018; 9:178. [PMID: 29487579 PMCID: PMC5816757 DOI: 10.3389/fmicb.2018.00178] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/25/2018] [Indexed: 02/02/2023] Open
Abstract
Initial indications that retroviruses are connected to neoplastic transformation were seen more than a century ago. This concept has also been tested for endogenized retroviruses (ERVs) that are abundantly expressed in many transformed cells. In healthy cells, ERV expression is commonly prevented by DNA methylation and other epigenetic control mechanisms. ERVs are remnants of former exogenous forms that invaded the germ line of the host and have since been vertically transmitted. Several examples of ERV-induced genomic recombination events and dysregulation of cellular genes that contribute to tumor formation have been well documented. Moreover, evidence is accumulating that certain ERV proteins have oncogenic properties. In contrast to these implications for supporting cancer induction, a recent string of papers has described favorable outcomes of increasing human ERV (HERV) RNA and DNA abundance by treatment of cancer cells with methyltransferase inhibitors. Analogous to an infecting agent, the ERV-derived nucleic acids are sensed in the cytoplasm and activate innate immune responses that drive the tumor cell into apoptosis. This "viral mimicry" induced by epigenetic drugs might offer novel therapeutic approaches to help target cancer cells that are normally difficult to treat using standard chemotherapy. In this review, we discuss both the detrimental and the new beneficial role of HERV reactivation in terms of its implications for cancer.
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Affiliation(s)
- Norbert Bannert
- HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Henning Hofmann
- HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Adriana Block
- HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Oliver Hohn
- HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
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37
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Zare M, Mostafaei S, Ahmadi A, Azimzadeh Jamalkandi S, Abedini A, Esfahani-Monfared Z, Dorostkar R, Saadati M. Human endogenous retrovirus env genes: Potential blood biomarkers in lung cancer. Microb Pathog 2018; 115:189-193. [DOI: 10.1016/j.micpath.2017.12.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 02/07/2023]
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38
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HIV-1 Infection of Primary CD4 + T Cells Regulates the Expression of Specific Human Endogenous Retrovirus HERV-K (HML-2) Elements. J Virol 2017; 92:JVI.01507-17. [PMID: 29046457 DOI: 10.1128/jvi.01507-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/14/2017] [Indexed: 11/20/2022] Open
Abstract
Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathological states, such as viral infections and certain cancers, coincide with ERV expression, suggesting that transcriptional reawakening is possible. HML-2 elements are reportedly induced during HIV-1 infection, but the conserved nature of these elements has, until recently, rendered their expression profiling problematic. Here, we provide comprehensive HERV-K HML-2 expression profiles specific for productively HIV-1-infected primary human CD4+ T cells. We combined enrichment of HIV-1 infected cells using a reporter virus expressing a surface reporter for gentle and efficient purification with long-read single-molecule real-time sequencing. We show that three HML-2 proviruses-6q25.1, 8q24.3, and 19q13.42-are upregulated on average between 3- and 5-fold in HIV-1-infected CD4+ T cells. One provirus, HML-2 12q24.33, in contrast, was repressed in the presence of active HIV replication. In conclusion, this report identifies the HERV-K HML-2 loci whose expression profiles differ upon HIV-1 infection in primary human CD4+ T cells. These data will help pave the way for further studies on the influence of endogenous retroviruses on HIV-1 replication.IMPORTANCE Endogenous retroviruses inhabit big portions of our genome. Moreover, although they are mainly inert, some of the evolutionarily younger members maintain the ability to express both RNA and proteins. We have developed an approach using long-read single-molecule real-time (SMRT) sequencing that produces long reads that allow us to obtain detailed and accurate HERV-K HML-2 expression profiles. We applied this approach to study HERV-K expression in the presence or absence of productive HIV-1 infection of primary human CD4+ T cells. In addition to using SMRT sequencing, our strategy also includes the magnetic selection of the infected cells so that levels of background expression due to uninfected cells are kept at a minimum. The results presented here provide a blueprint for in-depth studies of the interactions of the authentic upregulated HERV-K HML-2 elements and HIV-1.
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39
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Ho XD, Nguyen HG, Trinh LH, Reimann E, Prans E, Kõks G, Maasalu K, Le VQ, Nguyen VH, Le NTN, Phung P, Märtson A, Lattekivi F, Kõks S. Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma. Front Genet 2017; 8:193. [PMID: 29250102 PMCID: PMC5714928 DOI: 10.3389/fgene.2017.00193] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 02/05/2023] Open
Abstract
Osteosarcoma (OS) is a rare malignant bone tumor. It affects mostly young persons and has poor outcome with the present treatment. No improvement was observed since the introduction of chemotherapy. The better understanding of osteosarcoma development could indicate better management strategy. Repetitive DNA elements were found to play a role in cancer mechanism especially in epithelial tumors but not yet analyzed in osteosarcoma. We conducted the study to analyse the expression profile of repetitive elements (RE) in osteosarcoma. Methods: Fresh bone paired (tumor and normal bone) samples were obtained from excised parts of tumors of 18 patients with osteosarcoma. We performed sequencing of RNA extracted from 36 samples (18 tumor tissues and 18 normal bone for controls), mapped raw reads to the human genome and identified the REs. EdgeR package was used to analyse the difference in expression of REs between osteosarcoma and normal bone. Results: 82 REs were found differentially expressed (FDR < 0.05) between osteosarcoma and normal bone. Out of all significantly changed REs, 35 were upregulated and 47 were downregulated. HERVs (THE1C-int, LTR5, MER57F and MER87B) and satellite elements (HSATII, ALR-alpha) were the most significantly differential expressed elements between osteosarcoma and normal tissues. These results suggest significant impact of REs in the osteosarcoma. The role of REs should be further studied to understand the mechanism they have in the genesis of osteosarcoma.
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Affiliation(s)
- Xuan D Ho
- Department of Oncology, College of Medicine and Pharmacy, Hue University, Hue, Vietnam.,Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Hoang G Nguyen
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Le H Trinh
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Ene Reimann
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Ele Prans
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Gea Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.,Clinic of Traumatology and Orthopaedics of Tartu University Hospital, Tartu, Estonia
| | - Van Q Le
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Van H Nguyen
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Nghi T N Le
- Department of Orthopedics, College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Phuong Phung
- Department of Oncology, College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Aare Märtson
- Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.,Clinic of Traumatology and Orthopaedics of Tartu University Hospital, Tartu, Estonia
| | - Freddy Lattekivi
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Sulev Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
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40
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Schulz WA. Does HERV-K represent a potential therapeutic target for prostate cancer? Expert Opin Ther Targets 2017; 21:921-924. [PMID: 28847189 DOI: 10.1080/14728222.2017.1373095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wolfgang A Schulz
- a Department of Urology, Medical Faculty , Heinrich Heine University , Düsseldorf , Germany
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41
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Terry SN, Manganaro L, Cuesta-Dominguez A, Brinzevich D, Simon V, Mulder LCF. Expression of HERV-K108 envelope interferes with HIV-1 production. Virology 2017; 509:52-59. [PMID: 28605635 DOI: 10.1016/j.virol.2017.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022]
Abstract
The human endogenous retroviruses (HERV)-K of the HML-2 group include full-length or near full-length elements encoding functional proteins, and are classified as type-1 or type-2 (type-1 has a deletion in the 5' end of the env gene). Because proteins of different retroviruses can interact, we hypothesized that HERV-K envelope (Env) could influence HIV-1 replication. Here we describe the negative effect of envelope expression of certain type-2 HERV-Ks on HIV-1 production. All HIV-1 and SIV strains tested were susceptible to various degrees to inhibition by the HERV-K108 envelope. We identified four residues within HERV-K108 Env as being critical to inhibit HIV-1 production. No inhibition was observed on EGFP expression, indicating that HERV-K Env does not affect general protein production. These findings demonstrate that envelope proteins from some endogenous retroviruses can limit production of exogenous lentiviruses such as HIV-1. Future studies will elucidate the mechanism mediating HIV-1 inhibition by HERV Envs.
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Affiliation(s)
- Sandra N Terry
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lara Manganaro
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alvaro Cuesta-Dominguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daria Brinzevich
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lubbertus C F Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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42
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Manghera M, Magnusson A, Douville RN. The sense behind retroviral anti-sense transcription. Virol J 2017; 14:9. [PMID: 28088235 PMCID: PMC5237517 DOI: 10.1186/s12985-016-0667-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/09/2016] [Indexed: 12/15/2022] Open
Abstract
Retroviruses are known to rely extensively on the expression of viral proteins from the sense proviral genomic strand. Yet, the production of regulatory retroviral proteins from antisense-encoded viral genes is gaining research attention, due to their clinical significance. This report will discuss what is known about antisense transcription in Retroviridae, and provide new information about antisense transcriptional regulation through a comparison of Human Immunodeficiency Virus (HIV), Human T-cell Lymphotrophic Virus (HTLV-1) and endogenous retrovirus-K (ERVK) long terminal repeats (LTRs). We will attempt to demonstrate that the potential for antisense transcription is more widespread within retroviruses than has been previously appreciated, with this feature being the rule, rather than the exception.
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Affiliation(s)
- Mamneet Manghera
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Alycia Magnusson
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
| | - Renée N Douville
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada.
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43
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Rastogi A, Ali A, Tan SH, Banerjee S, Chen Y, Cullen J, Xavier CP, Mohamed AA, Ravindranath L, Srivastav J, Young D, Sesterhenn IA, Kagan J, Srivastava S, McLeod DG, Rosner IL, Petrovics G, Dobi A, Srivastava S, Srinivasan A. Autoantibodies against oncogenic ERG protein in prostate cancer: potential use in diagnosis and prognosis in a panel with C-MYC, AMACR and HERV-K Gag. Genes Cancer 2017; 7:394-413. [PMID: 28191285 PMCID: PMC5302040 DOI: 10.18632/genesandcancer.126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Overdiagnosis and overtreatment of prostate cancer (CaP) is attributable to widespread reliance on PSA screening in the US. This has prompted us and others to search for improved biomarkers for CaP, to facilitate early detection and disease stratification. In this regard, autoantibodies (AAbs) against tumor antigens could serve as potential candidates for diagnosis and prognosis of CaP. Towards this, our goals were: i) To investigate whether AAbs against ERG oncoprotein (overexpressed in 25-50% of Caucasian American and African American CaP) are present in the sera of CaP patients; ii) To evaluate an AAb panel to enhance CaP detection. The results using an enzyme-linked immunosorbent assay (ELISA) showed that anti-ERG AAbs are present in a significantly higher proportion in the sera of CaP patients compared to healthy controls (p = 0.0001). Furthermore, a panel of AAbs against ERG, AMACR and human endogenous retrovirus-K Gag successfully differentiated CaP patient sera from healthy controls (AUC = 0.791). These results demonstrate for the first time that anti-ERG AAbs are present in the sera of CaP patients. In addition, the data also suggest that AAbs against ERG together with AMACR and HERV-K Gag may be a useful panel of biomarkers for diagnosis and prognosis of CaP.
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Affiliation(s)
- Anshu Rastogi
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Amina Ali
- Urology Service, Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Shyh-Han Tan
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Sreedatta Banerjee
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Yongmei Chen
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Charles P Xavier
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Ahmed A Mohamed
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Lakshmi Ravindranath
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jigisha Srivastav
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Denise Young
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - David G McLeod
- Urology Service, Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Inger L Rosner
- Urology Service, Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Albert Dobi
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shiv Srivastava
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Alagarsamy Srinivasan
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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44
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Walsh SR, Gerpe MCR, Wootton SK. Construction of a molecular clone of ovine enzootic nasal tumor virus. Virol J 2016; 13:209. [PMID: 28038674 PMCID: PMC5203713 DOI: 10.1186/s12985-016-0660-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enzootic nasal tumor virus (ENTV-1) is an ovine betaretrovirus that has been linked to enzootic nasal adenocarcinoma (ENA), a contagious tumor of the ethmoid turbinates of sheep. Transmission experiments performed using virus isolated from cell free nasal tumor homogenates suggest that ENTV-1 is the causative agent of ENA; however, this etiological relationship has not been conclusively proven due to the fact that the virus cannot be propagated in vitro nor is there an infectious molecular clone of the virus. METHODS Here we report construction of a molecular clone of ENTV-1 and demonstrate that transfection of this molecular clone into HEK 293T cells produces mature virus particles. RESULTS Analysis of recombinant virus particles derived from the initial molecular clone revealed a defect in the proteolytic processing of Gag; however, this defect could be corrected by co-expression of the Gag-Pro-Pol polyprotein from the highly related Jaagsiekte sheep retrovirus (JSRV) suggesting that the polyprotein cleavage sites in the ENTV-1 molecular clone were functional. Mutagenesis of the molecular clone to correct amino acid variants identified within the pro gene did not restore proteolytic processing; whereas deletion of one proline residue from a polyproline tract located in variable region 1 (VR1) of the matrix resulted in production of CA protein of the mature (cleaved) size strongly suggesting that normal virion morphogenesis and polyprotein cleavage took place. Finally, electron microscopy revealed the presence of spherical virus particles with an eccentric capsid and an average diameter of about 100 nm. CONCLUSION In summary, we have constructed the first molecular clone of ENTV-1 from which mature virus particles can be produced. Future experiments using virus produced from this molecular clone can now be conducted to fulfill Koch's postulates and demonstrate that ENTV-1 is necessary and sufficient to induce ENA in sheep.
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Affiliation(s)
- Scott R Walsh
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - María Carla Rosales Gerpe
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Sarah K Wootton
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.
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45
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Ondrésik M, Azevedo Maia FR, da Silva Morais A, Gertrudes AC, Dias Bacelar AH, Correia C, Gonçalves C, Radhouani H, Amandi Sousa R, Oliveira JM, Reis RL. Management of knee osteoarthritis. Current status and future trends. Biotechnol Bioeng 2016; 114:717-739. [DOI: 10.1002/bit.26182] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/13/2016] [Accepted: 09/09/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Marta Ondrésik
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
| | - Fatima R. Azevedo Maia
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
| | - Alain da Silva Morais
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
- Stemmatters, Biotecnologia e Medicina Regenerativa SA; Guimaraes Portugal
| | - Ana C. Gertrudes
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
- Stemmatters, Biotecnologia e Medicina Regenerativa SA; Guimaraes Portugal
| | - Ana H. Dias Bacelar
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
- Stemmatters, Biotecnologia e Medicina Regenerativa SA; Guimaraes Portugal
| | - Cristina Correia
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
- Stemmatters, Biotecnologia e Medicina Regenerativa SA; Guimaraes Portugal
| | - Cristiana Gonçalves
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
- Stemmatters, Biotecnologia e Medicina Regenerativa SA; Guimaraes Portugal
| | - Hajer Radhouani
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
- Stemmatters, Biotecnologia e Medicina Regenerativa SA; Guimaraes Portugal
| | - Rui Amandi Sousa
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
- Stemmatters, Biotecnologia e Medicina Regenerativa SA; Guimaraes Portugal
| | - Joaquim M. Oliveira
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
| | - Rui L. Reis
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; Universidade do Minho, Headquarters of the European Institute Regenerative Medicine; AvePark 4806-909, Caldas das Taipas Guimaraes Portugal
- ICVS/3B's-PT Government Associated Laboratory; Braga/Guimaraes Portugal
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Li W, Lee MH, Henderson L, Tyagi R, Bachani M, Steiner J, Campanac E, Hoffman DA, von Geldern G, Johnson K, Maric D, Morris HD, Lentz M, Pak K, Mammen A, Ostrow L, Rothstein J, Nath A. Human endogenous retrovirus-K contributes to motor neuron disease. Sci Transl Med 2016; 7:307ra153. [PMID: 26424568 DOI: 10.1126/scitranslmed.aac8201] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The role of human endogenous retroviruses (HERVs) in disease pathogenesis is unclear. We show that HERV-K is activated in a subpopulation of patients with sporadic amyotrophic lateral sclerosis (ALS) and that its envelope (env) protein may contribute to neurodegeneration. The virus was expressed in cortical and spinal neurons of ALS patients, but not in neurons from control healthy individuals. Expression of HERV-K or its env protein in human neurons caused retraction and beading of neurites. Transgenic animals expressing the env gene developed progressive motor dysfunction accompanied by selective loss of volume of the motor cortex, decreased synaptic activity in pyramidal neurons, dendritic spine abnormalities, nucleolar dysfunction, and DNA damage. Injury to anterior horn cells in the spinal cord was manifested by muscle atrophy and pathological changes consistent with nerve fiber denervation and reinnervation. Expression of HERV-K was regulated by TAR (trans-activation responsive) DNA binding protein 43, which binds to the long terminal repeat region of the virus. Thus, HERV-K expression within neurons of patients with ALS may contribute to neurodegeneration and disease pathogenesis.
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Affiliation(s)
- Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myoung-Hwa Lee
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa Henderson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richa Tyagi
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Muzna Bachani
- Neurotherapeutics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Steiner
- Neurotherapeutics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emilie Campanac
- Molecular Neurophysiology and Biophysics Section, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dax A Hoffman
- Molecular Neurophysiology and Biophysics Section, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gloria von Geldern
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kory Johnson
- Bioinformatics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 21042, USA
| | - Dragan Maric
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - H Douglas Morris
- Mouse Imaging Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 21042, USA
| | - Margaret Lentz
- Integrated Research Facility, National Institute of Allergy and Infectious Disease, National Institutes of Health, Fort Detrick, Frederick, MD 21042, USA
| | - Katherine Pak
- Laboratory of Muscle Stem Cell and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 21042 , USA
| | - Andrew Mammen
- Laboratory of Muscle Stem Cell and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 21042 , USA
| | - Lyle Ostrow
- Department of Neurology, Johns Hopkins University, Baltimore, MD 28217, USA
| | - Jeffrey Rothstein
- Department of Neurology, Johns Hopkins University, Baltimore, MD 28217, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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Goering W, Schmitt K, Dostert M, Schaal H, Deenen R, Mayer J, Schulz WA. Human endogenous retrovirus HERV-K(HML-2) activity in prostate cancer is dominated by a few loci. Prostate 2015; 75:1958-71. [PMID: 26384005 DOI: 10.1002/pros.23095] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/02/2015] [Indexed: 11/11/2022]
Abstract
BACKGROUND Increased expression of human endogenous retroviruses, especially HERV-K(HML-2) proviruses, has recently been associated with prostate carcinoma progression. In particular, a HML-2 locus in chromosome 22q11.23 (H22q) is upregulated in many cases. We therefore aimed at delineating the extent and repertoire of HML-2 transcription in prostate cancer tissues and cell lines and to define the transcription pattern and biological effects of H22q. METHODS Sanger and high throughput amplicon sequencing was used to define the repertoire of expressed HML-2 in a selected set of samples. qRT-PCR was used to quantify expression of selected proviruses in an extended set of prostate cancer tissues. Transcription factor binding sites (TFBS) were compared bioinformatically using the Transfac database. Expression of H22q was further characterized by siRNA-mediated knockdown, 5' RACE mapping of transcriptional start sites (TSS) and identification of splice sites. Functional effects of H22q knockdown were investigated by viability and apoptosis assays. RESULTS In addition to H22q, a limited number of other proviruses were found expressed by sequencing. Of these, provirus ERVK-5 and to a lesser degree ERVK-15 were frequently upregulated in prostate cancer. In contrast, expression of ERVK-24, predominant in germ cell tumors, was not detectable in prostatic tissues. While HML-2 LTRs contain binding sites for the androgen receptor and cofactors, no consistent differences in transcription factor binding sites were found between expressed and non-expressed proviruses. The H22q locus contains two 5'-LTRs of which the upstream LTR is predominantly used in prostatic cells, with an imprecise TSS. Splicing of H22q transcripts is complex, generating, among others, a transcript with an Np9-like ORF. Knockdown of H22q did not significantly affect proliferation or apoptosis of prostate cancer cells. CONCLUSIONS Our findings further underline that HML-2 expression is commonly highly tissue-specific. In prostate cancer, a limited number of loci become activated, especially H22q and ERVK-5. As expressed and non-expressed proviruses do not differ significantly in TFBS, tissue- and tumor-specific expression may be governed primarily by chromatin context. Overexpression of HML-2 H22q is more likely consequence than cause of prostate cancer progression.
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Affiliation(s)
- Wolfgang Goering
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Katja Schmitt
- Institute of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany
| | - Melanie Dostert
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - René Deenen
- GTL, Biomedical Research Center, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens Mayer
- Institute of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Schmitt K, Heyne K, Roemer K, Meese E, Mayer J. HERV-K(HML-2) rec and np9 transcripts not restricted to disease but present in many normal human tissues. Mob DNA 2015; 6:4. [PMID: 25750667 PMCID: PMC4351823 DOI: 10.1186/s13100-015-0035-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/12/2015] [Indexed: 01/03/2023] Open
Abstract
Background Human endogenous retroviruses of the HERV-K(HML-2) group have been associated with the development of tumor diseases. Various HERV-K(HML-2) loci encode retrovirus-like proteins, and expression of such proteins is upregulated in certain tumor types. HERV-K(HML-2)-encoded Rec and Np9 proteins interact with functionally important cellular proteins and may contribute to tumor development. Though, the biological role of HERV-K(HML-2) transcription and encoded proteins in health and disease is less understood. We therefore investigated transcription specifically of HERV-K(HML-2) rec and np9 mRNAs in a panel of normal human tissues. Results We obtained evidence for rec and np9 mRNA being present in all examined 16 normal tissue types. A total of 18 different HERV-K(HML-2) loci were identified as generating rec or np9 mRNA, among them loci not present in the human reference genome and several of the loci harboring open reading frames for Rec or Np9 proteins. Our analysis identified additional alternative splicing events of HERV-K(HML-2) transcripts, some of them encoding variant Rec/Np9 proteins. We also identified a second HERV-K(HML-2) locus formed by L1-mediated retrotransposition that is likewise transcribed in various human tissues. Conclusions HERV-K(HML-2) rec and np9 transcripts from different HERV-K(HML-2) loci appear to be present in various normal human tissues. It is conceivable that Rec and Np9 proteins and variants of those proteins are part of the proteome of normal human tissues and thus various cell types. Transcription of HERV-K(HML-2) may thus also have functional relevance in normal human cell physiology. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0035-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Schmitt
- Institute of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, 66424 Homburg/Saar, Germany ; Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, K703, Elisabeth Kuhn Street, Frankfurt/Main, 65926 Germany
| | - Kristina Heyne
- José Carreras Research Center, Medical Faculty, University of Saarland, 66424 Homburg/Saar, Germany
| | - Klaus Roemer
- José Carreras Research Center, Medical Faculty, University of Saarland, 66424 Homburg/Saar, Germany
| | - Eckart Meese
- Institute of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, 66424 Homburg/Saar, Germany
| | - Jens Mayer
- Institute of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, 66424 Homburg/Saar, Germany ; Center of Human and Molecular Biology, University of Saarland, 66424 Homburg/Saar, Germany
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Downey RF, Sullivan FJ, Wang-Johanning F, Ambs S, Giles FJ, Glynn SA. Human endogenous retrovirus K and cancer: Innocent bystander or tumorigenic accomplice? Int J Cancer 2014; 137:1249-57. [PMID: 24890612 PMCID: PMC6264888 DOI: 10.1002/ijc.29003] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 05/02/2014] [Accepted: 05/09/2014] [Indexed: 12/20/2022]
Abstract
Harbored as relics of ancient germline infections, human endogenous retroviruses (HERVs) now constitute up to 8% of our genome. A proportion of this sequence has been co-opted for molecular and cellular processes, beneficial to human physiology, such as the fusogenic activity of the envelope protein, a vital component of placentogenesis. However, the discovery of high levels of HERV-K mRNA and protein and even virions in a wide array of cancers has revealed that HERV-K may be playing a more sinister role–a role as an etiological agent in cancer itself. Whether the presence of this retroviral material is simply an epiphenomenon, or an actual causative factor, is a hotly debated topic. This review will summarize the current state of knowledge regarding HERV-K and cancer and attempt to outline the potential mechanisms by which HERV-K could be involved in the onset and promotion of carcinogenesis.
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Affiliation(s)
- Ronan F Downey
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland
| | - Francis J Sullivan
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland.,Department of Radiation Oncology, Galway University Hospitals, Galway, Ireland
| | | | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD
| | - Francis J Giles
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland.,HRB Clinical Research Facilities Galway & Dublin, National University of Ireland Galway and Trinity College Dublin, Galway, Ireland
| | - Sharon A Glynn
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland
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