Mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE84275 | GEO | 2017/10/13
SECONDARY ACCESSION(S): PRJNA328504
REPOSITORIES: GEO
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Project description:The biological function and disease association of human endogenous retroviral (HERV) elements remains largely elusive. We addressed the physiological role of HERV-K(HML-2) in neuronal differentiation by manipulating HERV-K(HML-2) expression levels. We used CRISPR engineering to activate or repress HERV-K(HML-2) and demonstrate that elevated HERV-K(HML-2) transcription is detrimental for development, functionality and growth of cortical neurons. Effects are cell-type specific, as dopaminergic neurons were unaffected. We further show that layer formation is altered during forebrain organoid formation following activation of HERV-K(HML-2) transcription. HERV-K(HML-2) transcriptional activation concurrently elevated Neurotrophic Tyrosine Receptor Kinase 3 (NTRK3) expression along with other neurodegeneration-related genes. Direct transcriptional activation of NTRK3 resembled the HERV-K(HML-2) activation phenotype. Intriguingly, reduction of NTRK3 levels in HERV-K(HML-2)-activated cortical neurons restored differentiated cortical neurons. Hence, our findings unravel a unique cell type-specific mechanism of HERV-K(HML-2) during cortical neuronal differentiation.
2021-03-30 | GSE171101 | GEO
Project description:Increasing evidence suggests that repetitive elements may play a role in host gene regulation, particularly through the donation of alternative promoters, enhancers, splice sites, and termination signals. Elevated transcript expression of the endogenous retrovirus group HERV-K (HML-2) is seen in many human cancers, although the identities of the individual proviral loci contributing to this expression as well as their mechanisms of activation have been unclear. Using high-throughput next-generation sequencing techniques optimized for the capture of HML-2 expression, we characterized the HML-2 transcriptome and means of activation in an in vitro model of human mammary epithelial cell transformation. Our analysis showed significant expression originating from 15 HML-2 full-length proviruses, through four modes of transcription. The majority of expression was in the antisense orientation and from proviruses integrated within introns. We found two instances of long terminal repeat (LTR)-driven provirus transcription but no evidence to suggest that these active 5' LTRs were influencing nearby host gene expression. Importantly, LTR-driven transcription was restricted to tumorigenic cells, suggesting that LTR promoter activity is dependent upon the transcriptional environment of a malignant cell.IMPORTANCE Here, we use an in vitro model of human mammary epithelial cell transformation to assess how malignancy-associated shifts in the transcriptional milieu of a cell may impact HML-2 activity. We found 15 proviruses to be significantly expressed through four different mechanisms, with the majority of transcripts being antisense copies of proviruses located within introns. We saw active 5' LTR use in tumorigenic cells only, suggesting that the cellular environment of a cancer cell is a critical component for induction of LTR promoter activity. These findings have implications for future studies investigating HML-2 as a target for immunotherapy or as a biomarker for disease.
| S-EPMC5730778 | biostudies-literature
Project description:Identification of transcribed HERV-K(HML-2) loci in amyotrophic lateral sclerosis
| PRJEB23125 | ENA
Project description:The human genome consists of considerable portions derived from retroviruses typically inherited already for millions of years. So-called human endogenous retroviruses (HERVs) are usually severely mutated, yet some coding-competent HERV sequences exist. The HERV-K(HML-2) group includes evolutionarily young proviruses that still encode typical retroviral proteins. HERV-K(HML-2) has been implicated in various human diseases because transcription is often upregulated and encoded proteins are known to affect cell biology. HERV-K(HML-2) protease has received little attention so far. With findings for Human Immunodeficiency Virus (HIV) protease in mind we set out to identify human cellular proteins being substrates of HERV-K(HML-2) protease employing a modified Terminal Amine Isotopic Labeling of Substrates (TAILS) procedure. Thousands of significantly processed human proteins were revealed by TAILS and we could verify cleavage of a majority of selected human proteins in vitro. Our analysis suggests that hundreds, if not thousands of cellular proteins are potential substrates of HERV-K(HML-2) protease. As identified proteins participate in diverse, often disease-relevant cellular processes, it is conceivable that expression of HERV-K(HML-2) protease has functional consequences for cell biology and thus development of human diseases. Endogenous retrovirus-encoded protease may also be relevant for disease development in species other than human.
2019-09-02 | PXD010159 | Pride
Project description:Background: The human genome consists of considerable portions derived from retroviruses inherited for millions of years. So-called human endogenous retroviruses (HERVs) are usually severely mutated, yet some coding-competent HERVs exist. The HERV-K(HML-2) group includes evolutionarily young proviruses that still encode typical retroviral proteins. HERV-K(HML-2) has been implicated in various human diseases because transcription is often upregulated and some of the encoded proteins are known to affect cell biology. HERV-K(HML-2) Protease (Pro) has received little attention so far, although it appears expressed in some disease contexts and other retroviral proteases are known to process cellular proteins. Results: We set out to identify human cellular proteins being substrates of HERV-K(HML-2) Pro employing a modified Terminal Amine Isotopic Labeling of Substrates (TAILS) procedure. Thousands of human proteins were identified as significantly processed by HERV-K(HML-2) Pro. Identified proteins locate to various cellular compartments and participate in diverse, often disease-relevant cellular processes. We verified cleavage of a majority of selected human proteins in vitro and in vivo. Conclusions: Hundreds, if not thousands of cellular proteins are potential substrates of HERV-K(HML-2) Pro. It is conceivable that even low-level expression of HERV-K(HML-2) Pro has a functional impact on cell biology and thus relevance for human diseases. Specific studies will be required to elucidate effects of HERV-K(HML-2) Pro expression regarding human substrate proteins, cell biology and disease. Endogenous retrovirus-encoded Pro activity may also be relevant for disease development in species other than human.
2019-09-02 | PXD013296 | Pride
Project description:The endogenous retrovirus type W (HERV-W) is a human specific entity, which was initially discovered in multiple sclerosis (MS) patient derived cells. We initially found that the HERV-W envelope (ENV) protein negatively affects oligodendrogenesis and controls microglial cell polarization towards a myelinated axon associated and damaging phenotype. Such first functional assessments were conducted ex vivo, given the human specific origin of HERV-W. Recent experimental evidence gathered on a novel transgenic mouse model, mimicking activation and expression of the HERV-W ENV protein, revealed that all glial cell types are impacted and that cellular fates, differentiation, and functions were changed. In order to identify a HERV-W specific signature in glial cells, the current study analyzed the transcriptome of ENV stimulated microglial- and astroglial cells and compared the transcriptomic signature to lipopolysaccharide (LPS) stimulated cells, owing to the fact that both ligands can activate toll-like receptor-4 (TLR-4). Additionally, a comparison between published disease associated glial signatures and the transcriptome of HERV-W ENV stimulated glial cells was conducted. We, therefore, provide here for the first time a detailed molecular description of specific HERV-W ENV evoked effects on those glial cell populations that are involved in smoldering neuroinflammatory processes relevant for progression of neurodegenerative diseases.
2024-03-30 | GSE262029 | GEO
Project description:Human Endogenous Retroviruses (HERVs) are exogenous viral elements that integrated into the germline millions of years ago. They comprise 8% of the human genome and play a critical role in cellular differentiation during development. HERV-K(HML-2) is the most recently integrated and actively transcribed HERV. It is found to be highly expressed in pluripotent stem cells and strongly downregulated during cellular differentiation. Moreover, expression of HERV-K in terminally differentiated neurons results in cytotoxicity. Expression of HERVs has been implicated in carcinogenesis and is suggested to confer stem cell like features important for cell growth. Atypical Teratoid / Rhabdoid Tumor (AT/RT) is a rare pediatric brain cancer that results from incomplete neuronal differentiation during embryonic development. In this paper, we investigated the cytopathic effect of Ouabain, a cardiac glycoside that induces cytotoxicity in stem cells, on AT/RT cells. We characterized four AT/RT cell lines by immunostaining and observed variable levels of stem cell, Oct4 and Pax6, and neuronal differentiation markers, TUBB3 and MAP2, as well as HERV-K envelope (env), polymerase (pol), and gag transcripts. We stained formalin-fixed brain tissues from 20 AT/RT patients and 5 unaffected controls for HERV-K ENV protein expression. 40% of AT/RT patient tissues showed ENV expression. In contrast, no ENV immunostaining was observed in all 5 control brain tissues. We used Ouabain, known to be cytotoxic to stem cells, observed up to 50% toxicity at 24 hr and 80% toxicity at 48 hr after treatment. While AT/RT primarily exist as large cell aggregates in suspension, Ouabain treatment downregulated HERV-K ENV protein and caused disruption of cell-to-cell interactions. Similarly, when AT/RT cells were transfected with a CRISPR/Cas9 construct designed to repress HERV-K promotor activity, cell aggregates separated and cell viability decreased significantly. Using a luciferase reporter construct under the control of a HERV-K promotor, we observed a significant decrease in HERV-K promotor activity at 8 to 72 hr post treatment with 0.5 uM Ouabain. Given that downregulation of HERV-K alone was sufficient to cause cytotoxicity in the cells, HERV-K expression may be essential for AT/RT growth and survival. Ouabain and other compounds that modulate HERV expression may provide an alternative or adjunctive therapeutic option for treatment of embryonal tumors.
2021-06-28 | GSE124210 | GEO
Project description:The HERV-K(HML2) family is a group of elements of retroviral origin that are present in the human genome. They are silenced in most normal tissues, but are induced in a number of human cancers. In order to assess the relevance of their expression in these pathologies, the consequences of ectopic expression of the HERV-K(HML2) envelope protein were analysed in human 293T cells. The cells were transfected with a control vector, or an expression vector for the HERV-K(HML2) envelope protein. Total RNA was extracted 24h and 48h post transfection, and duplicate samples were analysed on whole genome transcriptional microarrays.
2017-06-17 | E-MTAB-5509 | biostudies-arrayexpress
Project description:Activation of HERV-K(HML-2) limits cortical neuronal differentiation by modulating Neurotrophic Tyrosine Receptor Kinase 3 expression
| PRJNA718326 | ENA