Patent Application
20220332799
The present invention relates to inhibitors of endogenous retrovirus (ERV) components, including Env and Gag proteins or fragments thereof, for use in treating a tauopathy, Parkinson's disease, or ALS (Amyothrophic Lateral Sclerosis). The present invention further relates to inhibitors of receptors which bind HERV Env proteins for use in treating a tauopathy, Parkinson's disease, or ALS (Amyothrophic Lateral Sclerosis). The present invention further relates to molecules binding to HERV Env and/or Gag proteins, or fragments thereof, or to a nucleic acid molecule encoding said HERV Env and/or Gag proteins, or fragments thereof, for use in diagnosing a tauopathy, Parkinson's disease, or ALS.
The deposition of intracellular fibrillar phosphorylated Tau in the central nervous system is a pathologic hallmark of a heterogeneous group of at least 20 neurodegenerative diseases, collectively termed tauopathies. These include Alzheimer's Disease (AD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD) and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17) and others (Williams, Intern Med J (2006), 36: 652-660). AD, the most common tauopathy, is characterized by the presence of senile plaques composed of amyloid-8 peptide, as well as by the formation of intraneuronal tangles composed of phosphorylated Tau. With a prevalence of approx. 46.8 million AD patients worldwide in 2015 and an estimated number of 131.5 million cases by 2050 due to demographic changes, AD and other tauopathies pose a tremendous social and economic burden to society. Unfortunately, therapeutic strategies are lacking that could halt the disease. Recent approaches that aimed at reducing amyloid-8 levels in AD have been unsuccessful, and clinical trials are gradually centering on Tau as the major drug target Congdon et al., Nat Rev Neurol (2018), 14: 399-415). Tau is a microtubule-stabilizing protein involved in intracellular trafficking (Vershinin et al., PNAS (2007), 87-92). Aberrant Tau aggregation is believed to start locally in specific brain regions, from where Tau pathology spreads to other regions of the brain (Braak et al., Acta Neuropathol (1991), 82: 239-259; Braak et al., Neurobiol Aging (1997), 18: 351-357). Misfolded Tau has been implicated in neuronal loss and disease severity (Nelson et al., J Neuropathol Exp Neurol (2007), 66: 1136-1146). Tau is subject to several posttranslational modifications such as hyperphosphorylation, acetylation or truncation, which can contribute to aberrant Tau polymerization into small oligomers and filaments. Tau aggregates associated with different tauopathies differ in their anatomical distribution, cell tropism, isoform composition and structure (Kovacs, Neuropathol Appl Neurobiol (2015): 41: 3-23).
Several lines of evidence suggest that transcellular spreading of distinct Tau aggregates may underlie the diversity and progression of tauopathies (Goedert, Science (2015), 349: 1255555). For example, in the case of sporadic AD, Tau aggregate spreading has been proposed to cause disease progression from the locus coeruleus to the transentorhinal cortex and finally to hippocampus and surrounding brain regions (Braak et al., Acta Neuropathol (2011), 121: 589-595). The mechanism of intercellular Tau aggregate transmission is only insufficiently understood. It is possible that so-far unidentified factors contribute to the sequential pathologic Tau spreading pattern and clinical diversity of distinct tauopathies (Braak et al., Neurobiol Aging (1995), 16: 271-278). Increasing evidence argues that extracellular vesicles (EVs) play a prominent role in disseminating aberrant Tau species to neighboring cells. Insoluble Tau was detected in EVs isolated either from cell culture or from patient CSF (Asai et al., Nat Neuroscie (2015), 18: 1584-1593; Saman et al., J Biol Chem (2012), 287: 3842-3849). Although EV-associated Tau represented only a small fraction of released Tau, it showed pathology-dependent phosphorylation at Thr-181 in CSF of AD patients early in disease (Saman, loc. cit.; Wang et al., Mol Neurodegener (1017), 12: 5; Frost et al., J Biol Chem (2009), 284: 12845-12852). Importantly, both pharmacological inhibition of EV release and disruption of exosomal membranes by sonication successfully halted Tau propagation in recipient cells or in a Tau transgenic mouse model, highlighting the important role of EVs in spreading of Tau pathology (Sama, loc. cit.; Wang, loc. cit.). So far it is unclear how exactly Tau is sorted into EVs and how these EVs target recipient cells.
As Tau pathology correlates better with the degree of cognitive decline in AD patients than with amyloid-β pathology, greater clinical efficacy may be achieved with Tau-based-therapeutic approaches (Nelson, loc. cit.). Current therapeutic interventions aim at reducing Tau expression, the formation of pathogenic Tau seeds or clearing pathogenic Tau. Strategies include reducing Tau expression by antisense oligonucelotides (Guo et al., Acta Neuropathol (2017), 133: 665-704), increasing cellular Tau degradation or reducing Tau posttranslational modifications, using phosphatase activators, kinase inhibitors, acetylation and deglycosylation inhibitors (Congdon, loc. cit.). Tau aggregation inhibitors such as a methylene blue derivative or curcumin so far had limited effects in phase II/III clinical trials (Congdon, loc. cit.). Likewise, a phase III clinical trial with microtubule stabilizer Davunetide in PSP patients did not result in cognitive improvements (Boxer et al., Lancet Neurol (2014), 13: 676-685).
An alternative approach to treating tauopathies is to halt disease progression by targeting the spreading of pathologic Tau throughout the brain. Antibodies against different forms of phosphorylated, oligomeric or misfolded Tau have been shown to modulate Tau pathology in mouse models. For example, passive immunotherapies with Tau specific antibodies were shown to slow progression of Tau pathology in transgenic mice (d'Abramo et al., PLoS One (2013), 8: e62402; Castillo-Carranza et al., J Neurosci (2014), 34: 4260-4272; Yanamandra et al., Neuron (2013), 80: 402-414). However, little is known how anti-Tau antibodies can reduce intracellular neurofibrillary tangle burden (Congdon, loc. cit.). It has been proposed that Tau antibodies achieve therapeutic effects by capturing extracellular Tau and thereby preventing the spreading of Tau pathology. Alternatively, antibodies might also enter neurons and target cytosolic Tau. Several antibodies used in these studies are currently undergoing early clinical trials. A difficulty with Tau-directed antibodies is the insufficient knowledge about the specific type of Tau that causes toxicity and/or is capable of transcellular spreading. Moreover, Tau efficiently spreads via EVs and is thus most likely shielded from extracellular antibody recognition. Consequently, antibodies targeting Tau directly might not be able to terminate the progression of Tau pathology. One way to prevent EV mediated spreading of Tau is to impair efficient transmission of Tau aggregates by targeting EV uptake. The advantage of such approach is that it could impair Tau spreading regardless of the Tau species packaged into EVs. However, very little is known how EVs dock onto target cells and release their cargo into the cytosol.
The gold standard for the diagnosis of tauopathies is still autopsy. Three major tauopathies, PSP, CBD and Pick's disease, are classified based on their characterized neuropathological characteristics. For example, PSP exhibits Tau-positive glial inclusions in the form of “tufted astrocytes” in gray matter; CBD is characterized by typical Tau-positive ballooned neurons and astrocytic deposits; Pick's disease contains Tau-positive “Pick bodies” in neurons. The autopsy diagnosis correlates not well with the syndrome diagnosis. Although CBD and PSP are most commonly associated with CBD clinical syndrome and PSP clinical syndrome, respectively, these syndromes are also shared by other tauopathies. For example, only 50% of cases with CBD clinical syndrome are CBD cases, the rest of cases are diagnosed with AD, PSP, Pick's disease and FTLD-TDP at autopsy (Coughlin et al., Curr Neurol Neurosci Rep (2017), 17: 72). Thus, for specific therapy, it is essential to establish antemortem diagnosis for classification of these tauopathies.
Several different methods have been developed for antemortem diagnosis, including neuroimaging, molecular imaging, and fluid biomarkers. Neuroimaging techniques using MRI proved useful in the diagnosis of PSP with 72.7% specificity but not for other tauopathies (Coughlin, loc. cit.). Molecular imaging, Tau positron emission tomography (PET), has been used in some clinical studies to distinguish AD from control patients. However, the second-generation of Tau specific PET ligands showed very weak binding to pure 3R- or 4R-Tau pathology in post mortem tissue in PSP, CBD and Pick's disease. Moreover, the observed potential off-target binding in susceptible brain regions in PSP and CBD, limits its use in diagnosis of tauopathies that represent with mixtures of 3R- and 4R-Tau pathology (Scholl et al., Mol Cell Neurosci (2018), doi: 10.1016/j.mcn.2018.12.001).
Fluid biomarkers for tauopathies include CSF total Tau and phosphorylated Tau. Total Tau in CSF has been postulated to correlate with neurodegenerative changes in AD patients. However, the increase is not specific for AD and also occurs in other neurodegenerative diseases, such as Creutzfeldt-Jakob disease and brain injury. Phosphorylated Tau in CSF is significantly increased in AD but not in other tauopathies, like PSP. Plasma Tau correlates poorly with CSF Tau levels, which limits its use in the diagnosis of AD (Scholl, loc. cit.). Thus, while determination of phosphorylated Tau levels in CSF in combination with Tau PET imaging could have implications for clinical diagnosis of AD, no suitable ante mortem methods are available for identification of other tauopathies.
Accordingly, the technical problem underlying the present invention was to comply with the disadvantages set out above.
The present invention addresses the technical problem by providing compounds for use in treating tauopathy, Parkinson's disease and ALS as set forth herein below and as defined by the claims.
Accordingly, the present invention relates to an inhibitor of HERV proteins comprising HERV Env and Gag, or a fragment thereof (i.e. fragment of HERV Env and/or HERV Gag protein(s)), for use in treating tauopathies (e.g., Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17)), Parkinson's disease, or ALS.
As surprisingly found in context with the present invention, human endogenous retrovirus (HERV) Env proteins (e.g., from HERV species HERV-W (Syncytin 1), HERV-K, HERV-H, HERV-T, HERV-FRD, HERV-F(c)1, HERV-F(c)2, HERV-E, HERV-P(b1), HERV-VR(b), and HERV-MER34) are upregulated in tauopathies. This applies mutatis mutandis also for HERV Gag proteins given that env and gag mRNA is transcribed together. As has been shown in context with the present invention, there is a correlation between increased HERV Env expression and accelerated intercellular Tau aggregate spreading. Particularly, in accordance with the present invention, ERV Env proteins serve as ligands that mediate the interaction of cellular membranes, resulting in increased transfer of protein aggregate seeds from one cell to another. As shown herein, interruptions of involved ligand-receptor interactions significantly impair the spreading of diverse proteopathic seeds, including Tau aggregates. Furthermore, retroviruses generally depend on proteolytic maturation of the structural protein Gag. Thus, in accordance with the present invention, Env activity is regulated by the maturation status of Gag (cf. Johnson, Nature Reviews Microbiol (2019), 17: 355-370). Without being bound by theory, the maturation of Gag changes the conformation of Gag in the particle and renders Env fusogenic. In other words, again without being bound by theory, in accordance with the present invention, (maturating) Gag activates Env. Accordingly, in context with the present invention, it has surprisingly been found that inhibition of HERV proteins (e.g., inhibition of the maturation or expression of ERV Env and Gag proteins, and/or binding of said ERV Env protein to a receptor; or inhibiting a HERV Env protein receptor from binding the HERV Env protein) is useful for treating tauopathies (e.g., Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17)). Without being bound by theory, by inhibiting HERV proteins (Env or Gag, or fragments thereof) as described and provided herein, spreading of pathogenic Tau seeds is inhibited or decreased. Also, again without being bound by theory, protein aggregates and the subsequent aggregation of proteins of the same kind in recipient cells is thus inhibited or decreased. Accordingly, in accordance with the present invention, inhibition of HERV proteins (Env or Gag, or fragments thereof) as described and provided herein can also be used for treating associated disorders undelaying such mechanisms such as Parkinson's disease and ALS (Amyothrophic Lateral Sclerosis).
As used herein, the term “HERV Env and/or Gag proteins” comprises all types and variants of HERV Env and/or Gag proteins, respectively, including—but not limited to—those Env and Gag proteins of the HERV species HERV-W (Syncytin 1), HER-K, HERV-H, HERV-T, HERV-FRD, HERV-F(c)1, HERV-F(c)2, HERV-E, HERV-P(b1), HERV-R, HERV-R(b), HERV-V and HERV-MER34. In one embodiment of the present invention, specifically those HERV Env and Gag proteins are meant which have been shown to be increased, upregulated or overexpressed in one or more tauopathies, Parkinson's disease, and/or ALS (Amyothrophic Lateral Sclerosis).
As shown in context with the present invention, HERV transcripts are upregulated in different tauopathies. For example, as has been found in context with the present invention, HERV-W is upregulated in AD patients, while HERV-FRD, —H and -R(b) are associated with CBD disease, and HERV-K and -F(c)1 are increased in PSP patients. Accordingly, in a specific embodiment of the present invention, the HERV Env and/or Gag protein is selected from the group consisting of Env and/or Gag of HERV-W, -FRD, —H, -R(b), —K, and -F(c)1, preferably HERV-W and HERV-K. Accordingly, in one embodiment of the present invention, an inhibitor of a specific HERV Env and/or Gag protein (or fragments thereof) may be particularly useful in treating a specific tauopathy which is associated with upregulation/increase/overexpression of the respective HERV Env protein. For example, in accordance with the present invention, an inhibitor of Env and/or Gag (or fragments thereof) from HERV-W may be used for treating AD, an inhibitor of Env and/or Gag (or fragments thereof) from HERV-FRD, -H and/or -R(b) may be used for treating CBD, and an inhibitor of Env and/or Gag (or fragments thereof) from HERV-K and/or -F(c)1 may be used for treating PSP.
The HERV Env and Gag proteins from HERV-W (Syncytin 1), HER-K, HERV-H, HERV-T, HERV-FRD, HERV-F(c)1, HERV-F(c)2, HERV-E, HERV-P(b1), HERV-R, HERV-R(b), HERV-V and HERV-MER34 are well known in the art.
For example, in accordance with the present invention, HERV Env proteins (or fragments thereof) as used and described herein may have amino acid sequences encoded by nucleotide sequences being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to those nucleotide sequences shown in SEQ ID NOs. 1 to 13 (particularly Env from HERV-H: SEQ ID NO: 1; HERV-K: SEQ ID NO: 2; HERV-T: SEQ ID NO: 3; HERV-W: SEQ ID NO: 4; HERV-FRD: SEQ ID NO 5; HERV-R: SEQ ID NO: 6; HERV-R(b): SEQ ID NO: 7; HERV-F(c)2: SEQ ID NO: 8; HERV-F(c)1: SEQ ID NO: 9; HERV-E: SEQ ID NO: 10; HERV-P(b1): SEQ ID NO: 11; HERV-V: SEQ ID NO: 12; HERV-MER34: SEQ ID NO: 13). That is, for example, in accordance with the present invention, HERV-H Env as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 1, and HERV-H Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the amino acid sequence shown in SEQ ID NO: 132 to 137, HERV-K Env as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 2, and HERV-K Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the amino acid sequence shown in SEQ ID NO: 101 to 128, HERV-T Env as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 3, HERV-W Env as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 4, and HERV-W Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the amino acid sequence shown in SEQ ID NO: 129 to 131, HERV-R Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the amino acid sequence shown in SEQ ID NO: 138 to 139, and so forth. In this context, preferred are those nucleotide sequences encoding a HERV Env protein as used and described herein which differ from the respective nucleotide sequences of SEQ ID NOs. 1 to 13, respectively, in a manner that any nucleotide difference results only in a conservative or highly conservative amino acid substitution (compared to the amino acid sequences encoded by the nucleotide sequence of the respective SEQ ID NO.), or is silent (i.e. does not translate into an amino acid substitution compared to the amino acid sequences encoded by the nucleotide sequence of the respective SEQ ID NO.).
As a further example, in accordance with the present invention, HERV Gag proteins (or fragments thereof) as used and described herein may have amino acid sequences encoded by nucleotide sequences being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to those nucleotide sequences shown in SEQ ID NOs. 14 to 21 (particularly Gag from HERV-H: SEQ ID NO: 14; HERV-K (consensus): SEQ ID NO: 15; HERV-K (orico, codon optimized): SEQ ID NO: 16; HERV-T: SEQ ID NO: 17; HERV-W: SEQ ID NO: 18; HERV-R: SEQ ID NO: 19; HERV-E: SEQ ID NO: 20; HERV-V: SEQ ID NO: 21), or have amino acid sequences being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or (preferably) identical to those amino acid sequences shown in SEQ ID NOs. 22 (Gag HERV-F(c)2) to 23 (Gag HERV-F(c)2). That is, for example, in accordance with the present invention, HERV-H Gag as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 14, HERV-K (consensus) Gag as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 15, HERV-T Gag as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 17, HERV-W Gag as used herein may have an amino acid sequence encoded by a nucleotide sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% identical to the nucleotide sequence shown in SEQ ID NO: 18, and so forth. In this context, preferred are those nucleotide sequences encoding a HERV Gag protein as used and described herein which differ from the respective nucleotide sequences of SEQ ID NOs. 14 to 21, respectively, in a manner that any nucleotide difference results only in a conservative or highly conservative amino acid substitution (compared to the amino acid sequences encoded by the nucleotide sequence of the respective SEQ ID NO.), or is silent (i.e. does not translate into an amino acid substitution compared to the amino acid sequences encoded by the nucleotide sequence of the respective SEQ ID NO.). Likewise, preferred are those HERV Gag proteins as used and described herein having amino acid sequences which differ from the respective amino acid sequences of SEQ ID NOs. 22 to 23, respectively, in a manner that only in a conservative or highly conservative amino acid substitutions/insertions/additions/deletions appear (compared to the amino acid sequences of the respective SEQ ID NO.).
Likewise, as used herein and in accordance with the present invention, HERV Env proteins as used and described herein may have amino acid sequences being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to those amino acid sequences encoded by nucleotide sequences shown in SEQ ID NOs. 1 to 13 (particularly Envs from HERV-H: SEQ ID NO: 1; HERV-K: SEQ ID NO: 2; HERV-T: SEQ ID NO: 3; HERV-W: SEQ ID NO: 4; HERV-FRD: SEQ ID NO 5; HERV-R: SEQ ID NO: 6; HERV-R(b): SEQ ID NO: 7; HERV-F(c)2: SEQ ID NO: 8; HERV-F(c)1: SEQ ID NO: 9; HERV-E: SEQ ID NO: 10; HERV-P(b1): SEQ ID NO: 11; HERV-V: SEQ ID NO: 12; HERV-MER34: SEQ ID NO: 13). That is, for example, in accordance with the present invention, HERV-H Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 1, HERV-K Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 2, HERV-T Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 3, HERV-W Env as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 4, and so forth.
Likewise, as used herein and in accordance with the present invention, HERV Gag proteins as used and described herein may have amino acid sequences being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to those amino acid sequences encoded by nucleotide sequences shown in SEQ ID NOs. 14 to 21 (particularly Gag from HERV-H: SEQ ID NO: 14; HERV-K (consensus): SEQ ID NO: 15; HERV-K (orico, codon optimized): SEQ ID NO: 16; HERV-T: SEQ ID NO: 17; HERV-W: SEQ ID NO: 18; HERV-R: SEQ ID NO: 19; HERV-E: SEQ ID NO: 20; HERV-V: SEQ ID NO: 21). That is, for example, in accordance with the present invention, HERV-H Gag as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 14, HERV-K (consensus) Gag as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 15, HERV-T Gag as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 17, HERV-W Gag as used herein may have an amino acid sequence being at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.8%, or 100% similar or identical to the amino acid sequence encoded by the nucleotide sequence shown in SEQ ID NO: 18, and so forth.
In accordance with the present invention, as used herein in context with amino acid sequences, the term “similar” means that a given amino acid sequence comprises identical amino acids or only conservative or highly conservative substitutions compared to the amino acid sequence of the respective SEQ ID NO. As used herein, “conservative” substitutions mean substitutions as listed as “Exemplary Substitutions” in Table I herein. “Highly conservative” substitutions as used herein mean substitutions as shown under the heading “Preferred Substitutions” in Table I herein.
As used herein, unless specifically defined otherwise, the term “nucleic acid” or “nucleic acid molecule” is used synonymously with “oligonucleotide”, “nucleic acid strand”, or the like, and means a polymer comprising one, two, or more nucleotides. In this context, also the term “target sequence” as used herein comprises nucleic acid molecules.
As used herein, “silent” mutations mean base substitutions within a nucleic acid sequence which do not change the amino acid sequence encoded by the nucleic acid sequence. “Conservative” substitutions mean substitutions as listed as “Exemplary Substitutions” in Table I. “Highly conservative” substitutions as used herein mean substitutions as shown under the heading “Preferred Substitutions” in Table I.
The term “position” when used in accordance with the present invention means the position of an amino acid within an amino acid sequence depicted herein. The term “corresponding” in this context also includes that a position is not only determined by the number of the preceding nucleotides/amino acids.
The level of identity between two or more sequences (e.g., nucleic acid sequences or amino acid sequences) can be easily determined by methods known in the art, e.g., by BLAST analysis. Generally, in context with the present invention, if two sequences (e.g., polynucleotide sequences or amino acid sequences) to be compared by, e.g., sequence comparisons differ in identity, then the term “identity” may refer to the shorter sequence and that part of the longer sequence that matches said shorter sequence. Therefore, when the sequences which are compared do not have the same length, the degree of identity may preferably either refer to the percentage of nucleotide residues in the shorter sequence which are identical to nucleotide residues in the longer sequence or to the percentage of nucleotides in the longer sequence which are identical to nucleotide sequence in the shorter sequence. In this context, the skilled person is readily in the position to determine that part of a longer sequence that matches the shorter sequence. Furthermore, as used herein, identity levels of nucleic acid sequences or amino acid sequences may refer to the entire length of the respective sequence and is preferably assessed pair-wise, wherein each gap is to be counted as one mismatch. These definitions for sequence comparisons (e.g., establishment of “identity” values) are to be applied for all sequences described and disclosed herein.
Moreover, the term “identity” as used herein means that there is a functional and/or structural equivalence between the corresponding sequences. Nucleic acid/amino acid sequences having the given identity levels to the herein-described particular nucleic acid/amino acid sequences may represent derivatives/variants of these sequences which, preferably, have the same biological function. They may be either naturally occurring variations, for instance sequences from other varieties, species, etc., or mutations, and said mutations may have formed naturally or may have been produced by deliberate mutagenesis. Furthermore, the variations may be synthetically produced sequences. The variants may be naturally occurring variants or synthetically produced variants, or variants produced by recombinant DNA techniques. Deviations from the above-described nucleic acid sequences may have been produced, e.g., by deletion, substitution, addition, insertion and/or recombination. The term “addition” refers to adding a nucleic acid residue/amino acid to the beginning or end of the given sequence, whereas “insertion” refers to inserting a nucleic acid residue/amino acid within a given sequence. The term “deletion” refers to deleting or removal of a nucleic acid residue or amino acid residue in a given sequence. The term “substitution” refers to the replacement of a nucleic acid residue/amino acid residue in a given sequence. Again, these definitions as used here apply, mutatis mutandis, for all sequences provided and described herein.
Generally, as used herein, the terms “polynucleotide” and “nucleic acid” or “nucleic acid molecule” are to be construed synonymously. Generally, nucleic acid molecules may comprise inter alia DNA molecules, RNA molecules, oligonucleotide thiophosphates, substituted ribo-oligonucleotides or PNA molecules. Furthermore, the term “nucleic acid molecule” may refer to DNA or RNA or hybrids thereof or any modification thereof that is known in the art (see, e.g., U.S. Pat. Nos. 5,525,711, 4,711,955, 5,792,608 or EP 302175 for examples of modifications). The polynucleotide sequence may be single- or double-stranded, linear or circular, natural or synthetic, and without any size limitation. For instance, the polynucleotide sequence may be genomic DNA, cDNA, mitochondrial DNA, mRNA, antisense RNA, ribozymal RNA or a DNA encoding such RNAs or chimeroplasts (Gamper, Nucleic Acids Research, 2000, 28, 4332-4339). Said polynucleotide sequence may be in the form of a vector, plasmid or of viral DNA or RNA. Also described herein are nucleic acid molecules which are complementary to the nucleic acid molecules described above and nucleic acid molecules which are able to hybridize to nucleic acid molecules described herein. A nucleic acid molecule described herein may also be a fragment of the nucleic acid molecules in context of the present invention. Particularly, such a fragment is a functional fragment. Examples for such functional fragments are nucleic acid molecules which can serve as primers.
The term “amino acid” or “amino acid residue” as used herein typically refers to an amino acid having its art recognized definition such as an amino acid selected from the group consisting of: alanine (Ala or A); arginine (Arg or R); asparagine (Asn or N); aspartic acid (Asp or D); cysteine (Cys or C); glutamine (Gln or Q); glutamic acid (Glu or E); glycine (Gly or G); histidine (His or H); isoleucine (He or I): leucine (Leu or L); lysine (Lys or K); methionine (Met or M); phenylalanine (Phe or F); pro line (Pro or P); serine (Ser or S); threonine (Thr or T); tryptophan (Trp or W); tyrosine (Tyr or Y); and valine (Val or V), although modified, synthetic, or rare amino acids may be used as desired. Generally, amino acids can be grouped as having a nonpolar side chain (e.g., Ala, Cys, He, Leu, Met, Phe, Pro, Val); a negatively charged side chain (e.g., Asp, Glu); a positively charged sidechain (e.g., Arg, His, Lys); or an uncharged polar side chain (e.g., Asn, Cys, Gln, Gly, His, Met, Phe, Ser, Thr, Trp, and Tyr).
As has been shown in context with the present invention, inhibitors that block maturation of HERV Env proteins also impair spreading of pathogenic aggregates. The same applies mutatis mutandis for inhibitors of HERV Gag protein maturation as this inhibits activation of Env as described above. Ways of inhbiting processing/maturation of Env or Gag proteins are generally known in the art; cf. Freed, Nature Review Microbiol (2015), 13: 484-496; Tedbury et al., Curr Topics Microbiol and Immunol (2015), 389: 171-201; Venanzi Rullo et al., Mol Med Reports (2019), 19: 1987-1995; Waheed et al., AIDS Res Human Retroviruses (2012), 28: 54-75. Accordingly, in one embodiment of the present invention, in context with the inhibitor of HERV Env and/or Gag proteins (or fragments thereof) as described and provided herein, HERV Env and/or Gag proteins (or fragments thereof) can be inhibited by inhibiting maturation of the respective HERV Env and/or Gag protein (or fragments thereof). Accordingly, in this embodiment of the present invention, the inhibitor of HERV Env and/or Gag proteins may inhibit maturation of the respective HERV Env and/or Gag protein (or fragments thereof). In a specific embodiment of the present invention, the inhibitor of HERV Env and/or Gag proteins (or fragments thereof) inhibits maturation of the respective HERV proteins, wherein said inhibitor is a HERV protease inhibitor which inhibits the respective protease which processes the respective Env or Gag protein for maturation. Due to the similarity to other retroviral gene products (e.g., those of HIV), protease inhibitors which are applied or applicable for treating HIV may also be used in accordance with the present invention to inhibit HERV Env and/or Gag protein (or fragments thereof) for use in treating tauopathy (e.g., Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17)), Parkinson's disease and ALS as described herein. Accordingly, in a specific embodiment of the present invention, the inhibitor of HERV Env and/or Gag proteins (or fragments thereof) may be an HIV-1 retroviral protease inhibitor, e.g., a (HERV) protease inhibitor selected from the group consisting of amprenavir, lopinavir, darunavir, indinavir, atazanavir, fosamprenavir, nelfinavir, ritonavir, saquinavir, and tipranavir, preferably amprenavir and atazanavir. Envisaged herein is a (HERV) protease inhibitor for use in treating Tauopathy, or Parkinson's disease. Said protease inhibitor may be any one of amprenavir, lopinavir, darunavir, indinavir, atazanavir, fosamprenavir, nelfinavir, ritonavir, saquinavir, tipranavir, amprenavir or atazanavir, preferably amprenavir, atazanavir, or lopinavir.
In accordance with the present invention, the inhibitor of HERV Env and/or Gag proteins (or fragments thereof) as described and provided herein may also be an inhibitor of expression of respective HERV Env and/or Gag proteins. For example, it may inhibit transcription or translation of the HERV Env and/or Gag genes or mRNAs, respectively. Accordingly, in one embodiment of the present invention, the inhibitors of HERV Env and/or Gag proteins as described and provided herein are nucleic acid molecules hybridizing or being complementary to at least a portion of the nucleic acid sequence encoding said HERV Env and/or Gag proteins, thereby inhibiting or preventing transcription or translation of the nucleic acid molecules encoding the HERV Env and/or Gag proteins. In context with the present invention, a suitable nucleic acid molecule for inhibiting expression (e.g., transcription or translation) of a HERV Env and/or Gag protein may be a small interference RNA (siRNA), microRNA (miRNA, miR), Tough Decoys (TuD) (e.g., Tough Decoy RNA), Decoys, antisense oligonucleotides (antisense RNA or DNA, chimeric antisense molecules), ribozymes, external guide sequence (EGS), oligonucleotides, small temporal RNA (stRNA), short hairpin RNA (shRNA), small RNA-induced gene activation (RNAa), small activating RNA (saRNA), locked nucleic acids (LNA), antagomirs, aptamers (DNA, RNA, XNA), peptide nucleic acids (PNA), and other oligomeric nucleic acid molecules, which are able to inhibit or suppress the expression (e.g., transcription or translation) of the nucleic acid molecule encoding the respective HERV Env and/or Gag proteins (e.g., by hybridizing to at least a portion of the nucleic acid molecule encoding the respective HERV Env and/or Gag proteins).
As used herein, an inhibitor hybridizing or being complementary to “at least a portion” of the nucleic acid sequence encoding said HERV Env protein means that said inhibitor (preferably itself being a nucleic acid molecule as described above) hybridizes or is complementary to at least about 3, 4, 5, 6, 7, 8, 9, 20, 11, 12, 13, 14 or 15 (preferably consecutive) nucleotides of the nucleotide sequence of the respective HERV Env protein (e.g., gene or transcribed mRNA thereof). For example, such inhibitor hybridizes or is complementary to at least about 3, 4, 5, 6, 7, 8, 9, 20, 11, 12, 13, 14 or 15 (preferably consecutive) nucleotides of a nucleotide sequence shown in any one of SEQ ID NOs. 1 to 13 (particularly HERV-H: SEQ ID NO: 1; HERV-K: SEQ ID NO: 2; HERV-T: SEQ ID NO: 3; HERV-W: SEQ ID NO: 4; HERV-FRD: SEQ ID NO 5; HERV-R: SEQ ID NO: 6; HERV-R(b): SEQ ID NO: 7; HERV-F(c)2: SEQ ID NO: 8; HERV-F(c)1: SEQ ID NO: 9; HERV-E: SEQ ID NO: 10; HERV-P(b1): SEQ ID NO: 11; HERV-V: SEQ ID NO: 12; HERV-MER34: SEQ ID NO: 13). That is, for example, in accordance with this embodiment of the present invention, an inhibitor (preferably itself being a nucleic acid molecule as described above) of HERV-H hybridizes or is complementary to at least about 3, 4, 5, 6, 7, 8, 9, 20, 11, 12, 13, 14 or 15 (preferably consecutive) nucleotides of the nucleotide sequence of SEQ ID NO: 1, an inhibitor (preferably itself being a nucleic acid molecule as described above) of HERV-K hybridizes or is complementary to at least about 3, 4, 5, 6, 7, 8, 9, 20, 11, 12, 13, 14 or 15 (preferably consecutive) nucleotides of the nucleotide sequence of SEQ ID NO: 2, an inhibitor (preferably itself being a nucleic acid molecule as described above) of HERV-T hybridizes or is complementary to at least about 3, 4, 5, 6, 7, 8, 9, 20, 11, 12, 13, 14 or 15 (preferably consecutive) nucleotides of the nucleotide sequence of SEQ ID NO: 3, an inhibitor (preferably itself being a nucleic acid molecule as described above) of HERV-W hybridizes or is complementary to at least about 3, 4, 5, 6, 7, 8, 9, 20, 11, 12, 13, 14 or 15 (preferably consecutive) nucleotides of the nucleotide sequence of SEQ ID NO: 4, and so forth. The same applies mutatis mutandis with respect to the Gag HERV proteins encoded by nucleotide sequences corresponding to SEQ ID NOs. 14 to 21 as set forth herein, as well as to Gag HERV proteins having amino acids corresponding to SEQ ID NOs. 22 and 23. In specific examples of the present invention, an inhibitor of a HERV Env protein may have a nucleotide sequence according to any one of SEQ ID NOs. 42-72 (upper letters; corresponding to the respective HERV species as indicated below), wherein up to 3, 2, 1, or (preferably) 0 nucleotides are added, inserted, substituted or deleted compared to said respective nucleotide sequences of SEQ ID NOs. 42-72. Further examples of inhibitors of a HERV Env protein may have a nucleotide sequence according to any one of the murine RNAs shown in SEQ ID NOs: 25-29, wherein up to 3, 2, 1, or (preferably) 0 nucleotides are added, inserted, substituted or deleted compared to said respective nucleotide sequences of SEQ ID NOs: 25 to 29. Additionally, SEQ ID NO: 98 may be another example of such an inhibitor with a loop sequence capable of silencing syncytin-1.
It is apparent from the abovemetioned, that the HERV Gag protein may be encoded by a nucleotide sequence shown in any one of SEQ ID NOs: 14 to 21, or encoded by a nucleotide sequence that has at least about 85% sequence identity to any one of SEQ ID NOs: 14 to 21. Thus, a nucleic acid molecule hybridizing to at least a portion of the nucleotide sequence of HERV Gag as shown in any one of SEQ ID NOs: 14 to 21, is envisaged herein and may be used for treating Tauopathy, or Parkinson's disease. Further examples of a nucleic acid molecule may comprise any one of the nucleotide sequence shown in any one of SEQ ID NOs: 30 to 35 which may be use for treating Tauopathy, or Parkinson's disease.
The term “hybridization”, “hybridizing” or “hybridizes” as used herein in context of nucleic acid molecules/DNA or RNA sequences may relate to hybridizations under stringent or non-stringent conditions. If not further specified, the conditions are preferably non-stringent. Said hybridization conditions may be established according to conventional protocols described, for example, in Sambrook, Russell “Molecular Cloning, A Laboratory Manual”, Cold Spring Harbor Laboratory, N. Y. (2001); Current Protocols in Molecular Biology, Update May 9, 2012, Print ISSN: 1934-3639, Online ISSN: 1934-3647; Ausubel, “Current Protocols in Molecular Biology”, Green Publishing Associates and Wiley Interscience, N. Y. (1989), or Higgins and Hames (Eds.) “Nucleic acid hybridization, a practical approach” IRL Press Oxford, Washington D.C., (1985). The setting of conditions is well within the skill of the artisan and can be determined according to protocols described in the art. Thus, the detection of only specifically hybridizing sequences will usually require stringent hybridization and washing conditions such as 0.1×SSC, 0.1% SDS at 65° C. Non-stringent hybridization conditions for the detection of homologous or not exactly complementary sequences may be set at 6×SSC, 1% SDS at 65° C. As is well known, the length of the probe and the composition of the nucleic acid to be determined constitute further parameters of the hybridization conditions. Variations in the above conditions may be accomplished through the inclusion and/or substitution of alternate blocking reagents used to suppress background in hybridization experiments. Typical blocking reagents include Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations. The inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility. In accordance to the invention described herein, low stringent hybridization conditions for the detection of homologous or not exactly complementary sequences may, for example, be set at 6×SSC, 1% SDS at 65° C. As is well known, the length of the probe and the composition of the nucleic acid to be determined constitute further parameters of the hybridization conditions.
Hybridizing nucleic acid molecules also comprise fragments of the above described molecules. Such fragments may represent nucleic acid molecules which code for a functional aaRS as described herein or a functional fragment thereof which can serve as a primer. Furthermore, nucleic acid molecules which hybridize with any of the aforementioned nucleic acid molecules also include complementary fragments, derivatives and variants of these molecules. Additionally, a hybridization complex refers to a complex between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary G and C bases and between complementary A and T bases; these hydrogen bonds may be further stabilized by base stacking interactions. The two complementary nucleic acid sequences hydrogen bond in an antiparallel configuration. A hybridization complex may be formed in solution (e.g., Cot or Rot analysis) or between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., membranes, filters, chips, pins or glass slides to which, e.g., cells have been fixed). The terms complementary or complementarity refer to the natural binding of polynucleotides under permissive salt and temperature conditions by base-pairing. For example, the sequence “A-G-T” binds to the complementary sequence “T-C-A”. Complementarity between two single-stranded molecules may be “partial”, in which only some of the nucleic acids bind, or it may be complete when total complementarity exists between single-stranded molecules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, which depend upon binding between nucleic acids strands. The term “hybridizing sequences” preferably refers to sequences which display a sequence identity of at least 45%, more preferably at least 50%, more preferably at least 55%, more preferably at least 60%, more preferably at least 65%, more preferably at least 70%, more preferably at least 75%, more preferably at least 80%, more preferably at least 85%, more preferably at least 90%, more preferably at least 95%, more preferably at least 96%, more preferably at least 97%, more preferably at least 98% more preferably at least 99%, more preferably at least 99.5%, and most preferably 100% identity with a nucleic acid sequence as described herein encoding an aaRS as described and provided herein.
In accordance with the present invention, the inhibitor of HERV Env proteins as described and provided herein may also be an inhibitor of binding of said HERV Env protein to a receptor of said HERV Env protein. As used herein, such receptors of HERV Env proteins generally comprise any receptor for which a HERV Env protein as used and described herein may be a natural ligand, or to which a HERV Env protein as used and described herein binds to with specific affinity. Typically, as generally used herein unless specified otherwise, binding is considered “specific” when the binding affinity is higher than 10−6 M. Preferably, as generally used herein unless specified otherwise, binding is considered specific when binding affinity is about 10−11 to 10−6 M (KD), preferably of about 10−11 to 10−9 M. If necessary, nonspecific binding can be reduced without substantially affecting specific binding by varying the binding conditions. Whether the recognition molecule specifically reacts as defined herein above can easily be tested, inter alia, by comparing the reaction of said recognition molecule with an epitope with the reaction of said recognition molecule with (an) other protein(s). In accordance with the present invention, non-limiting examples for receptors for HERV Env proteins, e.g., for HERV-W, comprise ASCT1 (gene: SLC1A4) or ASCT2 (gene: SLC1A5). A further possible receptor of HERV-K Env may be a complex of CD98HC and LAT1, as recent studies suggested. This complex may serve as another example of an HERV-K Env receptor.
In context with the present invention, binding of a HERV Env protein as used and described herein to a corresponding HERV Env protein receptor as described herein can be inhibited by any binding agent either (specifically) binding the respective HERV Env protein, or the corresponding HERV Env protein receptor. In accordance with the present invention, non-limiting examples for such binding agents binding to HERV Env protein or to its respective receptor comprise antibodies, protein aptamers, affimers, small compounds (e.g., those blocking the binding center of a HERV Env receptor), etc.
In one embodiment of the present invention, the inhibitor of Env protein is an antibody (specifically) binding to a respective Env protein as used and described herein. Preferably, such antibody thus inhibits binding of the respective Env protein to a receptor of the Env protein. In another embodiment of the present invention, the inhibitor is a binding agent as defined herein (e.g., an antibody) (specifically) binding to a receptor of a respective HERV Env protein as used and described herein. Preferably, such antibody thus inhibits binding of a respective HERV Env protein to the receptor of the HERV Env protein.
Accordingly, the present invention further relates to an inhibitor of a receptor binding a HERV Env protein as used and described herein for use in treating tauopathy (e.g., Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17)), Parkinson's disease and ALS. In context with the present invention, in one example, such inhibitor of a HERV Env receptor may be a binding agent (e.g., antibody) as described herein (thereby inhibiting binding of a respective HERV Env protein to the receptor of the HERV Env protein), for example an antibody (specifically) binding to said HERV Env protein receptor. In another example of the present invention, the HERV Env protein receptor inhibitor may inhibit the expression (e.g., transcription or translation) of the HERV Env protein receptor as described herein. For example, it may inhibit transcription or translation of the HERV Env receptor gene or mRNA, respectively. Accordingly, in one embodiment of the present invention, the inhibitor of HERV Env protein receptor as described and provided herein is a nucleic acid molecule hybridizing or being complementary to at least a portion of the nucleic acid sequence encoding said HERV Env protein receptor, thereby inhibiting or preventing transcription or translation of the nucleic acid molecule encoding the HERV Env protein receptor. In context with the present invention, a suitable nucleic acid molecule for inhibiting expression (e.g., transcription or translation) of a HERV Env protein receptor may be a small interference RNA (siRNA), microRNA (miRNA, miR), Tough Decoys (TuD) (e.g., Tough Decoy RNA), Decoys, antisense oligonucleotides (antisense RNA or DNA, chimeric antisense molecules), ribozymes, external guide sequence (EGS), oligonucleotides, small temporal RNA (stRNA), short hairpin RNA (shRNA), small RNA-induced gene activation (RNAa), small activating RNA (saRNA), locked nucleic acids (LNA), antagomirs, aptamers (DNA, RNA, XNA), peptide nucleic acids (PNA), and other oligomeric nucleic acid molecules, which are able to inhibit or suppress the expression (e.g., transcription or translation) of the nucleic acid molecule encoding the respective HERV Env protein receptor (e.g., by hybridizing to at least a portion of the nucleic acid molecule encoding the respective HER Env protein receptor).
As used herein, an inhibitor hybridizing or being complementary to “at least a portion” of the nucleic acid sequence encoding said HERV Env protein receptor means that said inhibitor (preferably itself being a nucleic acid molecule as described above) hybridizes or is complementary to at least about 3, 4, 5, 6, 7, 8, 9, 20, 11, 12, 13, 14 or 15 (preferably consecutive) nucleotides of the nucleotide sequence of the respective HERV Env protein receptor (e.g., gene or transcribed mRNA thereof).
Generally, as used herein, such receptors of HERV Env proteins comprise any receptor for which a HERV Env protein as used and described herein may be a natural ligand, or to which a HERV Env protein as used and described herein binds to with specific affinity. In accordance with the present invention, non-limiting examples for receptors for HERV Env proteins, e.g., for HERV-W, comprise SLC1A4 or SLC1A5. Accordingly, in a specific embodiment of the present invention, the HERV Env protein receptor is selected from the group consisting of SLC1A4 and SLC1A5 (Lavillette et al., J Virol (2002), 76: 6442-6452; and Marin et al., J Virol (2003), 77: 2936-2945). In this context, an inhibitor of SLC1A4 or SLC1A5 may be particularly useful in treating tauopathies.
The term “antibody” as used herein may be a protein comprising one or more polypeptides (comprising one or more binding domains, preferably antigen binding domains) substantially or partially encoded by immunoglobulin genes or fragments of immunoglobulin genes. The term “immunoglobulin” (Ig) is used interchangeably with “antibody” herein. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as myriad immunoglobulin variable region genes.
In particular, an “antibody” when used herein, may comprise tetrameric glycosylated proteins composed of two light (L) chains of approximately 25 kDa each and two heavy (H) chains of approximately 50 kDa each. Two types of light chain, termed lambda and kappa, may be found in antibodies. Depending on the amino acid sequence of the constant domain of heavy chains, immunoglobulins can be assigned to five major classes: A, D, E, G, and M, and several of these may be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2. An IgM antibody consists of 5 of the basic heterotetramer unit along with an additional polypeptide called a J chain, and contains 10 antigen binding sites, while IgA antibodies comprise from 2-5 of the basic 4-chain units which can polymerize to form polyvalent assemblages in combination with the J chain. In the case of IgGs, the 4-chain unit comprises in most cases about 150,000 daltons.
Each light chain includes an N-terminal variable (V) domain (VL) and a constant (C) domain (CL). Each heavy chain includes an N-terminal V domain (VH), three or four C domains (CHs), and a hinge region. The constant domains are not involved directly in binding an antibody to an antigen.
The pairing of a VH and VL together forms a single antigen-binding site. The CH domain most proximal to VH is designated as CH1. Each L chain is linked to an H chain by one covalent disulfide bond, while the two H chains are linked to each other by one or more disulfide bonds depending on the H chain isotype. The VH and VL domains consist of four regions of relatively conserved sequences called framework regions (FR1, FR2, FR3, and FR4), which form a scaffold for three regions of hypervariable sequences (complementarity determining regions, CDRs). The CDRs contain most of the residues responsible for specific interactions of the antibody with the antigen. CDRs are referred to as CDR 1, CDR2, and CDR3. Accordingly, CDR constituents on the heavy chain are referred to as H1, H2, and H3, while CDR constituents on the light chain are referred to as L1, L2, and L3. The term “variable” refers to the portions of the immunoglobulin domains that exhibit variability in their sequence and that are involved in determining the specificity and binding affinity of a particular antibody (i.e. the “variable domain(s)”). Variability is not evenly distributed throughout the variable domains of antibodies; it is concentrated in sub-domains of each of the heavy and light chain variable regions. These sub-domains are called “hypervariable” regions or “complementarity determining regions” (CDRs). The more conserved (i.e. non-hypervariable) portions of the variable domains are called the “framework” regions (FRM). The variable domains of naturally occurring heavy and light chains each comprise four FRM regions, largely adopting a β-sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases forming part of, the β-sheet structure. The hypervariable regions in each chain are held together in close proximity by the FRM and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site. The constant domains are not directly involved in antigen binding, but exhibit various effector functions, such as, for example, antibody-dependent, cell-mediated cytotoxicity and complement activation.
The terms “CDR”, and its plural “CDRs”, refer to a complementarity determining region (CDR) of which three make up the binding character of a light chain variable region (CDRL1, CDRL2 and CDRL3) and three make up the binding character of a heavy chain variable region (CDRH1, CDRH2 and CDRH3). CDRs contribute to the functional activity of an antibody molecule and are separated by amino acid sequences that comprise scaffolding or framework regions. The exact definitional CDR boundaries and lengths are subject to different classification and numbering systems. Despite differing boundaries, each of these systems has some degree of overlap in what constitutes the so called “hypervariable regions” within the variable sequences. CDR definitions according to these systems may therefore differ in length and boundary areas with respect to the adjacent framework region. See for example Kabat, Chothia, and/or MacCallum (Kabat et al., loc. cit.; Chothia et al., J Mol Biol (1987), 196: 901; and MacCallum et al., J Mol Biol (1996), 262: 732). However, the numbering in accordance with the so-called Kabat system is preferred.
The term “hypervariable region” (also known as “complementarity determining regions” or CDRs) as used herein refers to the amino acid residues of an antibody which are (usually three or four short regions of extreme sequence variability) within the V-region domain of an immunoglobulin which form the antigen-binding site and are the main determinants of antigen specificity. There are at least two methods for identifying the CDR residues: (1) An approach based on cross-species sequence variability (i.e. Kabat et al., loc. cit.); and (2) An approach based on crystallographic studies of antigen-antibody complexes (Chothia, C. et al., J Mol Biol (1987), 196: 901-917). However, to the extent that two residue identification techniques define regions of overlapping, but not identical regions, they can be combined to define a hybrid CDR. However, in general, the CDR residues are preferably identified in accordance with the so-called Kabat (numbering) system. The term “framework region” refers to the art-recognized portions of an antibody variable region that exist between the more divergent (i.e. hypervariable) CDRs. Such framework regions are typically referred to as frameworks 1 through 4 (FR1, FR2, FR3, and FR4) and provide a scaffold for the presentation of the six CDRs (three from the heavy chain and three from the light chain) in three dimensional space, to form an antigen-binding surface. The term “canonical structure” refers to the main chain conformation that is adopted by the antigen binding (CDR) loops. From comparative structural studies, it has been found that five of the six antigen binding loops have only a limited repertoire of available conformations. Each canonical structure can be characterized by the torsion angles of the polypeptide backbone. Correspondent loops between antibodies may, therefore, have very similar three dimensional structures, despite high amino acid sequence variability in most parts of the loops (Chothia and Lesk, J Mol Biol (1987), 196: 901; Chothia et al., Nature (1989), 342: 877; Martin and Thornton, J Mol Biol (1996), 263: 800, each of which is incorporated by reference in its entirety). Furthermore, there is a relationship between the adopted loop structure and the amino acid sequences surrounding it. The conformation of a particular canonical class is determined by the length of the loop and the amino acid residues residing at key positions within the loop, as well as within the conserved framework (i.e. outside of the loop). Assignment to a particular canonical class can therefore be made based on the presence of these key amino acid residues. The term “canonical structure” may also include considerations as to the linear sequence of the antibody, for example, as catalogued by Kabat (Kabat et al., loc. cit.). The Kabat numbering scheme (system) is a widely adopted standard for numbering the amino acid residues of an antibody variable domain in a consistent manner and is the preferred scheme applied in the present invention as also mentioned elsewhere herein. Additional structural considerations can also be used to determine the canonical structure of an antibody. For example, those differences not fully reflected by Kabat numbering can be described by the numbering system of Chothia et al and/or revealed by other techniques, for example, crystallography and two or three-dimensional computational modeling. Accordingly, a given antibody sequence may be placed into a canonical class which allows for, among other things, identifying appropriate chassis sequences (e.g., based on a desire to include a variety of canonical structures in a library).
CDR3 is typically the greatest source of molecular diversity within the antibody-binding site. H3, for example, can be as short as two amino acid residues or greater than 26 amino acids. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known in the art. For a review of the antibody structure, see Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, eds. Harlow et al., 1988. One of skill in the art will recognize that each subunit structure, e.g., a CH, VH, CL, VL, CDR, FR structure, comprises active fragments, e.g., the portion of the VH, VL, or CDR subunit the binds to the antigen, i.e., the antigen-binding fragment, or, e.g., the portion of the CH subunit that binds to and/or activates, e.g., an Fc receptor and/or complement. The CDRs typically refer to the Kabat CDRs, as described in Sequences of Proteins of immunological Interest, US Department of Health and Human Services (1991), eds. Kabat et al. Another standard for characterizing the antigen binding site is to refer to the hypervariable loops as described by Chothia. See, e.g., Chothia et al., J Mol Biol (1992), 227:799-817; and Tomlinson et al., EMBO J (1995), 14: 4628-4638. Still another standard is the AbM definition used by Oxford Molecular's AbM antibody modelling software. See, generally, e.g., Protein Sequence and Structure Analysis of Antibody Variable Domains. In: Antibody Engineering Lab Manual (Ed.: Duebel, S. and Kontermann, R., Springer-Verlag, Heidelberg). The sequence of antibody genes after assembly and somatic mutation is highly varied, and these varied genes are estimated to encode 1010 different antibody molecules (Immunoglobulin Genes, 2nd ed., eds. Jonio et al., Academic Press, San Diego, Calif., 1995). Accordingly, the immune system provides a repertoire of immunoglobulins. The term “repertoire” refers to at least one nucleotide sequence derived wholly or partially from at least one sequence encoding at least one immunoglobulin. The sequence(s) may be generated by rearrangement in vivo of the V, D, and J segments of heavy chains, and the V and J segments of light chains. Alternatively, the sequence(s) can be generated from a cell in response to which rearrangement occurs, e.g., in vitro stimulation. Alternatively, part or all of the sequence(s) may be obtained by DNA splicing, nucleotide synthesis, mutagenesis, and other methods, see, e.g., U.S. Pat. No. 5,565,332. A repertoire may include only one sequence or may include a plurality of sequences, including ones in a genetically diverse collection.
As used herein, unless specified otherwise, the term “antibody” does not only refer to an immunoglobulin (or intact antibody), but also to a fragment thereof, and encompasses any polypeptide comprising an antigen-binding fragment or an antigen-binding domain. Preferably, the fragment such as Fab, F(ab)2, Fv, scFv, Fd, dAb, and other antibody fragments that retain antigen-binding function. Typically, such fragments would comprise an antigen-binding domain and have the same properties as the antibodies described herein.
The term “antibody” as used herein includes antibodies that compete for binding to the same epitope as the epitope bound by the antibodies of the present invention, preferably obtainable by the methods for the generation of an antibody as described herein elsewhere. To determine if a test antibody can compete for binding to the same epitope, a cross-blocking assay e.g., a competitive ELISA assay can be performed. In an exemplary competitive ELISA assay, epitope-coated wells of a microtiter plate, or epitope-coated sepharose beads, are pre-incubated with or without candidate competing antibody and then a biotin-labeled antibody of the invention is added. The amount of labeled antibody bound to the epitope in the wells or on the beads is measured using avidin-peroxidase conjugate and appropriate substrate. Alternatively, the antibody can be labeled, e.g., with a radioactive or fluorescent label or some other detectable and measurable label. The amount of labeled antibody that binds to the antigen will have an inverse correlation to the ability of the candidate competing antibody (test antibody) to compete for binding to the same epitope on the antigen, i.e. the greater the affinity of the test antibody for the same epitope, the less labeled antibody will be bound to the antigen-coated wells. A candidate competing antibody is considered an antibody that binds substantially to the same epitope or that competes for binding to the same epitope as an antibody of the invention if the candidate competing antibody can block binding of the antibody by at least 20%, preferably by at least 20-50%, even more preferably, by at least 50% as compared to a control performed in parallel in the absence of the candidate competing antibody (but may be in the presence of a known noncompeting antibody). It will be understood that variations of this assay can be performed to arrive at the same quantitative value.
The term “antibody” also includes but is not limited to polyclonal, monoclonal, monospecific, polyspecific such as bispecific, non-specific, humanized, human, single-chain, chimeric, synthetic, recombinant, hybrid, mutated, grafted, and in vitro generated antibodies. In one embodiment of the present invention, the antibody binding to an HERV Env protein or to its respective receptor is a monoclonal antibody (mAb; MAb). In context with the present invention, commercially available antibodies that may be employed in accordance with the present invention comprise those listed in Table II herein.
Accordingly, the term “antibody” also relates to a purified serum, i.e. a purified polyclonal serum. Accordingly, said term preferably relates to a serum, more preferably a polyclonal serum and most preferably to a purified (monoclonal or polyclonal) serum. The antibody/serum is obtainable, and preferably obtained, for example, by the method or use described herein. “Polyclonal antibodies” or “polyclonal antisera” refer to immune serum containing a mixture of antibodies specific for one (monovalent or specific antisera) or more (polyvalent antisera) antigens which may be prepared from the blood of animals immunized with the antigen or antigens. A non-limiting example of such an antibody beyond the examples given in table II may be an antibody which is capable of binding to the amino acid sequence shown in SEQ ID NOs: 22-23 or to a portion thereof.
Furthermore, the term “antibody” as employed in the invention also relates to derivatives or variants of the antibodies described herein which display the same specificity as the described antibodies. Examples of “antibody variants” include humanized variants of non-human antibodies, “affinity matured” antibodies (see, e.g., Hawkins et al., J Mol Biol (1992), 254, 889-896; and Lowman et al., Biochemistry (1991), 30: 10832-10837) and antibody mutants with altered effector function (s) (see, e.g., U.S. Pat. No. 5,648,260). The terms “antigen-binding domain”, “antigen-binding fragment” and “antibody binding region” when used herein refer to a part of an antibody molecule that comprises amino acids responsible for the specific binding between antibody and antigen. The part of the antigen that is specifically recognized and bound by the antibody is referred to as the “epitope” as described herein above. As mentioned above, an antigen-binding domain may typically comprise an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH); however, it does not have to comprise both. Fd fragments, for example, have two VH regions and often retain some antigen-binding function of the intact antigen-binding domain. Examples of antigen-binding fragments of an antibody include (1) a Fab fragment, a monovalent fragment having the VL, VH, CL and CH1 domains; (2) a F(ab′)2 fragment, a bivalent fragment having two Fab fragments linked by a disulfide bridge at the hinge region; (3) a Fd fragment having the two VH and CH1 domains; (4) a Fv fragment having the VL and VH domains of a single arm of an antibody, (5) a dAb fragment (Ward et al., (1989) Nature 341:544-546), which has a VH domain; (6) an isolated complementarity determining region (CDR), and (7) a single chain Fv (scFv). Although the two domains of the Fv fragment, VL and VH> are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al., (1988) Science (1988), 242: 423-426; and Huston et al., (1988) PNAS USA (1988), 85: 5879-5883). These antibody fragments are obtained using conventional techniques known to those with skill in the art, and the fragments are evaluated for function in the same manner as are intact antibodies.
The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e. the individual antibodies comprising the population are identical except for possible naturally occurring mutations and/or post-translation modifications (e.g., isomerizations, amidations) that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they are synthesized by the hybridoma culture, uncontaminated by other immunoglobulins. The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al., Nature (1975), 256: 495, or may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567). The “monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature (1991), 352: 624-628; and Marks et al., J Mol Biol (1991), 222: 581-597, for example. The monoclonal antibodies herein specifically include “chimeric” antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain (s) is (are) identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; Morrison et al., PNAS USA (1984), 81: 6851-6855). Chimeric antibodies of interest herein include “primitized” antibodies comprising variable domain antigen-binding sequences derived from a non-human primate (e.g., Old World Monkey, Ape etc.) and human constant region sequences. “Humanized” forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F (ab′) 2 or other antigen-binding subsequences of antibodies) of mostly human sequences, which contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region (also CDR) of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity, and capacity. In some instances, Fv framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, “humanized antibodies” as used herein may also comprise residues which are found neither in the recipient antibody nor the donor antibody. These modifications are made to further refine and optimize antibody performance. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al., Nature (1986), 321: 522-525; Reichmann et al., Nature (1988), 332: 323-329; and Presta, Curr. Op. Struct Biol (1992), 2: 593-596.
The term “human antibody” includes antibodies having variable and constant regions corresponding substantially to human germline immunoglobulin sequences known in the art, including, for example, those described by Kabat et al. (See Kabat et al., loc. cit.). The human antibodies of the invention may include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo), for example in the CDRs, and in particular, CDR3. The human antibody can have at least one, two, three, four, five, or more positions replaced with an amino acid residue that is not encoded by the human germline immunoglobulin sequence. As used herein, “in vitro generated antibody” refers to an antibody where all or part of the variable region (e.g., at least one CDR) is generated in a non-immune cell selection (e.g., an in vitro phage display, protein chip or any other method in which candidate sequences can be tested for their ability to bind to an antigen). This term thus preferably excludes sequences generated by genomic rearrangement in an immune cell. A “bispecific” or “bifunctional antibody” is an artificial hybrid antibody having two different heavy/light chain pairs and two different binding sites. Bispecific antibodies can be produced by a variety of methods including fusion of hybridomas or linking of Fab′ fragments. See, e.g., Songsivilai & Lachmann, Clin Exp Immunol (1990), 79: 315-321; Kostelny et al., J Immunol (1992), 148: 1547-1553. In one embodiment, the bispecific antibody comprises a first binding domain polypeptide, such as a Fab′ fragment, linked via an immunoglobulin constant region to a second binding domain polypeptide.
Numerous methods known to those skilled in the art are available for obtaining antibodies or antigen-binding fragments thereof. For example, antibodies can be produced using recombinant DNA methods (U.S. Pat. No. 4,816,567). Monoclonal antibodies may also be produced by generation of hybridomas (see e.g., Kohler and Milstein, Nature (1975), 256: 495-499) in accordance with known methods. Hybridomas formed in this manner are then screened using standard methods, such as enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (BIACORE™) analysis, to identify one or more hybridomas that produce an antibody that specifically binds with a specified antigen. Any form of the specified antigen may be used as the immunogen, e.g., recombinant antigen, naturally occurring forms, any variants or fragments thereof, as well as antigenic peptide thereof. One exemplary method of making antibodies includes screening protein expression libraries, e.g., phage or ribosome display libraries. Phage display is described, for example, in U.S. Pat. No. 5,223,409; Smith, Science (1985), 228: 1315-1317; Clackson et al., Nature (1991), 352: 624-628; Marks et al., J Mol Biol (1991), 222: 581-597WO 92/18619; WO 91/17271; WO 92/20791; WO 92/15679; WO 93/01288; WO 92/01047; WO 92/09690; and WO 90/02809. In another embodiment, a monoclonal antibody may be obtained from the non-human animal, and then modified, e.g., humanized, deimmunized, chimeric, may be produced using recombinant DNA techniques known in the art. A variety of approaches for making chimeric antibodies have been described. See, e.g., Morrison et al., PNAS USA (1985), 81: 6851; Takeda et al., Nature (1985), 314: 452; U.S. Pat. Nos. 4,816,567; 4,816,397; EP 171496; EP 173494, GB 2177096. Humanized antibodies may also be produced, for example, using transgenic mice that express human heavy and light chain genes, but are incapable of expressing the endogenous mouse immunoglobulin heavy and light chain genes. Winter describes an exemplary CDR-grafting method that may be used to prepare the humanized antibodies described herein (U.S. Pat. No. 5,225,539). All of the CDRs of a particular human antibody may be replaced with at least a portion of a non-human CDR, or only some of the CDRs may be replaced with non-human CDRs. It is only necessary to replace the number of CDRs required for binding of the humanized antibody to a predetermined antigen. Humanized antibodies or fragments thereof can be generated by replacing sequences of the Fv variable domain that are not directly involved in antigen binding with equivalent sequences from human Fv variable domains. Exemplary methods for generating humanized antibodies or fragments thereof are provided by Morrison, Science (1985), 229: 1202-1207; Oi et al., BioTechniques (1986), 4: 214; U.S. Pat. Nos. 5,585,089; 5,693,761; 5,693,762; 5,859,205; and 6,407,213. Those methods include isolating, manipulating, and expressing the nucleic acid sequences that encode all or part of immunoglobulin Fv variable domains from at least one of a heavy or light chain. Such nucleic acids may be obtained from a hybridoma producing an antibody against a predetermined target, as described above, as well as from other sources. The recombinant DNA encoding the humanized antibody molecule can then be cloned into an appropriate expression vector. In certain embodiments, humanized antibody may be optimized by the introduction of conservative substitutions, consensus sequence substitutions, germline substitutions and/or backmutations. Such altered immunoglobulin molecules can be made by any of several techniques known in the art, (e.g., Teng et al., PNAS USA (1983), 80: 7308-731; Kozbor et al., Immunology Today (1983), 4: 7279; Olsson et al., Meth Enzymol (1982), 92: 3-16), and may be made according to the teachings of WO 92/06193 or EP 239400).
Examples of anti-HERV Env protein-antibodies may bind to the amino acid sequence of the HERV Env protein. Illustrative and non-limiting examples of such amino acid sequences are shown in SEQ ID NO: 101 to 139. Thus, an anti-HERV Env protein-antibody capable of binding to the amino acid sequence of HERV K shown in SEQ ID NOs: 101 to 128 or to a portion thereof may be used in treating Tauopathy, or Parkinson's disease is envisaged herein. Further, an anti-HERV Env protein-antibody capable of binding to the amino acid sequence of HERV W shown in SEQ ID NOs: 129 to 131 or to a portion thereof may be used treating Tauopathy, or Parkinson's disease is encompassed. Likewise an anti-HERV Env protein-antibody capable of binding to the amino acid sequence of HERV H shown in SEQ ID NOs: 132 to 137 or to a portion thereof may be used in treating Tauopathy, or Parkinson's disease is an illustrative example. Finally, an anti-HERV Env protein-antibody capable of binding to the amino acid sequence of HERV R shown in SEQ ID NOs: 138 to 139 or to a portion thereof may be used in treating Tauopathy, or Parkinson's disease is also envisaged herein.
In a similar manner HERV Gag amino acid sequences may be targeted by antibodies and these antibodies thus may fulfill the task of an inhibitor as mentioned herein. Therefore, an anti-HERV Env protein-antibody capable of binding to the amino acid sequence of HERV Gag shown in SEQ ID NOs: 22 to 23 or to a portion thereof may be used in treating Tauopathy, or Parkinson's disease.
As has further been found in context with the present invention, HERV Env proteins as described and defined herein can be used as biomarkers for diagnosing a tauopathy (e.g., Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17)), Parkinson's disease and ALS. Particularly, as found in context with the present invention, HERV Env proteins are upregulated and overexpressed in different tauopathies. For example, as has been found in context with the present invention, HERV-W is upregulated in AD patients, while HERV-FRD, H and R(b) are associated with CBD disease, and HERV-K and F(c)1 are increased in PSP patients. Accordingly, in accordance with the present invention, molecules binding to HERV Env proteins or (a) fragment(s) or to nucleic acid molecules encoding such HERV Env proteins or (a) fragment(s) thereof may be used for diagnosing tauopathy (e.g., Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17), Parkinson's disease and ALS. In specific embodiments of the present invention, molecules binding to specific HERV-Env proteins or (a) fragment(s) which are associated with specific tauopathies or with nucleic acid molecules encoding such specific HERV Env proteins or (a) fragment(s) thereof may be used for diagnosing corresponding specific tauopathies. For example, in this context, such specific tauopathy-HERV Env protein association has been shown in context with the present invention for (1) HERV-W and AD, (2) HERV-FRD & HERV-H & HERV-R(b) and CBD, and (3) HERV-K & HERV-F(c)1 and PSP.
Accordingly, the present invention also relates to molecules binding to HERV Env protein or a fragment thereof, or to a nucleic acid molecule encoding said HERV Env protein or a fragment thereof, for use in diagnosing a tauopathy (e.g., Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17)), Parkinson's disease, or ALS. In one embodiment of the present invention, such molecule binding to HERV Env protein or a fragment thereof may be any binding agent as described and defined herein in context with inhibitors of HERV Env proteins. Preferably, such binding agent is suitable to be employed in a protein detection system, for example—but not limited to—ELISA, ELIA, Western blot, IHC, and other protein detection systems known in the art. In one embodiment, such HERV Env protein binding agent is an antibody as described and defined herein. In a further embodiment, such binding agents may be labelled (depending on the assay used as readily clear for the skilled person).
In another embodiment of the present invention, such molecule binding to a nucleic acid molecule encoding a HERV Env protein or a fragment thereof may be any nucleic acid molecule as described and defined herein in context with inhibitors of HERV Env protein expression (e.g., transcription or translation) which is suitable for specifically detecting a nucleic acid molecule. Preferably, it is a nucleotide probe, hybridizing (preferably under stringent conditions) or being complementary to at least a portion of a nucleic acid molecule encoding a HERV Env protein or a fragment thereof. For example, such nucleic acid molecules may be selected from the group consisting of decoy nucleic acid molecules, primers, or other probe molecules suitable in corresponding assays for specific DNA or RNA sequence identification. Such assays include inter alia PCR (incl. RT, real-time, quantitative), Southern/Northern blot, microarray, etc. In one embodiment, such probe molecules for specific DNA or RNA sequence identification may be labelled (depending on the assay used as readily clear for the skilled person).
In context with the present invention, the tauopathy to be treated or diagnosed as described herein is to be understood as known in the art and may comprise any disease or disorder associated with generation, aggregation, or overexpression of Tau protein. In accordance with the present invention, examples of tauopathies comprise Alzheimer's Disease (AD), Argyrophilic Grain Disease (AGD), Cortical Basal Degeneration (CBD), Progressive Supranuclear Palsy (PSP), Pick's Disease (PiD), and Frontotemporal Dementia with Parkinsonism related to chromosome 17 (FTDP-17), particularly AD, AGD, CBD and PSP, more particularly AD, CBD and PSP.
The inventors were able to demonstrate that an shRNA directed against HERV Env (here: HERV-W Syncytin-1) can reduce intercellular Tau aggregate spreading (breast cancer cell line MCF-7,
Thus, it is encompassed to use a nucleotide sequence against HERV Env proteins (e.g. HERV-W Syncytin-1 or HERV-W Syncytin-2), or the (HIV) protease inhibitor Lopinavir, to reduce Tau aggregate spreading. A nucleotide sequence directed against the nucleotide sequence of HERV Env shown in any one of SEQ ID NOs: 1 to 13, for use in treating Tauopathy, or Parkinson's disease is encompassed by the present invention. An illustrative example of such a nucleotide sequence may be the sequence shown in SEQ ID NOs: 42 to 72, or SEQ ID NO: 98 or the murine sequences shown in SEQ ID NOs: 25 to 29. Further, a nucleotide sequence directed against HERV-W Syncytin-1 for use in treating Tauopathy, or Parkinson's disease as well as a nucleotide sequence directed against HERV-W Syncytin-2 for use in treating Tauopathy, or Parkinson's disease are embodiments of the present invention.
Likewise, a nucleotide sequence directed against the nucleotide sequence of HERV Gag shown in any one of SEQ ID NOs: 14 to 21 or encoded by a nucleotide sequence that has at least about 85% sequence identity to any one of SEQ ID NOs: 14 to 21, for use in treating Tauopathy, or Parkinson's disease, is envisaged herein. A nucleic acid molecule hybridizing to at least a portion of the nucleotide sequence of HERV Gag shown in any one of SEQ ID NOs: 14 to 21 for use in treating Tauopathy, or Parkinson's disease, is directed to bind anywhere in the respective DNA sequence. Further, a nucleic acid molecule comprising any one of the nucleotide sequence shown in any one of SEQ ID NOs: 30 to 35 for use in treating Tauopathy, or Parkinson's disease, depicts different nucleotide sequence variants, capable of binding selectively to the respective Gag proteins. It is further envisaged that the interaction between HERV Env and its respective receptors ASCT1 (gene SLC1A4), ASCT2 (gene SLC1A4), (and the complex of CD98HC and LAT1 which may functions as HERV Env receptor) are blocked, to reduce aggregate spreading. Thus, an inhibitor of a HERV Env protein capable of blocking the binding of HERV Env to its receptor ASCT1 (gene SLC1A4), ASCT2 (gene SLC1A5) for use in treating Tauopathy, Parkinson's disease, is encompassed herein. Said inhibitor may be a nucleic acid hybridizing to at least a portion of the nucleotide sequence of SLC1A4 (SEQ ID NO: 99) or SLCA4 (SEQ ID NO: 100). Thus, a nucleic acid molecule capable of blocking the HERV Env receptor ASCT1 (gene SLC1A4) or ASCT2 (gene SLC1A5) by hybridizing to at least a portion of the nucleotide sequence shown in SEQ ID NO: 99 or SEQ ID NO: 100 for use in treating Tauopathy, Parkinson's disease.
The present invention may also be characterized by the following items:
The embodiments which characterize the present invention are described herein, shown in the Figures, illustrated in the Examples, and reflected in the claims.
It must be noted that as used herein, the singular forms “a”, “an”, and “the”, include plural references unless the context clearly indicates otherwise. Thus, for example, reference to “a reagent” includes one or more of such different reagents and reference to “the method” includes reference to equivalent steps and methods known to those of ordinary skill in the art that could be modified or substituted for the methods described herein.
Unless otherwise indicated, the term “at least” preceding a series of elements is to be understood to refer to every element in the series. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the present invention.
The term “and/or” wherever used herein includes the meaning of “and”, “or” and “all or any other combination of the elements connected by said term”.
The term “about” or “approximately” as used herein means within 20%, preferably within 10%, and more preferably within 5% of a given value or range.
Throughout this specification and the claims which follow, unless the context requires otherwise, the word “comprise”, and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integer or step. When used herein the term “comprising” can be substituted with the term “containing” or “including” or sometimes when used herein with the term “having”.
When used herein “consisting of” excludes any element, step, or ingredient not specified in the claim element. When used herein, “consisting essentially of” does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim.
In each instance herein any of the terms “comprising”, “consisting essentially of” and “consisting of” may be replaced with either of the other two terms.
It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such can vary. The terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the scope of the present invention, which is defined solely by the claims.
All publications and patents cited throughout the text of this specification (including all patents, patent applications, scientific publications, manufacturer's specifications, instructions, etc.), whether supra or infra, are hereby incorporated by reference in their entirety. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. To the extent the material incorporated by reference contradicts or is inconsistent with this specification, the specification will supersede any such material.
Sequences referred to herein comprise:
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
H. sapiens
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Mus musculus
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
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The present invention is further illustrated by the following examples. Yet, the examples and specific embodiments described therein must not be construed as limiting the invention to such specific embodiments.
Upregulation of Endogenous Retrovirus Increases Intercellular Protein Aggregate Induction
The prion domain NM of the Saccharomyces cerevisiae prion protein Sup35 stably expressed in the cytosol of mouse neuroblastoma N2a cells was induced to aggregate by exposure to amyloid fibrils of recombinant NM protein (Krammer et al., PNAS (2009), 106: 462-467). To study cellular mechanisms of protein aggregate spreading, subclone N2a s2E was used, selected by two rounds of limiting dilution cloning. This clone was selected due to its ability to potently induce NM aggregation in cells expressing soluble NM upon coculture and EV addition (Liu et al., mBio (2016), 7:00915-00916). Donor clone s2E was cocultured with recipient cell line N2a expressing soluble NM-GFP (NM-GFPsol) and the percentage of recipient cells with induced NM-GFP aggregates was subsequently determined by automated microscopy (
It was determined whether the highly efficient aggregate induction by coculture or by EVs from donor cells of later passage was associated with active endogenous retroviral particles present in the exosomal fraction. To this end, the reverse transcriptase (RT) activity of released particles from donor cell clone s2E (P16) was compared with N2a NM-HAagg cell clones 1C and 3B that exhibit low aggregate induction rates in recipient cells (Hofmann et al., PNAS (2013), 10: 5951-5956; Liu et al., MBio (2016), 7). Only N2a NM-HAagg clone s2E released particles with increasing RT activity upon prolonged culture (
It was determined if endogenous retroviral particles or vesicles released by the donor cells contained infectious NM seeds. To separate EVs from viral particles, an Optiprep velocity gradient previously used to separate HIV-1 virions from non-viral extracellular vesicles was employed (Dettenhofer et al., J Virol (1999), 73: 1460-1467). Western blot analyses revealed the presence of NM-HA predominately in fractions that contained exosomal marker Alix (
ERV Gene Products are Required for Intercellular Aggregate Induction Via EVs
Experiment 1 showed that upregulated ERV Env and Gag proteins in donor cells are associated with EVs and facilitate efficient EV-mediated aggregate transmission to recipient cells. To further investigate if EV-mediated NM aggregate induction depends on the fusogenic activity of Env, anti-HIV-1 drugs were screened for their effects on NM aggregate induction in coculture, as well on EV- and fibril-mediated NM aggregate induction in recipient cells (
Neutralization experiments with antibodies targeting Env protein revealed a dose-dependent reduction of NM-GFP aggregate positive recipient cells cocultured with donor cells (
It was evaluated whether treatment with DNA methyl transferase inhibitors 5-Azacytidine (Aza) and Decitabine (Dec), capable of erasing epigenetic marks and thereby inducing ERV expression (Chiappinelli et al., Cell (2015), 162:974-986; Ramos et al., Epigenetics Chromatin (2015), 8:11) would result in increased intercellular aggregate induction efficiency. Clone s2E with low MuERVs expression (P1) was chosen for the experiment. Indeed, treatment of the cell clone s2E for three days with the epigenetic drugs and subsequent culture in the absence of the drugs for 5 days resulted in increased expression of total env and gag mRNA (
Alignment analysis showed substantial similarity of P10404 with MCF247, a polytropic MuLV (
XPR1 is a multiple-membrane spanning receptor with eight putative transmembrane domains and four extracellular loops (ECL) (Battini et al., PNAS (1999), 96: 1385-1390). Polymorphisms in ECL 3 and 4 affect the entry of certain X/P-MuLV subtypes. Analysis of XPR1 of N2a cells demonstrated that its Env recognition domain differed at 9 residues within ECL 3 and 4 from XPR1 expressed by HEK cells (
To examine this effect on Tau aggregate spreading, an N2a s2E cell clone stably propagating aggregated Tau-GFPCBD was produced (
Fusogenic Viral Glycoproteins Drastically Increase Intercellular Transmission of Proteinaceous Seeds
The foregoing experiments demonstrated that upregulation of endogenous retroviruses drastically increased intercellular aggregate transmission via receptor-ligand interactions. It was tested whether the expression of unrelated viral glycoproteins that target specific membrane proteins on recipient cells might also be able to increase intercellular aggregate transmission and induction. The vesicular stomatitis virus glycoprotein VSV-G is routinely used to pseudotype viral particles for efficient uptake by a broad spectrum of target cells expressing the LDL receptor. Recently, VSV-G has been successfully used to pseudotype EVs for enhanced protein delivery to recipient cells (Meyer et al., Int J Nanonmed (2017), 12: 3153-3170). It was tested if ectopic VSV-G expression also increased intercellular spreading of proteinaceous seeds. The N2a NM-HAagg clone 2E (precursor clone of s2E) and HEK NM-HAagg clone C3, two cell lines that are characterized by poor NM aggregate induction rates when cocultured with recipient cells, were transfected with plasmids coding for VSV-G. The presence of VSV-G on EVs isolated from both donor cell clones (
It was then tested if viral glycoproteins could also promote spreading of pathogenic protein aggregates between cells. Thus, the effect of VSV-G expression on the intercellular spreading of transmissible spongiform encephalopathy (TSE) agents was evaluated. TSE agents, the so far only bona fide mammalian prions, are composed of misfolded cellular prion protein PrP. The conversion of cellular (PrPC), a protein tethered to the cell membrane by a glycosylphosphatidyl-anchor, into its infectious aggregated isoform (PrPSc), occurs on the cell surface or along the endocytic pathway. It has previously been shown that N2a cells release prion infectivity associated with EVs. N2a cells persistently infected with TSE strain 22L (N2a22L) were transiently transfected with control plasmid or a plasmid coding for VSV-G. EVs were isolated from medium of transfected cells containing VSV-G (
We further tested if VSV-G expression also increased the intercellular transmission of Tau aggregates and subsequent induction of Tau aggregation in a reporter cell line. To this end, we established a Tau cell model that had been described previously by Diamond and coworkers (Sanders et al., Neuron (2014), 82:1271-1288). HEK cells were engineered to stably express the aggregation competent Tau core spanning amino acid residues 244-372 with two point mutations P301L/V337M fused to GFP (hereafter termed Tau-GFP). Cells were exposed to brain homogenates from patients who had suffered from Alzheimer's disease (AD), cortical basal degeneration (CBD), progressive supranuclear palsy (PSP) or frontotemporal lobar degeneration (FTLD). Upon limiting dilution cloning, cell clones HEK Tau-GFPAD, Tau-GFPFTLD Tau-GFPPSP and Tau-GFPCBD stably producing Tau aggregates were established (
Human Endogenous Retrovirus Proteins Contribute to Intercellular Protein Aggregate Transmission
To examine the effect of endogenous HERVs on protein aggregate transmission, T47D human breast tumor cells which exhibit highly increased HERV-K expression upon stimulation with female steroid hormones were used (Ono et al., J Virol (1987), 61: 2059-2062). It was first tested if HERV-K proteins contribute to the intercellular transmission of the model prion NM described above. To this end, a T47D cell clone stably expressing soluble NM-GFP (T47D NM-GFPsol) was exposed to in vitro formed NM fibrils for one day. The resulting T47D NM-GFPagg bulk cell population was cocultured with recipient HEK NM-mCherrysol cells in the presence or absence of Amprenavir, shown to also be effective against HERV-K (Tyagi et al., Retrovirology (2017), 14:21) (
To examine the effect of HERV-K proteins on Tau aggregate spreading, a T47D donor cell line stably expressing Tau-GFPsol was generated. As exposure of T47D cells to brain homogenates resulted in poor Tau-GFP aggregation (less than 0.5% of recipient cells), VSV-G pseudotyped EVs derived from HEK Tau-GFPAD and Tau-GFPFTLD cells (see
Elevated Transcripts of Distinct HERV Families in Postmortem Brains from Different Tauopathy Patients
The foregoing experiments indicated that murine and human ERV proteins expressed by donor cells facilitate efficient cell-to-cell and EV-mediated spreading of proteopathic seeds from donor to recipient cells. To test if HERV env expression is upregulated in tauopathies, quantitative real-time PCR was performed using predesigned primer sets against env sequences of nine HERV family members (de Parseval et al., J Virol (2003), 77:10414-10422; Strissel et al., Oncotarget (2012), 3:1204-1219). These primer sets locate in the coding elements that detect the expression of the coding copies of the env genes. It was found that transcripts of distinct HERVs were elevated in postmortem brain samples from individuals suffering from different tauopathies (
Methods
Human Brain Samples
Frozen brain tissue samples from neuropathologically confirmed cases of AD, CBD, PSP and controls were provided by Brain Bank Tubingen.
Ethics Statement
For all the patient sample experiments, the ethical approval has been obtained from ‘Medizinische Fakultät Ethik-Kommission, Rheinische Friedrich-Wilhelms-Universität, Project no. 236/18(2018)’.
Molecular Cloning
For the expression of lentiviral constructs Tau-GFP and Tau-FusionRed, the four repeat domain 4RN1 of human Tau (amino acid residues 244 to 372) containing the mutations P301L and V337M was fused aminoterminally to GFP or FusionRed (Evrogen) with an 18-amino acid flexible linker (EFCSRRYRGPGIHRSPTA), as described previously (Woerman et al., PNAS (2016), 113:E8187-E8196). Coding regions were cloned into the lentiviral vector pRRL.sin.PPT.hCMV.Wpre via BamHI and SalI (Hofmann et al., PNAS (2013), 10: 5951-5956). Murine and human receptor XPR1 were amplified from cDNA of N2a or HEK cells, respectively. The coding region of murine XPR1 tagged aminoterminally with a hemagglutinin epitope (HA) was cloned into a PiggyBac expression vector PB510B-1 (System Biosciences) using XbaI and NotI restriction sites.
Cell Lines
N2a, Hela, L929, CAD5 and HEK293T cells are from ATCC and were cultured in Opti-MEM (Gibco) supplemented with glutamine, 10% (v/v) fetal bovine serum (FCS) (PAN-Biotech GmbH) and antibiotics. Melan-a cells are from Wellcome Trust Functional Genomics Cell Bank and were cultured in RPMI 1640 (Gibco) with 2 mM glutamine, 10% FCS, antibiotics and 200 nM 12-0-tetradecanoyl phorbol acetate PMA and incubated at 37° C. and 10% CO2. T47D cells were cultured in DMEM (Gibco) supplemented with 2 mM Glutamine and 10 (v/v) FCS. Cells were incubated at 37° C. and 5% CO2. The total numbers of viable cells and the viability of cells were determined using the Vi-VELL™XR Cell Viability Analyzer (Beckman Coulter).
Isolation of Cortical Neurons
Preparation of cortical neurons was performed using postnatal day 13 SWISS pups as described previously (Hofmann et al., PNAS (2013), 10: 5951-5956). Neurons were transduced with lentivirus 2 days post preparation on 96 well plates or Sarstedt 8 slice chambers. After 2 days, EVs were added and neurons were incubated for 2 days. Subsequently, neurons were fixed for microscopy and imaging analysis.
Production and Transduction with Lentiviral Particles
HEK293T cells were cotransfected with plasmids pRSV-Rev, pMD2.VSV-G, pMDI.g/pRRE (all plasmids were published in Dull T, Zufferey R, Kelly M, Mandel R J, Nguyen M, Trono D, Naldini L A third-generation lentivirus vector with a conditional packaging system. J Virol. 1998 November 72(11):8463-71), and pRRI.sin.PPT.hCMV.Wpre (plasmid published in Follenzi, A. and L. Naldini (2002) HIV-based vectors. Preparation and use. Methods in molecular medicine 69: 259-274) containing Tau-GFP/FusionRed. Supernatants were harvested 30 and 54 h later and concentrated using PEG according to published protocols (Follenzi et al., Methods Mol Med (2002), 69:259-274). Cell lines and primary neurons were transduced with lentivirus, and stable cell clones expressing Tau-GFP/-FusionRed were produced by limiting dilution cloning (Krammer et al., PNAS (2009), 106:462-467).
EV Isolation
To prepare EV-depleted medium, FCS was ultracentrifuged at 100,000×g for 20 h at 4° C. Medium supplemented with the EV-depleted FCS and antibiotics was subsequently filtered through 0.22 μM and a 0.1 μM filter-sterilization devices (Millipore). For EV isolation, 2-4×106 cells were seeded in T175 flasks in 35 ml EV-depleted medium to reach confluence after 3 days. Cells and cell debris were pelleted by differential centrifugation (300×g, 10 min; 2,000×g, 20 min; 16,000×g, 30 min, 4° C.). The remaining supernatant (conditioned medium) was subjected to ultracentrifugation at 100,000×g for 1 h at 4° C. using rotors Ti45 or SW32Ti (Beckman Coulter). The pellet was rinsed in PBS and spun again using rotor SW55Ti at 100,000×g for 1 h at 4° C.
Aggregate Induction Assay
Recipient cells were cultured on CellCarrier-96 plates or 384 black microplates (PerkinElmer) at appropriate cell numbers for 1 h, and then treated with 5-10 μl of prepared samples (isolated EVs or recombinant NM fibrils). For aggregate induction by coculture, recipient and donor cells were mixed at different ratios based on the population doubling time of donor and recipient cells, and a total of 104 cells/per well was plated. After additional incubation for 16 h or 72 h (NM or Tau, respectively), cells were fixed in 4% paraformaldehyde and nuclei were counterstained with 4 μM Hoechst for 15 min. Cells were imaged with the automated confocal microscope CellVoyager CV6000 (Yokogawa Inc.) using a 20× or 40× objective. Maximum intensity projections were generated from Z-stacks. Images from 16 fields per well were taken. On average, a total of 3-4×104 cells per well and at least 3 wells per treatment were analyzed.
Sample Preparation for Mass Spectrometry
Cell pellets from five s2E cell culture replicates, and six replicates of EV pellets harvested from conditioned medium of s2E cells at passages 7 and 16 were collected for a quantitative proteomics analysis. Cell pellets were lysed in 150 μL SDT buffer (4% SDS (w/v), 100 mM Tris/HCl pH 7.6, 0.1 M DTT) by homogenization with a dounce tissue grinder and heated for 3 min at 95° C. Samples were sonicated 5 times for 30 s with intermediate cooling using a vialtweeter sonifier (amplitude 100%, duty cycle 50%; Hielscher, Germany). EV pellets were lysed in 100 μL STET lysis buffer (150 mM NaCl, 50 mM TrisHCl pH 7.5, 2 mM EDTA, 1% Triton X-100) on ice for 30 min with intermediate vortexing. Cell debris was removed by centrifugation at 16,000×g for 5 min. The protein concentration was determined using the colorimetric 660 nm assay (Thermo Fisher Scientific). For cell lysates, the assay solution was supplemented with the ionic detergent compatibility reagent (Thermo Fisher Scientific). A protein amount of 30 μg per sample for cell lysates and 10 μg for EV lysates was subjected to proteolytic digestion using the filter aided sample preparation (FASP) protocol (Wisniewski et al., Nat Methods (2009), 6:359-362) with 30 kDa Vivacon spin filters (Sartorius, Germany). Proteolytic peptides were desalted by stop and go extraction (STAGE) with C18 tips (Rappsilber et al., Anal Chem (2003), 75:663-670). The purified peptides were dried by vacuum centrifugation. Peptides from cell lysates and EV samples were dissolved in 40 or 20 μL of 0.1% formic acid, respectively.
LC-MS/MS Analyses
Samples were analyzed by LC-MS/MS for relative label free protein quantification. A peptide amount of approximately 1 μg per sample was separated on a nanoLC system (EASY-nLC 1000, Proxeon—part of Thermo Fisher Scientific) using in-house packed C18 columns (50 cm or 30 cm×75 μm ID, ReproSil-Pur 120 C18-AQ, 1.9 μm, Dr. Maisch GmbH, Germany) with a binary gradient of water (A) and acetonitrile (B) containing 0.1% formic acid at 50° C. column temperature and a flow rate of 250 nl/min. Peptides from cell lysates were separated on a 50 cm column using a gradient of 250 min length, whereas a 183 min gradient on a 30 cm column was used for peptides from EV samples (250 min. gradient: 0 min., 2% B; 5 min., 5% B; 185 min., 25% B; 230 min., 35% B; 250 min., 60% B; 183 min. gradient: 0 min., 2 B; 3:30 min., 5% B; 137:30 min., 25% B; 168:30 min., 35% B; 182:30 min., 60% B). The nanoLC was coupled online via a nanospray flex ion source (Proxeon—part of Thermo Fisher Scientific) equipped with a PRSO-V2 column oven (Sonation, Germany) to a Q-Exactive mass spectrometer (Thermo Fisher Scientific). Full MS spectra were acquired at a resolution of 70,000. The top 10 peptide ions were chosen for Higher-energy C-trap Dissociation (HCD) with a normalized collision energy of 25%. Fragment ion spectra were acquired at a resolution of 17,500. A dynamic exclusion of 120 s was used for peptide fragmentation.
Data Analysis and Label Free Quantification
The raw data was analyzed by the software Maxquant (maxquant.org, Max-Planck Institute Munich) version and 1.5.5.1 (Cox et al., Mol Cell Proteomics (2014), 13:2513-2526). The MS data was searched against a fasta database of Mus musculus from UniProt including also non-reviewed entries supplemented with databases of lentiviruses and murine leukemia viruses (download: Dec. 9, 2017, 52041+712+43 entries). Trypsin was defined as protease. Two missed cleavages were allowed for the database search. The option first search was used to recalibrate the peptide masses within a window of 20 ppm. For the main search, peptide and peptide fragment mass tolerances were set to 4.5 and 20 ppm, respectively. Carbamidomethylation of cysteine was defined as static modification. Acetylation of the protein N-term as well as oxidation of methionine were set as variable modifications. The false discovery rate for both peptides and proteins was adjusted to less than 1%. Label free quantification (LFQ) of proteins required at least two ratio counts of razor peptides. Only unique and razor peptides were used for quantification.
The LFQ values were log2 transformed and a two sided Student's t-test was used to evaluate statistically significant changed abundance of proteins between cell lysates from passages 16 and 7 as well as EV lysates from passages 15 and 6. A p-value less than 5% was set as significance threshold. Additionally, a permutation based false discovery rate estimation was used to account for multiple hypotheses (Tusher et al., PNAS (2001), 98:5116-5121).
OptiPrep Density Gradient
For separating EVs and virus, the discontinuous iodixanol gradient in 1.2% increments ranging from 6 to 18% were prepared as previously described (Dettenhofer et al., J Virol (1999), 73:1460-1467). The 100,000×g pellet from 1050 ml culture supernatant (30 T175 flasks) was resuspended in 1 ml PBS and overlaid onto the gradient. The gradient was subjected to high-speed centrifugation at 100,000×g for 2 h at 4° C. using a SW41Ti rotor (Beckman Coulter). 12 fractions of 1 ml each were collected from the top of the gradient, diluted with PBS in 5 ml, and centrifuged at 100,000×g for 1 h at 4° C. The pelleted fractions were resuspended in 100 μl PBS, and then used for further experiments. The reverse transcriptase activity of the viruses was measured by using a colorimetric reverse transcriptase assay (Roche).
Determination of Extracellular Vesicles Size and Number
ZetaView PMX 110-SZ-488 Nano Particle Tracking Analyzer (Particle Metrix GmbH) was used to determine the size and number of isolated extracellular vesicles. The instrument captures the movement of extracellular particles by utilizing a laser scattering microscope combined with a video camera. For each measurement, the video data is calculated by the instrument, resulting in a velocity and size distribution of the particles. For nanoparticle tracking analysis, the Brownian motion of the vesicles from each sample was followed at 22° C. with properly adjusted equal shutter and gain. At least six individual measurements of 11 subvolumes (positions) within the measurement cell and around 2200 traced particles in each measurement were detected for each sample.
Electron Microscopy (EM)
EM imaging of extracellular vesicle preparations was performed as previously described (Thery et al., Curr Protoc Cell Biol (2006), Chapter3:Unit3 22). Briefly, the 100,000×g pellets from conditioned medium were fixed in 2% paraformaldehyde, loaded on glow discharged Formvar/carbon-coated EM grids (Plano GmbH), contrasted in uranyl-oxalat (pH 7) for 5 min and embedded in uranyl-methylcellulose for 5 min. Samples were examined using a JEOL JEM-2200FS transmission electron microscope at 200 kV (JEOL).
Infectivity Assay
The infectivity assay was performed as previously described (Pothlichet et al., Int J Cancer (2006), 119:815-822). Briefly, melan-a cells were exposed to conditioned medium from different cell clones at either low or high passsages in the presence of 4 μg polybrene/ml for 24 h. The medium was then replaced with normal culture medium. After five days, cells were lysed for western blot analysis of retroviral Env and Gag proteins.
Drug Treatments
The treatment of cells with Amprenavir (10 μM; Santa Cruz) and DMSO was performed for 72 h in EV-depleted medium in T175 flasks. Afterwards, the total numbers of viable cells and the viability upon drug treatment were determined using the Vi-VELL™ XR Cell Viability Analyzer (Beckman Coulter). EVs were isolated from the conditioned medium via ultracentrifugation and processed for the aggregate induction assay as described above. NM aggregate induction by coculture of donor and recipient cells or by exposure of recipient cells to donor-derived EVs was performed in the absence of the drugs. For coculture and EV treatment of recipient Tau-FusonRed cells, donor s2E P21 or T47D cells with Tau-GFP aggregates were pretreated as above. Isolated EVs or pretreated donor cells were then incubated with recipient cells in the presence of compounds for 72 h.
To inhibit methyltransferases, s2E P1 donor cells were treated for three days with methyltransferase inhibitors 5-Azacytidine (Aza) 200 nM, Decitabine (Dec) 100 nM or DMSO as solvent control. Subsequently, the cells were cultured in the absence of the drugs for 5 days. Pre-treated donor cells were subsequently cocultured with recipient cells as described above to monitor aggregate induction efficiency in recipient N2a NM-GFPsol cells. Cell lysates of donor cells were also analyzed for MuERV Env and Gag expression levels by western blot. To increase DNA methylation, the s2E donor clone (P21) was treated with methyl group donors L-methionine (L-M) 80 mM, Betaine (B) 80 mM, Choline chloride (CC) 20 mM or medium control for 6 days. MuERV Env and Gag protein levels were analyzed by western blot. Subsequently, cells were cocultured with recipient cells for 16 h. The percentage of aggregate containing recipient cells was compared to the percentage of aggregate bearing recipients cocultured with solvent-treated donors.
Neutralization Assay
To block MuLVs Env on the surface of the donor cell clones s2E and s2E Tau-GFPCBD and on secreted EVs, mAb83A25, reactive against a broad range MuLVs (Evans et al., J Virol (1990), 64:6176-6183) was incubated with either EVs or donor cells in serial dilutions for 1 h at 37° C. with rotation at 20 rpm. Donor cells were subsequently mixed with recipient cells for 16 h. Alternatively, antibody-treated and untreated EVs were added to recipient cells for 16 h (NM) or 3 days (Tau) incubation time.
Transfection of siRNAs and Plasmids
To transiently knock-down the upregulated specific MuLV Env and Gag genes in s2E clones, custom-designed Silencer select siRNAs (Thermo Fisher Scientific) against AA037244.2 (env) and AID54952 (gag) were used. Pre-designed siRNAs against murine XPR1 and mCat-1 genes were used to knock-down genes coding for putative receptors. For transfection, 2-4×105 cells/well were seeded on 6 well plates. The next day, 30 nM siRNA or plasmid DNA was transfected using Lipofectamine RNAiMAX or Lipofectamine2000 transfection reagent, respectively, according to the manufacturer's instructions (Thermo Fisher Scientific). After 2 days, transfected cells were harvested for aggregate induction assays and qRT-PCR, western blot analysis.
PK Treatment for Detection of PrPSc
Cells from one well of 6 well plate were lysed in 1 ml lysis buffer. 900 μl of lysates were digested with 20 μg/ml proteinase K (PK) at 37° C. for 30 min for PrPSc detection. Proteolysis was terminated by adding 0.5 mM Pefabloc. To make the pellet visible, 10 μl blue dextran was added to each sample and the samples were centrifuged at 20,817×g for 1 h. Proteins in 100 μl untreated lysates were precipitated with 4× methanol overnight at −20° C. and pelleted at 2,120×g for 25 min at 4° C. Untreated samples were analysed with the PK-treated pellets for total PrP and PrPSc by western blot using monoclonal anti-PrP antibody 4H11.
Sedimentation Tau Polymers
The sedimentation assay was performed as described previously (Sanders et al., Neuron (2014), 82:1271-1288). Briefly, cell pellets were lysed in lysis buffer (150 mM NaCl (w/v), 50 mM (v/v) Tris-HCl, pH7.5, 1% (v/v) NP-40, protease inhibitor) on ice for 30 min. Cleared cell lysates were separated from cell debris by centrifugation at 2650×g for 2 min at 4° C. Cleared cell lysates adjusted to 100 μg total protein were subjected to centrifugation at 100,000×g for 1 h, 4° C. Pellets were washed with 1.5 ml PBS and insoluble material was pelleted again at 100,000×g for 30 min. Proteins in the supernatant fractions were precipitated with 4× methanol overnight at −20° C. and pelleted at 2,120×g for 25 min at 4° C. (soluble fraction). The pellet (insoluble fraction) and ⅓ of the soluble fraction dissolved in RIPA buffer with 4% SDS were loaded for western blot analysis.
Pronase digestion of Tau
The resistance of Tau aggregates to pronase treatment was probed as described previously (Sanders et al., Neuron (2014), 82:1271-1288). Briefly, 18 μl cleared cell lysates or brain homogenates (containing a total protein concentration of 20-100 μg dependening on Tau aggregates content) were incubated with 2 μl 1 mg/ml pronase (Roche) at 37° C. for 1 h. Afterwards, samples were boiled in 4× sample buffer with 1% SDS final. Pronase-resistant Tau bands were detected by western blot as described below with rabbit anti-Tau ab64193 (Abcam).
Preparation of Brain Homogenates
Frozen human brain samples were homogenized in complete OptiMEM culture medium (for cell culture), QIAzol lysis reagent (for RNA isolation) or lysis buffer (PBS with 1% Triton-X and protease, phosphotase inhibitors for protein analysis) using the Precellys® 24 (Bertin Instruments) with 1.4 mm ceramic beads at 4° C. for 4 cycles 5500 rpm 20 sec. For 10 brain homogenates for aggregate induction in cell cultures, crude homogenates were cleared of cell debris at 872×g for 5 min at 4° C. Supernatants were sonicated at 50% power for 6 min and stored at −80° C. RNA was isolated using the Qiagen RNeasy Lipid Tissue Mini Kit combined with genomic DNA digestion as described in the manufacturer's instruction. For protein analysis, brain homogenates were cleared of cell debris at 15000×g for 15 min, 4° C.
Tau Aggregate Induction Using Patient-Derived Brain Homogenate
To test the Tau aggregate induction by brain homogenates from different tauopathy patients, HEK Tau-GFPsol cells were plated on a CellCarrier-96 black microplate (PerkinElmer) at 2000 cells/well in 50 μl complete medium. The next day, 6 μl 10% brain homogenate and 0.2 μl lipofectamine2000 were diluted into OptiMEM without antibiotics (final 60 μl) for 20 min at RT. Brain homogenate-liposome mixtures were added to recipient cells for 5 h and 50 μl complete medium were added to cells afterwards. The induced cells were fixed 3 days later in 4% paraformaldehyde. Nuclei were counterstained with Hoechst. Cells were imaged using the automated confocal microscope CellVoyager CV6000 (Yokogawa Inc.) and a 40× objective.
qRT-PCR
Total RNA from cell pellets or brain samples was isolated using the RNeasy Mini Kit or RNeasy Lipid Tissue Mini Kit (Qiagen). RNA concentration and quality were determined using the Agilent 2100 Bioanalyzer System. For a 20 μl reaction, 1 μg RNAs were reversely transcribed to cDNA using the iScript™ cDNA Synthesis Kit (Bio-Rad). For a 20 μl qRT-PCR reaction, 2 μl of synthesized cDNA was used as template. For qRT-PCR of murine env AA037244.2 and gag AID54952, custom designed TaqMan probes were used (Thermo Fisher Scientific). Pre-designed TaqMan probes by the company for murine pan-env, xpr1, mcat-1 and gapdh as housekeeping control and TaqMan™ Gene Expression Master Mix (Thermo Fisher Scientific) were used. qRT-PCR using TaqMan probes was performed as described in the manufacturer's instruction. For qRT-PCR analyses of HERV family members, primers were designed using the corresponding cDNA sequences (cf. SEQ ID NOs. 73-92). PowerUP SYBR™ Green Master Mix (Thermo Fisher Scientific) was mixed with different cDNAs and corresponding primers as indicated in the instruction. The fast cycling mode was used for all primers.
Western Blotting
For Western blot analysis, protein concentrations were measured using the Quick Start™ Bradford Protein assay (Bio-Rad). Proteins were separated on NuPAGE®Novex® 4-12 Bis-Tris Protein Gels (Life Technologies) followed by transfer onto a PVDF membrane (GE Healthcare). Western blot analysis was performed using rat hybridoma anti-MuERV Env mAb83A25; anti-xenotropic MuLV virus antibody ABIN457298 for detecting both Env and Gag (antibodies-online); mouse anti-MuERV Gag ab100970 (Abcam); mouse anti-Alix (1:1000; BD Bioscience); rat anti-HA 3F10 (1:1000; Roche); mouse anti-GAPDH 6C5 (1:5000; Abcam); mouse anti-Hsc/Hsp70 N27F3-4 (1:1000; ENZO); mouse anti-VSV-G A5977 (Sigma); rabbit anti-Tau ab64193 (Abcam); mouse anti-HERV K Env HERM-1811-5 (Amsbio); mouse anti-HERV K Gag HERM-1841-5 (Amsbio). The membrane was incubated with Pierce™ ECL Western Blotting Substrate (Thermo Fisher Scientific) according to the manufacturer's recommendations.
Image Analysis
The image analysis was performed using the CellVoyager Analysis support software. An image analysis routine was developed for single cell segmentation and aggregate identification (Yokogawa Inc.). The total number of cells was determined based on the Hoechst signal, and recipient cells were detected by their GFP/FusionRed signal. Green aggregates were identified via morphology and intensity characteristics. The percentage of recipient cells with aggregated NM-GFP or Tau-FusionRed/Tau-GFP was calculated as the number of aggregate-positive cells to total recipient cells set to 100%. False positive recipient cells were detected due to the heterogeneity of Tau-GFP/-FusionRed expression of individual cells. The mean percentage of false positives determined in control recipient cells was subtracted from all samples. Of note, negative values were sometimes obtained when no induction was observed. For data presentation, the minimum of the Y Axis was set to 0.
Immunofluorescence Staining and Confocal Microscopy Analysis of Prion-Infected Cells
Cells were fixed in 4% paraformaldehyde for 20 min at 37° C. and permeabilized in 0.1 Triton X-100 for 10 min at RT. For PrPSc staining, proteins were denatured in 6 M guanidine hydrochloride for 10 min at RT to reduce PrPC staining and increase detection of PrPSc (Taraboulos et al., J Cell Biol (1990), 110:2117-2132). Cells were rinsed with PBS, blocked in 0.2% gelatine for 1 h and incubated for 2 h with anti-PrP 4H11 antibody hybridoma solution diluted 1:10 in blocking solution (Ertmer et al., JBC (2004), 279:41918-41927). After three washing steps in PBS, cells were incubated for 1 h with Alexa Fluor 488-conjugated anti-Mouse IgG secondary antibody diluted 1:800 in blocking solution (Thermo Fisher Scientific) and nuclei were counterstained for 15 min with 4 μg/ml Hoechst 33342 (Molecular Probes). 96 well plate was scanned with CellVoyager CV6000 (Yokogawa Inc.). Confocal laser scanning microscopy was performed on a Zeiss LSM 800 laser-scanning microscope with Airyscan (Carl Zeiss).
Statistical Analysis
All analyses were performed using the Prism 6.0 (GraphPad Software v.7.0c). Statistical inter-group comparisons were performed using the one-way ANOVA with a Bonferroni post-test or Student's t test. p values smaller than 0.05 were considered significant. All experiments were performed in triplicates or sextuplicates and repeated at least three times. Error bars represent the standard deviation (SD).
Downregulation of HERV-W Env Syncytin-1 Reduces Intercellular Aggregate Spreading
Human endogenous retroviruses (HERV) are usually silenced but become de-repressed during aging and in several human malignancies, including cancer, inflammatory diseases and neurodegeneration. To assess if HERV expression could affect intercellular spreading of protein aggregation, the inventors first made use of two cancer cell lines known to overexpress HERV. Human breast cell line MCF-7 was engineered to stably express Tau-GFP and exposed to AD brain homogenate to isolate clones propagating Tau-GFPAD. Cells were incubated with or without 5-Aza-2-deoxycytidine (Aza) for HERV de-repression and subsequently cocultured with recipient HEK Tau-FRsol cells (
HIV Protease Inhibitor Known to Inhibit HERV-K Maturation Reduces Intercellular Aggregate Spreading
The inventors further genetically engineered human A375 melanoma cells to express Tau-GFP and exposed them to AD brain homogenate to isolate a clone propagating Tau-GFPAD. Cells were treated with 10 μM Lopinavir, an HIV protease inhibitor shown to inhibit HERV-K protease required for HERV protein maturation. Upon coculture, the inventors observed a significant reduction of recipient cells with aggregates (
HERV Env/Receptor Interactions Contribute to the Spreading of Proteopathic Seeds
To assess if HERV Env can mediate contact between donor and recipient membranes and thereby contribute to proteopathic seed spreading, the inventors overexpressed HERV-W Syncytin-1 in two HEK cell models propagating either aggregated NM-HA (HEK NM-HAagg) or aggregated Tau-GFP (HEK Tau-GFPAD) (
Materials and Methods
Molecular Cloning
To generate the expression vector coding for SLC1A4 or SLC1A5, the corresponding cDNA for SLC1A4 (cataloge nr. #EX-A3396-Lv213; GeneCopoeia) or SLC1A5 (cataloge nr. #EX-Z2810-Lv213; GeneCopoeia) was cloned into cataloge nr. #PB510B-1 vector (SBI) under the CMV promoter. To generate the phCMV-Syncytin-1-100UTR plasmid, Syncytin-1 cDNA tagged with a Myc epitope sequence (cataloge nr. #EX-T0264-Lv213; GeneCopoeia) was cloned into phCMV-EcoENV (Addgene #15802) using EcoRI and XhoI to replace EcoENV. The 100 bp sequence from 3′-UTR of Syncytin-1 shown to enhance gene expression was amplified using primers (SEQ ID NO: 95 forward: 5′-CCGCTCGAGAGCGGTCGTCGGCCAAC-3′/ SEQ ID NO: 96 reverse: 5′-GAAGATCTCCTTCCCAGCTAGGCTTAGGG-3′) and genomic DNA from MCF-7 cells as template. The sequence was cloned into phCMV-Syncytin-1 using XhoI and BglII restriction sites. The three point mutations R314A, N315A and K316A, shown to destroy fusogenic activity, were introduced using the Q5 site-directed mutagenesis Kit (NEB).
Cell Lines
MCF-7 (ATCC HTB-22) cells were cultured in MEM (Gibco) with 10% FCS, P/S, 10 nM estrogen and 0.01 mg/ml human recombinant insulin. A375 (ATCC CRL-1619) cells were cultured in DMEM (Gibco) with 10% FCS, P/S.
Brain Homogenate Preparation and Clarification
Frozen human brain samples were homogenized in lysis buffer (for protein analysis) via Precellys® 24 (Bertin Instruments) with 1.4 mm ceramic beads at 4° C. for 4 cycles 5500 rpm 20 s. To prepare 10% (w/v) clear brain homogenate for aggregate induction, crude homogenates were centrifuged at 872×g for 5 min at 4° C., and then the supernatants were sonicated with 50% power for 6 min. These homogenates were frozen at −80° C. until use. For protein analysis, cleared supernatants were prepared by centrifugation of the crude homogenates at 15,000×g for 15 min.
Tau Aggregate Induction by Brain Homogenate and Liposomes
To induce Tau aggregation in MCF7/A375 Tau-GFPsol cells with brain homogenates from AD patients, cells were plated on 6-well plates at 1×106 cells/well in 2 ml complete medium one day before. Next day, 200 μl 10% brain homogenates and 4 μl lipofectamine2000 were incubated for 20 min and added to recipient cells to have final 1% brain homogenates on cells. After 3 days, cells were split and further expanded for limited dilution clone selection as previously described.
Production and Transduction with Lentiviral Particles
HEK293T cells were cotransfected with plasmids pRSV-Rev, pMD2.VSV-G, pMDI.g/pRRE (all plasmids were published in Dull T, Zufferey R, Kelly M, Mandel R J, Nguyen M, Trono D, Naldini L A third-generation lentivirus vector with a conditional packaging system. J Virol. 1998 November 72(11):8463-71), and pRRI.sin.PPT.hCMV.Wpre (plasmid published in Follenzi, A. and L. Naldini (2002) HIV-based vectors. Preparation and use. Methods in molecular medicine 69: 259-274) containing Tau-GFP for fluorescence tagged Tau expression or pSIH-shRNA-Syn GGCCCTCCCTTATCATATT (SEQ ID NO: 97) with the CTTCCTGTCAGA (SEQ ID NO: 98) loop sequence to silence Syncytin-1 expression, pSIH-puro-control (Addgene #26597) was used to produce control shRNA lentivirus. Supernatants were harvested and concentrated with PEG according to published protocols. MCF-7 and A375 cell lines were transduced with Tau-GFP lentivirus to produce MCF-7 and A375 Tau-GFPsol cells. MCF-7 Tau-GFPAD clones were transduced with shRNA-Syn or control lentiviruses, and selected with 2 μg/ml puromycin for 2 weeks.
Drug Treatment
To inhibit methyltransferase, MCF-7 Tau-GFPAD cells were treated with 2 μM Aza or DMSO for 4 d. Thereafter, the pretreated donor cells were cocultured with recipient HEK Tau-FRsol in the absence of the drugs for 3 d. The treatment of A375 melanoma cells with Lopinavir (10 μM; Selleckchem) and DMSO was performed for 72 h in EV-depleted medium in T175 flasks. Afterwards, the total numbers of viable cells and the viability upon drug treatments were determined using the Vi-VELLTMXR Cell Viability Analyzer (Beckman Coulter). EV were isolated from the conditioned medium via ultracentrifugation and processed for the assays as described above.
Transfection with siRNAs or Plasmids
To transiently knock-down specific genes, custom-designed Silencer select siRNAs from Thermo Fisher were used. Pre-designed siRNAs were used to knock-down genes. For transfection, cells were pre-seeded on 6 well plate one d before at 2×105 cells/well. The next day, either a final 60 nM (1:1 SLC1A4 (#s12914)/SLC1A5 (#s12918)) siRNAs (Lifetechnologies) was mixed with 1:20 diluted Lipofectamine RNAiMAX for siRNAs or 2 μl plasmid was mixed with 4 μl TransIT-2020 (Mirusbio) diluted in Opti-MEM for 30 min before addition to cells. After 1-3 d, transfected cells were harvested for aggregate induction assays, qRT-PCR or Western blot analysis.
qRT-PCR
Total RNAs from cell pellets were isolated using the RNeasy Mini Kit or RNeasy Lipid Tissue Mini Kit (Qiagen). RNA concentration and quality were determined with Agilent 2100 Bioanalyzer System. RNAs were reversely transcribed to cDNA using the iScript™ cDNA Synthesis Kit (Bio-Rad). For mRNA analysis, pre-designed TaqMan assays for human SLC1A4 (Hs00983079_m1), SLC1A5 (Hs01056542_m1), GAPDH (Hs02786624_g1) or ACTB (Hs01060665_g1) as housekeeping control were utilized with TaqMan™ Gene Expression Master Mix (Thermo Fisher).
Western Blotting
For Western blot analysis, protein concentrations were measured by Quick Start™ Bradford Protein assay (Bio-Rad) and proteins were separated on NuPAGE®Novex® 4-12% Bis-Tris Protein Gels (Life Technologies) followed by transfer onto a PVDF membrane (GE Healthcare) in a wet blotting chamber. Western blot analysis was performed using rabbit anti-Flotillin-1 ab133497 (Abcam); rat anti-HA 3F10 (1:1000; Roche); mouse anti-GAPDH 6C5 (1:5000; Abcam); mouse anti-Hsp70/72 N27F3-4 (1:1000; ENZO); rabbit anti-Tau ab64193 (Abcam); rat anti-c-myc-HRP 130-092-113 (Miltenyi Biotec). The membrane was incubated with Pierce™ ECL Western Blotting Substrate (Thermo Fisher Scientific) according to the manufacturer's recommendations.
Image Analysis
The image analysis was performed using the CellVoyager Analysis support software. An image analysis routine was developed for single cell segmentation and aggregate identification (Yokogawa Inc.) The total number of cells was determined based on the Hoechst signal, and recipient cells were detected by their GFP/-FR signal. Green aggregates were identified via morphology and intensity characteristics. The percentage of recipient cells with aggregated NM-GFP or Tau-FR/Tau-GFP was calculated as the number of aggregate-positive cells per total recipient cells set to 100%. False positive induced recipient cells were detected due to the heterogeneity in GFP/FR expression of individual cells. The mean percentage of false positives determined in control recipient cells was subtracted from all samples. Of note, negative values were sometimes obtained when no induction was observed. For data presentation, the minimum range of Y Axis was set to 0.
Statistical Analysis
All analyses were performed using the Prism 6.0 (GraphPad Software v.7.0c). Statistical inter-group comparisons were performed using the one-way ANOVA with a Bonferroni post-test or unpaired Student's t test. p values smaller than 0.03 (*), 0.002 (**) and 0.0002 (***) were considered significant. All experiments were performed in triplicates or sextuplicates and repeated at least two times. Error bars represent the standard deviation (SD).
| Number | Date | Country | Kind |
|---|---|---|---|
| 19195304.1 | Sep 2019 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2020/074809 | 9/4/2020 | WO |
