WO2004087748A1 - Protein with fusogenic activity, nucleic acid sequences encoding said protein and pharmaceutical compositions comprising the same - Google Patents

Protein with fusogenic activity, nucleic acid sequences encoding said protein and pharmaceutical compositions comprising the same Download PDF

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Publication number
WO2004087748A1
WO2004087748A1 PCT/EP2004/003552 EP2004003552W WO2004087748A1 WO 2004087748 A1 WO2004087748 A1 WO 2004087748A1 EP 2004003552 W EP2004003552 W EP 2004003552W WO 2004087748 A1 WO2004087748 A1 WO 2004087748A1
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Prior art keywords
protein
syncitin
seq
sequence
polypeptide
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PCT/EP2004/003552
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French (fr)
Inventor
Thierry Heidmann
Marie Dewannieux
Sandra Blaise
Laurence Benit
Nathalie De Parseval
Vladimir Lazar
Marianne Mangeney
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Centre National De La Recherche Scientifique
Inserm (Institut National De La Sante Et De La Recherche Medicale)
Institut Gustave Roussy
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Priority to EP04725350A priority Critical patent/EP1651667B1/en
Priority to AT04725350T priority patent/ATE551353T1/en
Publication of WO2004087748A1 publication Critical patent/WO2004087748A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/10022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Definitions

  • the present invention relates to a new protein with fusogenic properties, nucleic acid sequences encoding for said protein, and pharmaceutical compositions comprising them.
  • the human genome contains a large fraction (ca. 8%) of elements of retroviral origin, with thousands of sequences close to the integrated proviral form of infectious retroviruses, with two long terminal repeats (LTR) bordering internal regions homologous to the gag, pol and env genes (Lower, R., Lower, J. & Kurth, R. (1996) Proc. Natl. Acad. Sci. USA 93, 5177-5184; Boeke, J. D. & Stoye, J. P. (1997) in Retroviruses, eds. Coffin, J. M., Hughes, S. H. & Varmus, H. E. (Cold Spring Harbor Laboratory Press, New York), pp. 343-436; Lander, E.
  • HERV Human Endogenous RetroViruses
  • HERV and present-day retroviruses can be infened from phylogenetic analyses on the Reverse Transcriptase domain of the pol gene or the TransMembrane moiety (TM) of the env gene, which disclose interspersion of both classes of elements and suggest a common history and shared ancestors (Tristem, M. (2000) J. Virol. 1A, 3715-3730; Benit, L., Dessen, P. & Heidmann, T. (2001) J. Virol. 15. 11709-11719). Similarities are also observed at the functional level.
  • Syncitin 1 the envelope protein of a HERV-W family member, Syncitin (hereafter named Syncitin 1), has retained the ability to interact with the receptor of the D-type retroviruses (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329, Lavillette, D., Marin, M., Ruggieri, A., Mallet, F., Cosset, F. L. & Kabat, D. (2002) J.
  • Virol 76, 6442-6452 can confer infectivity on pseudotyped retroviral particles (Lavillette, D., Marin, M., Ruggieri, A., Mallet, F., Cosset, F. L. & Kabat, D. (2002) J. Virol. 16, 6442-6452, An, D. S., Xie, Y.-M. & Chen, I. S. Y. (2001) J. Virol. 75, 3488-3489). % As a consequence of the close relationship between HERVs and infectious retroviruses,
  • WO 01 16171 discloses that the HERV-
  • HERV-W envelope gene product (Syncitin 1) is a highly fusogenic glycoprotein which is specifically expressed in the placenta and can mediate cell-cell fusion ex vivo.
  • This HERV-W envelope could be used in cancer treatment by promoting the formation a syncitia by cancerous cells, thus leading to their death. Disorders in the expression of the HERV-W envelope could impair placental morphogenesis.
  • the HERV envelope can not mediate the fusion of all cell types, therefore it can
  • HERV-W envelope do not account for all placental morphogenesis disorders and other HERV envelopes might be implicated.
  • an object of the present invention is to provide a new fusogenic HERV envelope, with a cell-specificity different from that of HERV-W envelope and which accounts for all the placental morphogenesis disorders arising from disorders in the expression of a HERV envelope other than the HERV-W envelope.
  • Another object of the present invention is to provide a new HERV envelope which presents an immunosuppressive activity in addition to a fusogenic activity, said new HERV j envelope representing the sole example of a HERV envelope with both fusogenic activity and immunosuppressive activity.
  • the present invention relates to a protein or a polypeptide, characterized in that it corresponds to an amino acid sequence, comprising or being constituted by:
  • a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2, and/or an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2.
  • the present invention relates in particular to a protein or a polypeptide as defined above, characterized in that it corresponds to an amino acid sequence, comprising or being constituted by:
  • a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2, and/or an antigenic activity similar to that of Syncitin 2.
  • the present invention also relates to a protein or a polypeptide as defined above characterized in that it corresponds to an - amino acid sequence, comprising or being constituted by:
  • a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents an immunosuppressive activity similar to that of Syncitin 2, and/or an antigenic activity similar to that of Syncitin 2.
  • the present invention more particularly relates to a protein or a polypeptide as defined above, characterized in that it conesponds to an amino acid sequence, comprising or being constituted by:
  • the expression "fusogenic activity” relates to the ability of said protein or polypeptide to promote the fusion, i.e. the coalescence, of biological membranes, in particular the fusion of cellular membranes.
  • a syncitium is in particular characterized by the presence of several nuclei enclosed by a single cellular membrane.
  • Such a fusogenic activity can be detected according to the following procedure:
  • an expression vector carrying the coding sequence of said polypeptide or protein under the control of a promoter is transformed into host cells, to obtain host cells producing, said polypeptide or protein, the formation of a syncitium from said host cells being indicative of a fusogenic activity of said polypeptide or protein;
  • Syncitin 2 is a HERV envelope presenting a fusogenic activity.
  • Syncitin 2 is also refered to as HERV-FRD in the examples.
  • the expression "presents a fusogenic activity similar to that of Syncitin 2" means that the protein or the polypeptide to which it relates has the same cell-specificity than Syncitin 2 and/or a fusogenic activity which represents at least 50%> ofthe fusogenic activity of Syncitin 2 in the same conditions.
  • Syncitin 2 and the HERV-W envelope are the only two HERV envelopes with fusogenic activity normally expressed in the human body.
  • Syncitin 2 presents a fusogenic cell-specificity different from that of the HERV-W envelope. That is, the panel of cells which can be brought to form syncitia by Syncitin 2 is different from the panel which can be brought to form syncitia by Syncitin 1.
  • immunosuppressive activity relates to the ability of said protein or polypeptide to enable the cells canying it to escape immune control.
  • the expression "presents an immunosuppressive activity similar to that of Syncitin 2" means that the protein or the polypeptide to which it relates has an immunosuppressive activity which represents at least 50% of the immunosuppressive activity of Syncitin 2 in the same conditions.
  • antigenic activity relates to the ability of said protein or polypeptide to activate the immune system and to elicit an immune response directed against said protein or polypeptide.
  • the expression "presents an antigenic activity similar to that of Syncitin 2" means that the protein or the polypeptide to which it relates is liable to elicit an immune response directed against Syncitin 2.
  • Syncitin 2 is essentially expressed in the placenta, and impaired expression of Syncitin 2 may result in placental morphogenesis disorders, in particular syncitiotrophoblast disorders. Such disorders may arise either from an expression of Syncitin 2 higher or lower than normal. Higher than normal expression of Syncitin 2 leads to the formation and/or the development of unwanted syncitia, such as trophoblastic invasion which occurs in choriocarcmoma. Conversely, lower than normal expression of Syncitin 2 leads to the absence or to the underdevelopment of normally occurring syncitia, such as trophoblast underdevelopment, which may be a cause of unfertility. According to a particular embodiment, the invention relates to fragments ofthe Syncitin 2 protein, said fragments being constituted by a sequence deriving from SEQ ID NO: 2 by deletion of at least one amino acid and containing at least 20 contiguous amino acids.
  • a protein or a polypeptide according to the invention is characterized in that it corresponds to an amino acid sequence comprising or being constituted by a sequence derived from SEQ ID NO: 2 by deletion of at least the 17 contiguous amino acids from position 414 to position 430 of SEQ ID NO: 2.
  • SEQ ID NO: 65 The 17 contiguous amino acids from position 414 to position 430 of SEQ ID NO: 2 correspond to SEQ ID NO: 65.
  • This sequence has a major role in the immunosuppressive activity of Syncitin 2.
  • Proteins or polypeptides devoid of SEQ ID NO: 65 according to the invention, will not generally have any immunosuppressive activity.
  • Such proteins or polypeptides devoid of SEQ ID NO: 65 encompass in particular fragments comprising at least 20 amino acids selected from contiguous amino acids from position 1 to position 413 or from position 431 to 538 of SEQ ID NO: 2.
  • a protein or a polypeptide according to the invention is characterized in that it conesponds to SEQ ID NO: 64.
  • SEQ ID NO: 64 conesponds to SEQ ID NO: 2 from which SEQ ID NO: 65 has been deleted.
  • a protein or a polypeptide conesponding to such a sequence presents a fusogenic activity and an antigenic activity similar to that of Syncitin 2 but is devoid of any immunosuppressive activity.
  • Such a protein or polypeptide presents a better antigenic activity than Syncitin 2 as it is devoid of immunosuppressive activity, which makes it a good candidate for the manufacture of a vaccine composition.
  • the present invention also relates to a nucleic acid, characterized in that it conesponds to a sequence encoding a protein or a polypeptide as defined above, and or to its complementary sequence.
  • the present invention also relates to a nucleic acid, characterized in that it conesponds to a nucleic acid sequence comprising or being constituted by:
  • a homologous sequence presenting at least 66% nucleotide identity with SEQ ID NO: 1, provided that said homologous sequence encodes a protein or a polypeptide presenting a fusogenic activity similar to that of Syncitin 2, or • fragments of said sequences, such as SEQ ID NO: 3 or 4; and/or to its complementary sequence.
  • the present invention also relates to a nucleic acid, characterized in that it hybridizes with a nucleic acid as defined above under stringent conditions.
  • the present invention also relates to a prokaryotic or eukaryotic expression vector, characterized in that it comprises a nucleic acid as defined above and the elements required for its expression in a host cell.
  • An eukaryotic expression vector according to the invention is particularly useful for gene therapy, in particular to compensate for disorders resulting in an absence of expression or a lower than normal expression of fusogenic proteins, such as Syncitin 2.
  • Such vectors can also be used to transfect tumoral cells to induce the formation of a syncitium resulting from the fusion of transfected tumoral cells with transfected or untransfected tumoral cells.
  • Such vectors may be advantageously derived from vectors classically used in gene therapy protocols, such as retroviral or lentiviral vectors.
  • the present invention also relates to a prokaryotic or eukaryotic cell, characterized in that it comprises vector as defined above.
  • such cells express fusogenic polypeptide or protein and have the capacity of forming syncitia.
  • such cells can be administered to an individual suffering from cancer at a tumor site, to promote the formation of a syncitium resulting from the fusion of cells according to the invention with tumoral cells.
  • such cells can also be administered to an individual suffering from a placental morphogenesis disorders caused by the absence of formation or the underdevelopment of functional syncitia, such as the syncitiontrophoblast, to promote the formation and/or the development of syncitia, such as the syncitiotrophoplast.
  • patients suffering from cancers can be treated as follows:
  • healthy cells in particular healthy cells originating from a tissue similar to the tissue which carries tumoral cells, are taken from the patient,
  • - said healthy cells are transfected with a vector according to the invention, - transfected cells are administrated to the patient, in particular at a site close to the targeted tumor,
  • the tumoral cells are induced to form syncitia by the transfected cells, and die.
  • the present invention also relates to an antibody, characterized in that it is directed against a protein or a polypeptide as defined above.
  • antibody as intended herein relates to monoclonal or polyclonal antibodies, as well as to antibody fragments.
  • Antibodies according to the invention can be obtained by methods well known to the man skilled in the art. For instance monoclonal antibodies can be produced according to Kohler and Milstein (1975) Nature 256:495-497 or Galfre et al (1977) Nature 266:522-550 and polyclonal antibodies can be produced according to Roda and Bolelli (1980) Journal of Steroid Biochemistry, 13 :449-454.
  • Antibody fragments according to the invention relate more particularly to Fab, F(ab') , or scFv fragments.
  • Fab and F(ab') 2 fragments are particularly well known to the man skilled in the art, and can be obtained respectively by papain and pepsin proteolytic cleavage of antibodies.
  • scFv fragments are in particular described in Blazar et al. (1997) Journal of Immunology 159:5821-5833 or Bird et al. (1988) Science 242:423-426, advantageously scFv fragments are recombinant.
  • the present invention also relates to a purified natural human protein, characterized in that: it is recognized by an antibody as defined above and, it presents a fusogenic activity.
  • the present invention also relates to. a pharmaceutical or a vaccinal composition, comprising as active substance at least one substance selected from the group comprising: a protein or a polypeptide as defined above, a nucleic acid as defined above, a vector as defined above, or a cell as defined above; in association with a pharmaceutically acceptable vehicle.
  • a protein or a polypeptide according to the invention can be used for the treatment of abnormal syncitium formation and/or development, i.e. syncitium formation and/or development which does not occur under normal conditions, mediated by an above normal expression of Syncitin 2, by competing for Syncitin 2 receptor sites on cells.
  • a protein or a polypeptide according to the invention could also be used to target compounds, in particular therapeutic compounds to cells which cany receptors for Syncitin 2.
  • a protein or a polypeptide according to the invention can be used for the immunosuppressive treatment of patients, such as patients afflicted with allergy, autoimmune disease or graft rejection.
  • a protein according to the invention has anti-cancerous prophylactic properties and can be used for the manufacture of a vaccinal composition.
  • HERV-FRD is liable to be involved in cancer development due to its immunosuppressive activity which can induce immune tumor escape and due to its expression in tumors
  • administration of a protein according to the invention to a patient could help preventing the development of tumors expressing this protein thanks to immunological reactions elicited in response to said administration.
  • proteins or polypeptides devoid of immunosuppressive activity according to the invention are particularly useful since they have an antigenic activity similar to that of Syncitin 2 without the drawback of its immunosuppressive activity, they can therefore easily elicit an immune response against tumors expressing HERV-FRD.
  • Vaccinal compositions comprising such proteins or polypeptides devoid of immunosuppressive activity are therefore particularly useful in anti- tumor prevention and/or therapy.
  • a nucleic acid according to the invention and a vector according to the invention can be used in gene therapy to compensate for a lower than normal expression of a fusogenic protein, in particular of Syncitin 2, notably in the placenta.
  • a fusogenic protein in particular of Syncitin 2
  • such nucleic acids and vectors can be used to transfect tumor cells so as to induce tumor cell fusion and j consequently tumor destruction.
  • a cell according to the invention can be used to cure tissues which should undergo cell fusion but for which this function is impaired, or to promote the formation of syncitia in tumors.
  • the present invention relates to a vaccinal composition as defined above, comprising as active substance a protein or a polypeptide as defined above, in association with a pharmaceutically acceptable vehicle.
  • the present invention also relates to a pharmaceutical composition, comprising as active substance at least one substance selected from the group comprising: an antibody as defined above, an antisense sequence hybridizing to SEQ ID NO: 1, a RNAi comprising a sequence hybridizing to SEQ ID NO: 1, or an aptamer directed against a protein conesponding to SEQ ID NO: 2, in association with a pharmaceutically acceptable vehicle.
  • a pharmaceutical composition comprising as active substance at least one substance selected from the group comprising: an antibody as defined above, an antisense sequence hybridizing to SEQ ID NO: 1, a RNAi comprising a sequence hybridizing to SEQ ID NO: 1, or an aptamer directed against a protein conesponding to SEQ ID NO: 2, in association with a pharmaceutically acceptable vehicle.
  • An antibody according to the invention can be used to prevent the binding of Syncitin 2 to its receptor on cells, thus preventing syncitium formation and/or development.
  • an antisens sequence according to the invention is meant to impair the translation a Syncitin 2 encoding mRNA thus impairing its expression and as a consequence preventing syncitium formation and/or development.
  • RNAi interference RNA
  • An aptamer according to the invention is a nucleic acid, in particular a ribonucleic acid, the folding of which allows its binding to the Syncitin 2 protein so as to prevent the Syncitin 2 protein from promoting the formation and/or the develonce of syncitia.
  • the present invention also relates to the use of at least one substance selected from the group comprising: a protein or a polypeptide as defined above, a nucleic acid as defined above, a vector as defined above, or a cell as defined above; for the manufacture of a drug useful for the prevention and/or the treatment: - of cancers or,
  • a cellular fusogenicity disorder or a syncitium morphogenesis disorder such as a placental morphogenesis disorder or,
  • an immune system disorder in particular an immune system disorder requiring an immunosuppressive treatment, such as allergy, autoimmune disease or graft rejection.
  • Drugs according to the invention are useful for treating cancers by promoting the formation of syncitia by cancerous cells, which leads to cellular death.
  • the killing of tumor cells by syncitia formation promoted by fusogenic proteins is notably described in Bateman et al, (2002) Cancer Research 15: 6566-6578.
  • Drugs according to the invention can also be used to compensate for the absence of a functional Syncitin 2 in tissues in which it is normally present, such absence leading to a fusogenicity disorder or a syncitium morphogenesis disorder, in which the physiologic formation of a syncitium is impaired or prevented. In the case of placental morphogenesis, an impaired or deficient syncitium formation results in infertility.
  • drugs according to the invention could be used as anti-tumor vaccines, whereby the administration of said drugs to an individual could lead to an immunological reaction directed against said drugs, thus controlling and/or destroying tumor which express said the Syncitin 2 protein.
  • the present invention also relates to a method for detecting the Syncitin 2 protein or for measuring the concentration ofthe Syncitin 2 protein in a biological sample, characterized in that it comprises a step of contacting said biological sample with an antibody as defined above.
  • Such methods are useful for the diagnosis of pathologies in which the expression of Syncitin 2 is modified. Such methods are also useful for assessing transfection efficiency in gene therapy assays in which nucleic acids according to the invention are introduced into cells.
  • the biological sample is a placental sample.
  • the present invention also relates to a method for detecting the Syncitin 2 mRNA or for measuring the concentration of the expression of the Syncitin 2 mRNA in a biological sample, characterized in that it comprises a step of contacting said biological sample with at least one nucleic acid as defined above.
  • Syncitin 2 mRNA expression detection or measure methods which can be used with nucleic acids according to the invention notably comprise Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), Nuceic Acid Based Sequence Amplification
  • NASBA in situ hybridization and Northern blot.
  • NASBA in situ hybridization and Northern blot.
  • Such methods are useful for the diagnosis of pathologies in which the expression of Syncitin 2 is modified. Such methods are also useful for assessing transfection efficiency in gene therapy assays in which nucleic acids according to the invention are introduced into cells.
  • the biological sample is a placental sample.
  • nucleic acids conesponding to SEQ ID NO: 3 and 4 can be used as primers for the detection or for the assessment of the concentration of the Syncitin 2 mRNA by RT-PCR, in particular by real-time quantitative RT-PCR using the following procedure:
  • RNA is first extracted from biological samples in which the Syncitin 2 mRNA concentration is to be assessed, according to methods well known to the man skilled in the art. RNA concentration is then quantified spectrophotometrically. Five micrograms of each RNA sample are submitted to DNAse treatment to eliminate DNA contaminants. One microgram of RNA from each sample is reverse transcribed using a virus Reverse Transcriptase, notably in presence of a ribonuclease inhibitor, deoxynucleotides, MgCl 2 , KCl, and random hexamers. The complementary DNAs thus obtained are then diluted in nuclease-free water.
  • Real-Time quantitative PCR is achieved using a complementary DNA equivalent of 20 ng of total RNA notably in presence of a thermostable polymerase, the primers according to the invention, deoxynucleotides and MgCl 2 .
  • the amplification is performed using a 2 min step at 50°C, a 10 min denaturation step at 95°C, followed by 40 cycles of 15 s denaturation at 95°C, 1 min primer annealing and polymerization step at 60°C.
  • amplification of 18S total ribosomal RNA was performed as an endogenous control.
  • the relative expression in each sample is calculated with respect to a standard calibration curve (e.g. dilution series of genomic DNA).
  • a method for the in vitro diagnosis of pathologies linked to the level of expression of Syncitin 2 in a tissue comprising the following steps:
  • the present invention also relates to a method for the screening of drugs liable to modify the fusogenic activity of a polypeptide or a protein as defined above, characterized in that a drug to screen is contacted with cells expressing said polypeptide or protein, and the presence or the absence of formation of a syncitium by said cells is observed.
  • Drugs which lead to the absence of formation of a syncitium can be used to block abnormal syncitium formation and/or development, such as in trophoblast invasion which occurs in choriocarcinoma. Drugs which lead to the formation of a syncitium can be used to promote the formation and/or the development of syncitium, for instance in cases where there is an absence of formation and/or an underdevelopment of functional syncitia.
  • FIG. 1 Structural organization and characteristic features of the 16 identified HERV envelopes. Hydrophobicity profiles and characteristic domains of the 16 HERV envelope proteins (the 6 HERV-K HML2 envelopes being almost identical are represented by a unique protein) and ofthe Moloney murine leukemia virus envelope. The black rectangles delineate the open reading frames, and the gray rectangles at the end of R and Fc2 envelope represent the short reading frames present downstream of the stop codon.
  • the « CWLC » motifs (consensus C-X-X-C) and the proteolytic cleavage sites (consensus R/K-X-R/K-R) are represented with pale and dark gray vertical bars respectively, and their sequence are indicated in the right part of the figure;
  • the putative immunosuppressive domain is represented with a gray box.
  • FIG. 3 A and Figure 3B Envelope-mediated cell-cell fusion.
  • Figure 3 A Construction of envelope-expressing vectors and rationale of the fusion assay. Each ofthe 16 envelope genes was PCR-amplified from BAC DNA and cloned into the phCMV expression vector. The env genes inserted in-between the ⁇ -globin intron and pA sequences are schematized with the putative cleavage site between the surface (SU) and the transmembrane (TM) envelope subdomains. Cells were transfected with the env-expressing vectors and stained with May- Gr ⁇ nwald and Giemsa solutions 12 h (for the G355-5 cells) or 36 h (for the other cell types) after transfection.
  • FIG. 3B Syncytia formation by HERV envelope glycoproteins in various cell types. Cells were transfected with vectors expressing the HERV-FRD envelope (ez ⁇ vFRD), the HERV-W envelope (envW), or an 'empty' vector (none).
  • Figure 4 Primary sequence, hydrophobicity profile, and predicted features of the HERV- FRD envelope.
  • the SU and TM moities of the envelope are delineated, with the canonical RVRR cleavage site between the two subunits underlined (consensus: R/K-X-R/K-R); in the TM subunit, the hydrophobic fusion peptide and transmembrane domains are shaded in light gray, and the putative immunosuppressive domain (ISU) in dark grey; in the SU subunit, the canonical CWLC domain involved in SU-TM interaction, is underlined.
  • ISU immunosuppressive domain
  • FIG. 1 Northern blot analysis of HERV-FRD env expression in human tissues.
  • Poly(A) + RNAs (Ambion, Human Northern Blot 2) were probed with an antisense-strand HERV-FRD env riboprobe. Exposure time 12 h.
  • Figure 6A and Figure 6B Conservation of the HERV-FRD env locus and open reading frame upon primate evolution.
  • Figure 6A Slot-blot of genomic DNA from simian, prosimian, cat and mouse species, probed with a full-length HERV-FRD env fragment. The infened date of insertion of HERV-FRD is indicated with an anow on the primate phylogenetic tree on the left. NWM: New World Monkey.
  • Figure 6B In vitro transcription- translation assay of the human HERV-FRD env gene and of the orthologous genes from the indicated simian species. Env genes were PCR-amplified as schematized, submitted to in vitro transcription/translation ('control' is without DNA template), run on a polyacrylamide gel and autoradio graphed. The anow points the bands ofthe expected size.
  • FIG 7. Fusion activity of the orthologous primate ERV-FRD envelope glycoproteins.
  • Figure 8A and Figure 8B Infection assays using retroviral particles pseudotyped with the HERV-FRD and control envelopes.
  • Figure 8A Rationale of the assay.
  • conesponding pseudotype viruses were produced by cotransfecting 7.5 x 10 5 293T cells with 0.55 ⁇ g ofthe phCMV-HERV-FRD vector expressing the HERV-FRD envelope (or pcDNA3 for the negative -none- control, and phCMVampho for the amphotropic MLV envelope positive control), 1.75 ⁇ g of a vector encoding the retroviral proteins (except the envelope) of MLV (phCMVintron) HIV (pCMV ⁇ R8.91) or SIV (pSIV3+), and 1.75 ⁇ g of the conesponding defective retroviral vectors marked with a ⁇ -galactos
  • Target cells murine 3T3, feline G355-5, or human TE671, HeLa and 293T cells
  • 5-500 ⁇ l of virus samples containing 4 ⁇ g of Polybrene per ml were added to the cells and centrifuged for spinoculation at 1,200 x g for 2 h 30 min at 25°C (10). After removal of the supernatants, the cells were incubated in regular medium for 60 h at 37°C.
  • Viral titers were then measured upon by X-Gal staining of the cells and expressed as lacZ Colony Forming Unit (CFU) per milliliter of viral supernatant.
  • CFU lacZ Colony Forming Unit
  • Figure 9 Infection / cell-cell fusion, activities and host range of the HERV-FRD and simian orthologous envelopes.
  • Upper panel Infection of feline (G355.5), human (293T and HeLa) and murine (3T3) cells by STV-based particles pseudotyped with the indicated ERV-FRD envelopes. Same experimental conditions as in Figure 8A, with negative and positive control values as in Table 1.
  • NWM New World Monkey (Callithrix jacchus marmoset).
  • Lower panel Cell-cell fusion assay for the ERV-FRD envelopes and cells as in the upper panel.
  • the G355-5 and HeLa cells were transfected using Lipofectamine (Invitrogen, 2 ⁇ g of DNA for 5xl0 5 cells), and the 293T and TE671 cells using calcium phosphate precipitation (Invitrogen, 5 ⁇ g of DNA for 5xl0 5 cells). Fusion activities were measured 12 to 36 h post-transfection ofthe conesponding expression vectors. To visualize syncytia, cells were fixed in methanol and stained by adding May-Gr ⁇ nwald and Giemsa solutions (Sigma) according to the manufacturer's instructions.
  • the fusion index which represents the percentage of fusion events in a cell population is defined as [(N-S)/T] x 100, where N is the number of nuclei in the syncytia, S is the number of syncytia, and T is the total number of nuclei counted.
  • Figure 10A and Figure 10B Comparison of the simian ERV-FRD envelopes and identification of a unique point mutation responsible for the gibbon envelope loss-of- function.
  • Figure 10 A Aligned primary sequences ofthe HERV-FRD and simian orthologous envelopes. Abbreviations are: Hu:homo sapiens; Cpz: chimpanzee; Go: gorilla; Oo: orangutan; Gib: gibbon; Mcq: macaque; Nwm: New World Monkey. Accession numbers are AL136139 for the human gene, and AJ577595 to AJ577600 for the simian genes.
  • the RVRR canonical motif for SU-TM cleavage is darkened, and the predicted transmembrane hydrophobic domain is boxed. Aminoacids differing between the human and gibbon proteins are indicated with an asterisk, among which those unique to the gibbon sequence are grayed. The two aminoacids in the TM moiety of the gibbon protein that were mutated and assayed for reversion to the infectious phenotype are indicated with an arrow.
  • Figure 10B Infection of feline (G355-5) and human (293T) cells by SIV-based particles pseudotyped with the wild type (wt) and mutant (F490->L or T532->N) gibbon FRD envelopes, with the human FRD envelope as a control.
  • the indicated aminoacid changes in the gibbon envelope were performed by a three-fragment ligation, using PCR fragments generated with oligonucleotides containing the gibbon-to-human single-base mutations (TTT->CTT and AAT->ACT for aminoacid positions 490 and 532, respectively), and subsequent sequencing of the resulting constructs.
  • Infection assays were performed as described in Figure 8A. The viral titers are average from two independent experiments.
  • T7 promoter-containing PCR products were ethanol precipitated and 200 ng of the amplification products were used in the TNT Coupled Reticulocyte Lysate System (Promega Corp., Madison, WI) according to the manufacturer instructions, with ( H) methionine (ICN
  • BACPAC Resources Human BAC clones containing the identified coding envelope genes were purchased from BACPAC Resources (Oakland, CA). RNA from various human tissues were purchased from Clontech (Palo Alto, CA), Stratagene (La Jolla, CA) and Ambion (Austin, TX). Quality ofthe RNA was assessed on a RNA LabChip (Agilent 2100 Bioanalyzer), and RNA concentration was quantified spectrophotometrically. Five micrograms of each RNA sample were submitted to DNAse treatment (DNA-free, Ambion) to eliminate DNA contaminants.
  • DNAse treatment DNA-free, Ambion
  • RNA from each sample was reverse transcribed in a 20 ⁇ l volume reaction using 50U Moloney murine leukemia virus Reverse Transcriptase, 20U ribouclease inhibitor (Applied Biosystems, Foster City, CA), 1 mmol L dA/T/G/C (Amersham-Pharmacia Biotech, Upsala, Sweden), 5 mmol L MgCl 2 , 10 mmol/L Tris-HCl ( ⁇ H8.3), 10 mmol/L KCl, and 50 pmol/L of random hexamers (Applied Biosystems). The complementary DNAs were then diluted 1/25 in nuclease-free H 2 O (Promega Corp.).
  • Oligonucleotides were designed using the computer program Oligo (MedProbe, Oslo, Norway). The special requirements were a Tm of 60° and an amplicon length comprised between 80 and 350 bp. Oligonucleotides were purchased from MWG (Ebersberg, Germany). Real-Time quantitative PCR was achieved using a complementary DNA equivalent of 20 ng of total RNA. The reaction was performed in 25 ⁇ l using SYBR Green PCR Core Reagents (Applied Biosystems, Foster City, CA) according to the manufacturer's instructions. PCR was developed with the ABI PRISM 7000 Sequence Detection System (Applied Biosystems). Amplification was performed using a 2 min. step at 50°C then a 10 min.
  • control plasmid (p 11 env) containing the 11 envelope amplicons obtained with the primers listed in Table 3 was constracted by first cloning each amplicon into the pGEMT vector, and then by successive three-fragment ligations using fragments from these 11 plasmids and from construct intermediates.
  • a control tube containing 1 ng ofthe pllenv plasmid was included in each Real-Time PCR assay as a reference.
  • Table 3 Sequence of the primers used to detect the expression of the coding envelopes by quantitative RT-PCR analysis
  • HERV families were identified.
  • the envelope gene was tentatively delineated, with the pol gene (which was easily positioned due to its high conservation among retroviral elements) at its 5' end, and with the retroviral LTR at its 3' end.
  • the distance between the pol gene and LTR was higher than 1.4 kb (the average length of an envelope gene being 1.9 kb)
  • the envelope gene was considered as potentially complete and the HERV family retained.
  • Table 1 The resulting list of the 34 conesponding HERV families is given in Table 1.
  • Table 1 HERV families containing full-length envelope genes
  • HERV-ADP HERVP71A I 50 17 0
  • HERV-K HML-6 HERVK3 II 100 17 0
  • HERV-P HUERS-P3 I 100 13 0
  • HERV-U2 PRIMA41 III 100 10 0
  • HERV-FRD MER50 I 100 8 1
  • HERV-F(c)l - I 2 1 1 total -4,000 476 f 16 refers to names given in original publications, most ofthe time following the PBS-related nomenclature
  • BLAST query was then performed on human genome databases using the envelope gene as a probe. Overall, it yielded 476 potentially complete envelope genes (see Table 1 for their distribution among the HERV families). The coding status of each identified env gene was finally assessed, and only those with an open reading frame beginning at the first Met codon of the consensus envelope gene and uninterrupted over >90% of this gene were retained. Among the 476 envelope genes that were individually analyzed, only 16 genes were found to potentially encode envelope proteins.
  • Table 2 The 16 coding envelope genes ofthe human genome.
  • HML-2.HOM / K(C7) / HERV-K108 locus is organized as a tandem repeat in some individuals, with 100% nt identity for two the envelope genes.
  • HERV-K human endogenous retrovirus K proviruses are unique to humans. Cun. Biol. 9:861-868, Blond, J.-L., F. Beseme, L. Duret, O. Bouton, F. Bedin, H. Penon, B. Mandrand, and F. Mallet. 1999. Molecular characterization and placental expression of HERV-W, a new human endogenous retrovirus family. J. Virol. 73:1175-1185, Cohen, M., M. Powers, C. O'Connell, and N. Kato. 1985.
  • an in vitro transcription-translation assay was performed using human BAC clones containing the identified coding envelope genes.
  • the 16 BACs were obtained from BACPAC Resources (Oakland, CA), except for the HI, H2 and H3-containing BACs that had been cloned previously (de Parseval, N, J. F. Casella, L. Gressin, and T. Heidmann. 2001. Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates. Virology. 279:558-569).
  • the in vitro transcription-translation assay was performed directly on the env gene PCR products (generated using a forward T7-containing primer at the env 5' end and a reverse primer downstream of the stop codon).
  • translation products ofthe size expected from the sequences in the database were obtained (indicated with anowheads in Figure 2).
  • additional bands of lower molecular weight were observed, compatible with initiation at internal sites, and interestingly in one case (i.e. F(c)2) additional bands at higher molecular weight were detected, most probably associated with the presence at the gene 3' end of a frameshift signal (Benit, L., A. Calteau, and T. Heidmann. in press. Characterization of the low copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes. Virology).
  • the predicted hydrophobic profiles of the 16 proteins represented in Figure 1 allow the identification of characteristic domains of these envelopes, namely the fusion peptide, located just downstream ofthe proteolytic cleavage site between the SUrface (SU) and TransMembrane (TM) moieties of the envelopes, and the transmembrane domain of the TM subunit which permits the anchorage of the envelope in the membrane.
  • this analysis revealed that one envelope (EnvR) seems to be devoid of a fusion peptide, and that two envelopes (EnvR and EnvF(c)2) disclose a premature stop codon just upstream of their transmembrane hydrophobic domain. Two other domains are delineated in Figure 1.
  • the CWLC domain involved in the interaction between the SU and the TM moieties
  • Pinter A., R. Kopelman, Z. Li, S. C. Kayman, and D. A. Sanders. 1997. Localization of the labile disulfide bond between SU and TM of the murine leukemia virus envelope protein complex to a highly conserved CWLC motif in SU that resembles the active-site sequence of thiol-disulfide exchange enzymes. J. Virol. 71:8073-8077
  • the CKS17-like immunosuppressive domain (Cianciolo, G. J., T. Copeland, S.
  • the Inventors devised a Real-Time RT-PCR strategy which uses specific primers designed in such a way that only envelope genes with an open reading frame should be amplified among all the envelope genes of a given family.
  • env nucleotide sequences were aligned with the CLUSTALW program and primers were designed within domains of maximal divergence between the coding copy and the other copies.
  • Primers for Sybr Green amplification were devised with their 3 '-ends forced at nucleotide positions with, again, maximum divergence between the coding sequence and the others.
  • a first series of assays was performed by PCR amplification of human genomic DNA. As expected, in all cases a single band was observed, thus excluding non-specific amplifications or amplifications of elements of unusual size (data not shown). Then, PCR products for each couple of primers were cloned into a pGEM-T vector and at least 6 clones per amplicon were sequenced for each envelope (26 clones for the HERV-K (HML-2) family, see below), hi all cases, the 6 clones for a given envelope were identical and unambiguously corresponded to the coding sequence, being different from all the other aligned sequences within each HERV family.
  • HERV-K (HML-2) family 26 clones were sequenced, among which 21 had an identical sequence conesponding to the sequence of the 6 coding envelopes, and 5 which conesponded to two other HERV-K (HML-2) envelope genes. Despite this parasitic amplification of non coding envelopes, the HERV-K (HML-2) coding envelope primer set was retained since it allowed the amplification of at least all the coding envelopes.
  • Transcriptome of the coding Envelope genes survey of human tissues
  • the values are determined by real-time quantitative PCR. Each value is expressed as the mean standard deviation relative to the value for a reference control plasmid assayed in each real-time PCR experiment after correction for total RNA content in each tissue extract (using the 18S transcript as an internal control).
  • PBL peripheral blood lymphocytes.
  • RNA were submitted to DNAse treatment and reverse transcribed using MLV RT, and a first Real-Time quantitative PCR was performed using primers for rRNA 18S to normalize for differences in the amount of total RNA added to the reaction (less than a 3.5-fold variation among samples). Real-Time PCR was then performed for each couple of specific primer. Control PCRs performed on RNA without the RT step never resulted in any amplification, as expected.
  • the expression levels represented in Table 4 disclose several interesting features.
  • envelope genes which disclose a severe tissue-specificity together with an overall low expression level, namely the 3 envH, envR(b), envF(c)l and envF(c)2, and the envelope genes which are transcribed in the majority of the tissues, namely the 6 envK, envT, envW, envFRD and envR.
  • This latter gene is singular as its level of expression is extremely high in all tissues tested, with actually the highest value among all coding env genes (with the exception of the thyroid, for en T).
  • the status ofthe HERV-K (HML-2) family is unique among the coding env-containing families in several respects. Although elements of this family first entered the primate genome more than 30 million years ago (36), new proviral copies have been generated in the recent past. Actually, the entry date in the human genome of 4 out of the 6 HERV-K (HML-2) proviruses with a coding env gene has been estimated to be less than 5 million years ago (ref. 2 for K2, K3, K4, and data not shown for Kl). In addition, the latter two proviruses are polymorphic in humans with allele frequencies of 0.04 and 0.19 (ref. 41 for K5 and K6).
  • HERV-K (HML-2) proviruses with coding env have open reading frames in other genes (all 6 have ORFs in ' their gag genes, 4 in their re? genes and 4 in their pol genes, resulting in three completely coding HERV-K (HML-2) proviruses), and among the 29 other env gene-containing proviruses of this family, 10 additional retroviral coding genes can be found.
  • the other env gene-containing families can be considered as « old families » with no human-specific integrations.
  • the entry date in the primate genome ofthe coding env gene-containing proviruses vary from 10 million years (for the HERV-Hp62 provirus, (15) to more than 45 million years (for the the coding env- containing HERV-R(b) provirus, data not shown).
  • no entirely coding gene besides the env genes have been found so far among those families.
  • the Inventors have devised an efficient method to detect the expression of specific genes belonging to large multigenic families with high homology between their members. It allowed the quantitative and specific monitoring of the expression level of these endogenous retroviral genes, a task which would be impossible using the Northern blot or classical RT-PCR methods which detect the overall expression ofthe complete set of elements among each family.
  • testis is an organ in which all coding envelopes are transcribed is not a totally unexpected result since germline expression is a common feature of transposable elements in other species, including mice and drosophila (refs. 17 and 39 for the mouse, reviewed in refs. 11 and 18 for drosophila). In these species, expression in the germ line is associated with a high transpositional activity which may result in stably inherited mutations and most probably plays a role in the generation of genetic diversity in the course of evolution.
  • the high level expression of the newly identified envT detected in the thyroid is intriguing because it is one of the rare coding env gene highly expressed in a « permanent » healthy tissue and it is highly expressed only in this organ. This expression might be relevant to the hormone-producing status of the thyroid gland (and this interpretation might similarly hold for envR in the adrenal gland) and to specific sequences in the HERV LTR or in the vicinity of the proviral insertion site.
  • the envelope proteins of exogenous counterparts of HERVs possess several functions besides their primary role as key molecules for viral entry: most of them elicit immunosuppressive effects and some of them have the capacity to create cell-cell fusion. Consequently, the high level expression of three endogenous coding env genes observed in the placenta (namely envR, envW and the newly identified envFRD) could be implicated in two major physiological processes of this organ : fusion of the cytotrophoblast cells to form the syncytiotrophoblast layer, and local immunosuppression at the materno-foetal barrier.
  • the envW gene product is a highly fusogenic protein (Blond, J. L., D. Lavillette, V. Cheynet, O. Bouton, G. Oriol, S. Chapel-Fernandes, B. Mandrand, F. Mallet, and F.-L. Cosset. 2000.
  • An envelope glycoprotein of the human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J. Virol. 74:3321-3329).
  • envFRD also highly expressed in the placenta
  • envR it had been previously ruled out its possible implication in fundamental processes of placenta formation by the discovery of a premature stop mutation present in 16% of Caucasians in the heterozygous state, and in 1% in the homozygous state (de Parseval, N, and T. Heidmann. 1998. Physiological knock-out ofthe envelope gene of the single copy ERV-3 human endogenous retrovirus in a fraction ofthe Caucasian population. J. Virol. 72:3442-3445).
  • retroviral envelopes Another property of retroviral envelopes is to inhibit infection by retroviruses sharing the same receptor - i. e. receptor interference, reviewed in refs. Best, S., P. R. Le Tissier, and J. P. Stoye. 1997. Endogenous retroviruses and the evolution of resistance to retroviral infection. Trends Microbiol. 5:313-318 and Rosenberg, N, andP. Jolicoeur 1997. Retroviral Pathogenesis, p. 475-586. In J. M. Coffm, Hughes, C. L., Varmus, H. E. (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, New York -.
  • HERV-encoded proteins have also been tentatively involved in several human j pathologies including cancer, immune disorders and neurological diseases, (reviewed in refs.
  • the present survey of coding env genes of the human genome provides a comprehensive list of candidate genes for the possible involvement of HERVs in human physiology and physiopathology. Furthermore, it shown herein that all of the identified genes can be expressed at least in some tissues, and the invention provide tools to specifically evaluate their transcriptional status in physiological and pathological conditions.
  • the identified genes should allow further studies of their function via classical genetic approaches (identification of susceptibility loci, search for polymorphisms among the human population as previously performed for the HERV-R locus, ref. de Parseval, N., and T. Heidmann. 1998. Physiological knock-out of the envelope gene of the single copy ERV-3 human endogenous retrovirus in a fraction of the Caucasian population. J. Virol. 72:3442-3445), whereas the limited number of unraveled coding sequences downsizes an a priori insoluble multigenic analysis to a simpler one.
  • the human TE671 rhabdomyosarcoma cells (ATCC CRL8805), 293T embryonal kidney cells (ATCC CRL11268) and HeLa epithelioid carcinoma cells (ATCC CCL2), the Cos- 7 African green monkey kidney cells (ECACC 87021302), the G355-5 feline astrocyte cells (ATCC CRL2033), and the NIH3T3 mouse fibroblasts were grown in Dulbeco's modified Eagle's medium (DMEM) supplemented with 10 % fetal calf serum; the CHO Chinese hamster ovary cells (ATCC-CCL61) were grown in F12K nutrient medium (Gibco) supplemented with 7 % fetal calf serum. All cell culture media were supplemented with streptomycin (100 ⁇ g / mL) and penicillin (100 U / mL).
  • the FBA-RlessSALF expression vector (Lavillette, D., Maurice, M., Roche, C, Russell, S, J., Sitbon, M. & Cosset, F.-L. (1998) J. Virol. 72, 9955-9965) encoding the A-Rless hyperfusogenic mutant amphotropic MLV envelope glycoprotein and the phCMV-G expression plasmid (GenBank accession number AJ318514) were gifts from F-L Cosset (ENS, Lyon, France).
  • the HERV-W envelope expression vector (phCMV-EnvpH74) was a gift from F. Mallet (ENS, Lyon, France). The fifteen other endogenous envelope expression vectors were constracted as follows.
  • Cell-cell fusion assay Cells were transfected using Lipofectamine (Invitrogen, 2 ⁇ g of DNA for 5xl0 5 cells), except for 293T and T ⁇ 671 cells which were transfected using calcium phosphate precipitation (Invitrogen, 5 ⁇ g of DNA for 5x10 5 cells). Fusion activity of envelope glycoproteins was measured 12 to 36 h after transfection of the conesponding expression vectors. To visualize syncytia, cells were fixed in methanol and stained by adding May- Gr ⁇ nwald and Giemsa solutions (Sigma) according to the manufacturer's instructions.
  • the fusion index which represents the percentage of fusion events in a cell population is defined as [(N-S)/T] x 100, where N is the number of nuclei in the syncytia, S is the number of syncytia, and T is the total number of nuclei counted.
  • the envelope genes orthologous to the human HERV-FRD gene were PCR-amplified from simian (and human as a control) genomic DNAs. PCR were carried out for 25 cycles (10 sec at 93 °C, 30 sec at 56 °C, 4 min at 68 °C), in 50 ⁇ l, using 100 ng of genomic DNA, 48 pmol of each primer, 350 ⁇ M of each dNTP, 0.75 ⁇ l Expand long template enzyme mix and IX reaction buffer (Roche).
  • TzoI-containing primers were ATCACCTCGAGCACCATGGGCCTGCTCCTGCTGGTTCTCATTC (SEQ ID NO: 58) as forward primer and ATCACCTCGAGGCTTCAGTACAGGTGGATA (SEQ ID NO: 59) as reverse primer.
  • Each PCR product was then Xhol restricted and cloned into the phCMV-G vector opened with Xhol. Sequencing of the simian envelope genes was performed on the bulk of the PCR products before cloning (MWG-Biotech).
  • DNA slot-blot DNAs (3 ⁇ g) from each species were loaded on Hybond N+ membranes (Amersham) using a slot blot apparatus (Hoefer). Blots were hybridized overnight at 65 °C under standard conditions (24), using a 32 P-labelled full-length FRD env gene (1679 bp PCR- fragment) as a probe. Membranes were then washed at 65 °C, once with 2X SSC-0.1 % SDS for 15 min and once with IX SSC-0.1 % SDS for 15 min. Labelling was detected using a Phosphorhnager (FLA-3000 scanner).
  • the membrane was washed at 68 °C, twice with the NorthernMax low stringency buffer and once with the NorthernMax high stringency buffer (Ambion), and then exposed to X-ray film (Kodak) at -80 °C for 12 h.
  • Example 1 An assay for fusogenicity ofthe sixteen cloned envelopes genes identified in Example 1 was. performed. This assay relies on the fransfection of cells expected to cany a receptor for the conesponding envelope, with the expression vectors for the envelope proteins. Accordingly, fusion assays were performed for all sixteen envelope genes upon transfection of a large series of cells, including feline, murine, simian and human cells. In the latter case, different cell lines were used, namely Hela cells, 293T embryonic kidney cells, and TE671 cells which have been previously used as they possess the receptors for several retrovirus groups (Porter, C. D., Collins, M. K, Tailor, C. S., Parkar, M. H., Cosset, F.
  • retrovirus groups Portable, C. D., Collins, M. K, Tailor, C. S., Parkar, M. H., Cosset, F.
  • Fusion assay was performed with the following target cells : NIH3T3, CHO, G355-5, Cos-7, TE671, 293T and HeLa.
  • (-) indicates a negative result in all cell types ; (+) indicates a positive result in at least one cell type.
  • the properties ofthe HERV-FRD env gene was analyzed further and compared to that of HERV-W.
  • the syncytia-forming activity j of both envelopes although of quite related extent when using the syncytia forming index defined in Materials and Methods, do not coincide for a given cell-type: for instance, the HERV-FRD Env is highly fusogenic in feline cells where that of HERV-W has no activity, and within human cells where the HERV-W Env is fusogenic, that of HERV-FRD is not fusogenic in all cell types, with only limited effect in Hela cells.
  • retroviral envelope-mediated cell- fusion is dependent on the presence of an appropriate receptor on the cell surface, which may be different for different envelope proteins, as currently observed for most exogenous infectious animal retroviruses (reviewed in ref. Hunter, E. (1997) in Retroviruses, eds. Coffin, J. M., Hughes, S. H. & Varmus, H. E. (Cold Spring Harbor Laboratory Press, New York), pp. 71-119 and Overbaugh, J., Miller, A. D. & Eiden, M. V. (2001) Microbiol. Mol. Biol. Rev. 65, 371-389).
  • the receptor for the HERV- W envelope protein is the receptor for the D-type retroviruses (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329; Lavillette, D., Marin, M., Ruggieri, A., Mallet, F., Cosset, F. L. & Kabat, D. (2002) J. Virol. 76, 6442-6452).
  • the receptor for the HERV-FRD envelope is distinct, as the cell specificity for fusion for both envelopes is different. This was further confirmed by performing an interference assay using the panel of cells derived in (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel- Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J.
  • Virol 1A, 3321-3329 where no decrease in the fusogenic activity of the HERV-FRD Env could be detected, under conditions where the cells had been stably transfected with an expression vector for the envelope of a type-D retrovirus (RD114, not shown).
  • a Northern blot analysis was performed with a membrane containing polyA "1" RNA from a panel of human tissues that were hybridized with a riboprobe for the HERV- FRD envelope.
  • a strong band is observed in the placenta, and actually almost exclusively in this organ, at the expected position for a spliced subgenomic retroviral transcript.
  • a real-time RT-PCR analysis of the HERV-FRD env gene transcripts further disclosed high level expression in cytotrophoblast cells isolated from the placenta, not observed in the conesponding fibroblast cells.
  • the FRD family of endogenous retroviruses consists of approximately 50 provirus copies per haploid genome (Tristem, M. (2000) J. Virol. 74, 3715-3730; Seifarfh, W., Skladny, H., Krieg-Schneider, F., Reichert, A., Hehlmann, R. & Leib-Mosch, C. (1995) J. Virol. 69, 6408-6416).
  • This family is most probably a very ancient family whose members entered the primate genome after the divergence between prosimians and simians: this is demonstrated in the zoo-slot in Figure 6A.
  • the identified putative envelope genes were characterized further, along three lines: firstly, the PCR products were sequenced for an unambiguous identification of the env genes and the determination of their level of divergence in the course of primate evolution; secondly, an in vitro transcription/translation assay was performed to determine whether the genes are fully coding; and thirdly a fusion assay was performed as above, to determine if env gene function has been preserved.
  • the PCR env fragments were cloned into the phCMV expression vector and tested in the syncytia-forming assay, as above.
  • For each env gene at least six clones were assayed to circumvent possible mutations introduced by the PCR amplification procedure (a feature with no consequence on both the sequencing and the transcription/translation assay above, directly performed on the bulk of the PCR product), using both the highly fusogenic feline G355.5 cells, and human cells (see Figure 7).
  • fusion of the transduced feline cells could be observed for all env genes (with in each case at least four out of six cloned PCR-fragments positive, a result consistent with the expected rate of mutation of the DNA polymerase used for the conesponding genomic amplifications), with no significant difference in the extent of fusogenicity from human to New World Monkey.
  • the fusogenic function has been frequently hypothesized as being plausibly involved in placenta formation, via the fusion of the cytotrophoblast cells into the syncytiotrophoblast (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel- Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329; Mi, S., Lee, X., Li, X., Veldman, G.
  • the present invention now provides the required genetic tools to unambiguously address the issue: there are two identified HERV envelope genes with fusogenic properties in the human genome, and these two genes are expressed in the placenta.
  • the identified HERV-FRD envelope gene canies a domain -the immunosuppressive domain- which could play a physiological role in protecting the fetus against the maternal immune system, and as such have also participated in the 'positive selection' ofthe syncytin-2 gene in the course of primate evolution.
  • Retroviruses conferring infectivity and functional conservation among simians
  • HERV-W envelope gene is functional, since pseudotypes generated with HIV-l virions are infectious (An, D. S., Y.-M. Xie, and I. S. Y. Chen. 2001.
  • Envelope gene ofthe human endogenous retroviras HERV-W encodes a functional retrovirus envelope. J. Virol. 75:3488-3489; Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002.
  • the envelope glycoprotein of human endogenous retroviras type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442- 6452).
  • HERV-FRD envelope can also confer infectivity to pseudotypes generated with lentiviral virions.
  • the HERV-FRD envelope gene was cloned into a hCMV promoter-driven expression vector to be used in a previously described infection assay (Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002.
  • the envelope glycoprotein of human endogenous retroviras type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442-6452), as schematized in Figure 8A.
  • human 293T cells are co-transfected with an expression vector for the retroviral proteins -except the envelope- from type-C (MLV) or lenti (HIV-1 and SIV) virases, a conesponding lacZ gene-marked defective retroviral vector, and an expression vector for the env gene to be tested (or an empty vector as a negative control and a vector for the amphotropic MLV envelope as a positive control).
  • the pseudotype virions are assayed for infectivity after recovery of the transfected cell supernatant 36 h post-transfection, transfer of the supernatant onto target test cells and centrifugation of the plates (i.e. spinoculation, see Ref. Lavillette, D., M.
  • the HERV-FRD envelope when expressed on lentiviral particles, confers infectivity to the virions, with evidence for viral titers on feline (G355-5) and human (TE671 and 293T) cells in the 100-500 cm per ml range.
  • feline (G355-5) and human (TE671 and 293T) cells in the 100-500 cm per ml range.
  • the murine 3T3 cells and the human HeLa cells are refractory to infection (although they are positive for the confrol amphotropic MLV envelope), a result consistent with the absence of any detectable syncytia formation in a fusion assay carried out with these cells (see below).
  • the MLV core is much less efficient -if any- than the lentiviral cores, as similarly observed for the HERV-W envelope (An, D. S., Y.-M. Xie, and I. S. Y. Chen. 2001. Envelope gene of the human endogenous retrovirus HERV-W encodes a functional retrovirus envelope. J. Virol. 75:3488-3489; Blond, J.-L., D. Lavillette, V. Cheynet, O. Bouton, G. Oriol, S. Chapel-Fernandes, B. Mandrand, F. Mallet, and F.-L. Cosset. 2000.
  • An envelope glycoprotein ofthe human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J. Virol. 74:3321- 3329; Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002.
  • the envelope glycoprotein of human endogenous retrovirus type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442-6452).
  • the envelope glycoprotein of human endogenous retroviras type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442-6452; Lavillette, D., M. Maurice, C. Roche, S. J. Russell, M. Sitbon, and F.-L. Cosset. 1998. A proline-rich motif downstream of the receptor binding domain modulates conformation and fusogenicity of murine refroviral envelopes. J. Virol. 72:9955-9965).
  • the gibbon envelope discloses strong conservation with the other simian FRD envelopes, as it is 97 % identical to the human sequence, i.e.
  • the present functional characterization of the ERV-FRD envelopes is strongly suggestive of an 'ancestral' infection event by a functional retrovirus and its subsequent 'endogenization', with some of the envelope functions retained in evolution.
  • Close examination of the primate FRD envelope sequences indeed reveals a prevalence of synonymous versus nonsynonymous substitutions (ratios for all pairwise comparisons >3, using the SNAP.pl program at the www .hiv-web . lanl . gov site), thus suggesting positive selection for a physiological function -which remains to be unraveled.
  • the assay for measuring the immunosuppressive activity was performed following the general procedure described in Mangeney & Heidmann, PNAS 1998 and Mangeney et al, J. Gen. Virol 2001.
  • the cell line used in the assay was MCA205(methylcholanthrene-induced murine fibrosarcoma cells (Shu and Rosemberg, 1985). Cells were cultured in DMEM supplemented with 1 . 0% fetal calf serum, streptomycin (100 ⁇ g/ml) and penicillin (lOOunits/ml).
  • HERV-FRD envelope gene was PCR-amplified from the conesponding BAC DNA
  • TCGAGCTCTTAGGTCACCATGGGC SEQ ID NO: 66
  • Mlul- containing oligonucleotide AACGGACGCGTCTCTGTCGTGTTCC ACTA SEQ ID NO: j 67
  • PCR was carried out for only 15 cycles (1 min. at 94 °C, 1 min at 60 °C,
  • the PCR product was then cloned into the pDFG-MoTMtag vector (see below) opened at the
  • pDFG-MoTMtag was constructed by ligating pDFG-MoTM (Mangeney & Heidmann, 1998) opened with Bsu361 and Xhol and a PCR fragment (digested with the same enzymes) generated using primers 5' CGTCTTGTCTGCTGCAGCATC-3' (SEQ ID NO: 68) and 5'- CATACTCGAGTCAACGCGTAGAATCGAGACCGAGGAGAGGGTTAGGGATAGGCT TACCGTACGGCTCGTACTCTATAGGCTTC-3' (SEQ ID NO: 69) and pDFGMoTM as a template.
  • pDFG-envHERV-W was constracted by inserting the Agel-Dral Klenow treated fragment from pCR2.1 pH74 (Blond et al. J. Virol. (2000) Vol 74: 3321-3329) into the pDFG- MoTMTag vector digested by Agel and BsiWI and Klenow treated.
  • Retroviral expression vectors (1.75 ⁇ g) were packaged by transient cotransfection into 7.5 x 10 5 293T cells with 1.75 ⁇ g of CMV-gag-pol-MoMLV and 0.55 ⁇ g CMV-envAmpho, using the calcium phosphate method. Supernatants were recovered 2 days later, filtered and used for infection of 5 x 10 5 MCA205 tumor cells in the presence of 4 ⁇ g/ml polybrene, as described in Mangeney & Heidmann, 1988. Cells were maintained in selective medium (400 units/ml hygromycin) for 2 weeks.
  • tumor cells were trypsinized, centrifuged and resuspended in PBS at a concentration of 1 x 10 7 cells/ml. 100 ⁇ l of each suspension were injected s.c. in the shaved right flank of 3 C57/BL6 and 8 to 10 BALB/c mice. Tumor establishment was determined by palpation and tumor area (in mm 2 ) was determined by measuring perpendicular tumor diameters.
  • Synctin 1 is devoid of such an activity.
  • Syncitin 2 is the first HERV envelope described to date with both immunosuppressive and fusogenic activity.

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Abstract

The present invention notably relates to a protein or a polypeptide, characterized in that it corresponds to an amino acid sequence, comprising or being constituted by: a sequence corresponding to SEQ ID NO:2(Syncitin 2), or a sequence derived from SEQ ID NO:2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide corresponding to said derived sequence presents a fusogenic activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2, or a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO:2, provided that the protein or the polypeptide corresponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2, and/or an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2.

Description

PROTEIN WITH FUSOGENIC ACTIVITY, NUCLEIC ACID SEQUENCES ENCODING SAID PROTEIN AND PHARMACEUTICAL COMPOSITIONS COMPRISING THE SAME
The present invention relates to a new protein with fusogenic properties, nucleic acid sequences encoding for said protein, and pharmaceutical compositions comprising them.
The human genome contains a large fraction (ca. 8%) of elements of retroviral origin, with thousands of sequences close to the integrated proviral form of infectious retroviruses, with two long terminal repeats (LTR) bordering internal regions homologous to the gag, pol and env genes (Lower, R., Lower, J. & Kurth, R. (1996) Proc. Natl. Acad. Sci. USA 93, 5177-5184; Boeke, J. D. & Stoye, J. P. (1997) in Retroviruses, eds. Coffin, J. M., Hughes, S. H. & Varmus, H. E. (Cold Spring Harbor Laboratory Press, New York), pp. 343-436; Lander, E. S., Linton, L. M., Binen, B., Nusbaum, C, Zody, M. C, Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W. & al. (2001) Nature 409, 860-921). These elements, named Human Endogenous RetroViruses (HERV), are most probably the proviral remnants of ancestral germline infections by active retroviruses, which have thereafter been transmitted in a mendelian manner. HERV can be grouped according to sequence homologies into approximately 100 distinct families, each containing a few to several hundreds elements.
Strong similarities between HERV and present-day retroviruses can be infened from phylogenetic analyses on the Reverse Transcriptase domain of the pol gene or the TransMembrane moiety (TM) of the env gene, which disclose interspersion of both classes of elements and suggest a common history and shared ancestors (Tristem, M. (2000) J. Virol. 1A, 3715-3730; Benit, L., Dessen, P. & Heidmann, T. (2001) J. Virol. 15. 11709-11719). Similarities are also observed at the functional level.
Thus, the envelope protein of a HERV-W family member, Syncitin (hereafter named Syncitin 1), has retained the ability to interact with the receptor of the D-type retroviruses (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329, Lavillette, D., Marin, M., Ruggieri, A., Mallet, F., Cosset, F. L. & Kabat, D. (2002) J. Virol 76, 6442-6452) and can confer infectivity on pseudotyped retroviral particles (Lavillette, D., Marin, M., Ruggieri, A., Mallet, F., Cosset, F. L. & Kabat, D. (2002) J. Virol. 16, 6442-6452, An, D. S., Xie, Y.-M. & Chen, I. S. Y. (2001) J. Virol. 75, 3488-3489). % As a consequence of the close relationship between HERVs and infectious retroviruses,
" and despite the fact that most HERVs have accumulated mutations, deletions and/or truncations, it remains plausible that some elements still possess functions of infectious retroviruses, that may have been diverted by the host to its benefit. Along this line, it has been proposed (reviewed in ref. Venables, S., Brookes, M., Fan, W., Larsson, E., Maini, R. N. & Boyd, M. T. (1995)
Virology 211, 589-592, Harris, J. R. (1998) BioEssays 20, 307-316) that the HERV envelopes could play a role in several processes including i) protection against infection by present-day retroviruses through receptor interference (Best, S., Le Tissier, P. R. & Stoye, J. P. (1997)
Trends Microbiol 5, 313-318), ii) protection ofthe fetus against the maternal immune system via an immunosuppressive domain located in the envelope TM subunit (Cianciolo, G. J., Copeland,
T., Orozlan, S. & Snyderman, R. (1985) Science 230, 453-455; Mangeney, M. & Heidmann, T.
(1998) Proc. Natl. Acad. Sci. USA 95, 14920-14925), and iii) placenta morphogenesis through fusogenic effects allowing differentiation of cytotrophoblast cells into the syncytiotrophoblast
(Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S.,
Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329; Mi, S., Lee, X., Li, X.,
Veldman, G. M., Finnerty, H., Racie, L., LaVallie, E., Tang, X. Y., Edouard, P., Howes, S.,
Keith, J. C. J. & McCoy, J. M. (2000) Nature 403, 785-788).
In accordance with a symbiotic role for HERVs, WO 01 16171 discloses that the HERV-
W envelope gene product (Syncitin 1) is a highly fusogenic glycoprotein which is specifically expressed in the placenta and can mediate cell-cell fusion ex vivo. This HERV-W envelope could be used in cancer treatment by promoting the formation a syncitia by cancerous cells, thus leading to their death. Disorders in the expression of the HERV-W envelope could impair placental morphogenesis.
However, the HERV envelope can not mediate the fusion of all cell types, therefore it can
I not be used for the treatment of all cancer types. Besides, disorders in the expression of the
HERV-W envelope do not account for all placental morphogenesis disorders and other HERV envelopes might be implicated.
Therefore, an object of the present invention is to provide a new fusogenic HERV envelope, with a cell-specificity different from that of HERV-W envelope and which accounts for all the placental morphogenesis disorders arising from disorders in the expression of a HERV envelope other than the HERV-W envelope.
Another object of the present invention is to provide a new HERV envelope which presents an immunosuppressive activity in addition to a fusogenic activity, said new HERV j envelope representing the sole example of a HERV envelope with both fusogenic activity and immunosuppressive activity.
The present invention relates to a protein or a polypeptide, characterized in that it corresponds to an amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide conesponding to said derived sequence presents a fusogenic activity similar to that of Syncitin 2 and/or an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2, and/or an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2.
The present invention relates in particular to a protein or a polypeptide as defined above, characterized in that it corresponds to an amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide conesponding to said derived sequence presents a fusogenic activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2, and/or an antigenic activity similar to that of Syncitin 2.
The present invention also relates to a protein or a polypeptide as defined above characterized in that it corresponds to an - amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at . least one amino acid, provided that the protein or the polypeptide corresponding to said derived sequence presents an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents an immunosuppressive activity similar to that of Syncitin 2, and/or an antigenic activity similar to that of Syncitin 2.
The present invention more particularly relates to a protein or a polypeptide as defined above, characterized in that it conesponds to an amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide conesponding to said derived sequence presents a fusogenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2.
The expression "fusogenic activity" relates to the ability of said protein or polypeptide to promote the fusion, i.e. the coalescence, of biological membranes, in particular the fusion of cellular membranes.
Membrane fusions between eukaryotic cells lead to the formation of a syncitium. A syncitium is in particular characterized by the presence of several nuclei enclosed by a single cellular membrane.
Such a fusogenic activity can be detected according to the following procedure:
- an expression vector carrying the coding sequence of said polypeptide or protein under the control of a promoter is transformed into host cells, to obtain host cells producing, said polypeptide or protein, the formation of a syncitium from said host cells being indicative of a fusogenic activity of said polypeptide or protein;
- alternatively, it is possible to contact said host cells with untransformed cells of various lineages, the formation of a syncitium arising from the fusion of transformed cells with untransformed cells being indicative of a fusogenic activity of said polypeptide or protein and ofthe presence of a receptor of said polypeptide or protein in said untransformed cells.
Syncitin 2 is a HERV envelope presenting a fusogenic activity. Syncitin 2 is also refered to as HERV-FRD in the examples. The expression "presents a fusogenic activity similar to that of Syncitin 2" means that the protein or the polypeptide to which it relates has the same cell-specificity than Syncitin 2 and/or a fusogenic activity which represents at least 50%> ofthe fusogenic activity of Syncitin 2 in the same conditions.
Avantageously, Syncitin 2 and the HERV-W envelope (Syncitin 1) are the only two HERV envelopes with fusogenic activity normally expressed in the human body.
Equally advantageous, Syncitin 2 presents a fusogenic cell-specificity different from that of the HERV-W envelope. That is, the panel of cells which can be brought to form syncitia by Syncitin 2 is different from the panel which can be brought to form syncitia by Syncitin 1. The cells which are liable to specifically fusion with cells expressing respectively Syncitin 1 or 2, express membrane receptors respectively specific to Syncitin 1 or 2.
The expression "immunosuppressive activity" relates to the ability of said protein or polypeptide to enable the cells canying it to escape immune control.
Such an activity can be evidenced and measured following the procedure described in Mangeney & Heidmann, PNAS 1998, and Mangeney et al., J.Gen. Virol. 2001, and as described in Example 4. Advantageously Syncitin 2 presents an immunosuppressive activity.
The expression "presents an immunosuppressive activity similar to that of Syncitin 2" means that the protein or the polypeptide to which it relates has an immunosuppressive activity which represents at least 50% of the immunosuppressive activity of Syncitin 2 in the same conditions.
The expression "antigenic activity" relates to the ability of said protein or polypeptide to activate the immune system and to elicit an immune response directed against said protein or polypeptide.
The expression "presents an antigenic activity similar to that of Syncitin 2" means that the protein or the polypeptide to which it relates is liable to elicit an immune response directed against Syncitin 2.
Syncitin 2 is essentially expressed in the placenta, and impaired expression of Syncitin 2 may result in placental morphogenesis disorders, in particular syncitiotrophoblast disorders. Such disorders may arise either from an expression of Syncitin 2 higher or lower than normal. Higher than normal expression of Syncitin 2 leads to the formation and/or the development of unwanted syncitia, such as trophoblastic invasion which occurs in choriocarcmoma. Conversely, lower than normal expression of Syncitin 2 leads to the absence or to the underdevelopment of normally occurring syncitia, such as trophoblast underdevelopment, which may be a cause of unfertility. According to a particular embodiment, the invention relates to fragments ofthe Syncitin 2 protein, said fragments being constituted by a sequence deriving from SEQ ID NO: 2 by deletion of at least one amino acid and containing at least 20 contiguous amino acids.
According to another particular embodiment, a protein or a polypeptide according to the invention is characterized in that it corresponds to an amino acid sequence comprising or being constituted by a sequence derived from SEQ ID NO: 2 by deletion of at least the 17 contiguous amino acids from position 414 to position 430 of SEQ ID NO: 2.
The 17 contiguous amino acids from position 414 to position 430 of SEQ ID NO: 2 correspond to SEQ ID NO: 65. This sequence has a major role in the immunosuppressive activity of Syncitin 2. Proteins or polypeptides devoid of SEQ ID NO: 65 according to the invention, will not generally have any immunosuppressive activity. Such proteins or polypeptides devoid of SEQ ID NO: 65 encompass in particular fragments comprising at least 20 amino acids selected from contiguous amino acids from position 1 to position 413 or from position 431 to 538 of SEQ ID NO: 2.
According to a preferred embodiment, a protein or a polypeptide according to the invention is characterized in that it conesponds to SEQ ID NO: 64.
SEQ ID NO: 64 conesponds to SEQ ID NO: 2 from which SEQ ID NO: 65 has been deleted. Advantageously, a protein or a polypeptide conesponding to such a sequence presents a fusogenic activity and an antigenic activity similar to that of Syncitin 2 but is devoid of any immunosuppressive activity. Such a protein or polypeptide presents a better antigenic activity than Syncitin 2 as it is devoid of immunosuppressive activity, which makes it a good candidate for the manufacture of a vaccine composition.
The present invention also relates to a nucleic acid, characterized in that it conesponds to a sequence encoding a protein or a polypeptide as defined above, and or to its complementary sequence.
The present invention also relates to a nucleic acid, characterized in that it conesponds to a nucleic acid sequence comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 1, or
• a sequence derived from SEQ ID NO: 1 by insertion, deletion or substitution of at least one nucleotide, provided that said derived sequence encodes a protein or a polypeptide presenting a fusogenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 66% nucleotide identity with SEQ ID NO: 1, provided that said homologous sequence encodes a protein or a polypeptide presenting a fusogenic activity similar to that of Syncitin 2, or • fragments of said sequences, such as SEQ ID NO: 3 or 4; and/or to its complementary sequence.
The present invention also relates to a nucleic acid, characterized in that it hybridizes with a nucleic acid as defined above under stringent conditions.
Such stringent conditions according to the invention are defined in particular in Church, G. M. & Gilbert, W. (1984) Proc. Natl Acad. Sci. USA 81, 1991-1995 at a temperature of 65°C.
The present invention also relates to a prokaryotic or eukaryotic expression vector, characterized in that it comprises a nucleic acid as defined above and the elements required for its expression in a host cell.
An eukaryotic expression vector according to the invention is particularly useful for gene therapy, in particular to compensate for disorders resulting in an absence of expression or a lower than normal expression of fusogenic proteins, such as Syncitin 2. Such vectors can also be used to transfect tumoral cells to induce the formation of a syncitium resulting from the fusion of transfected tumoral cells with transfected or untransfected tumoral cells. Such vectors may be advantageously derived from vectors classically used in gene therapy protocols, such as retroviral or lentiviral vectors.
The present invention also relates to a prokaryotic or eukaryotic cell, characterized in that it comprises vector as defined above.
Advantageously, such cells express fusogenic polypeptide or protein and have the capacity of forming syncitia.
Advantageously, such cells can be administered to an individual suffering from cancer at a tumor site, to promote the formation of a syncitium resulting from the fusion of cells according to the invention with tumoral cells. Alternatively, such cells can also be administered to an individual suffering from a placental morphogenesis disorders caused by the absence of formation or the underdevelopment of functional syncitia, such as the syncitiontrophoblast, to promote the formation and/or the development of syncitia, such as the syncitiotrophoplast.
According to a particular embodiment ofthe present invention, patients suffering from cancers can be treated as follows:
- healthy cells, in particular healthy cells originating from a tissue similar to the tissue which carries tumoral cells, are taken from the patient,
- said healthy cells are transfected with a vector according to the invention, - transfected cells are administrated to the patient, in particular at a site close to the targeted tumor,
- the tumoral cells are induced to form syncitia by the transfected cells, and die.
The killing of tumor cells by syncitia formation promoted by fusogenic proteins is notably described in Bateman et al, (2002) Cancer Research 15: 6566-6578.
The present invention also relates to an antibody, characterized in that it is directed against a protein or a polypeptide as defined above.
The expression "antibody" as intended herein relates to monoclonal or polyclonal antibodies, as well as to antibody fragments.
Antibodies according to the invention can be obtained by methods well known to the man skilled in the art. For instance monoclonal antibodies can be produced according to Kohler and Milstein (1975) Nature 256:495-497 or Galfre et al (1977) Nature 266:522-550 and polyclonal antibodies can be produced according to Roda and Bolelli (1980) Journal of Steroid Biochemistry, 13 :449-454.
Antibody fragments according to the invention relate more particularly to Fab, F(ab') , or scFv fragments. Fab and F(ab')2 fragments are particularly well known to the man skilled in the art, and can be obtained respectively by papain and pepsin proteolytic cleavage of antibodies. scFv fragments are in particular described in Blazar et al. (1997) Journal of Immunology 159:5821-5833 or Bird et al. (1988) Science 242:423-426, advantageously scFv fragments are recombinant.
The present invention also relates to a purified natural human protein, characterized in that: it is recognized by an antibody as defined above and, it presents a fusogenic activity.
The present invention also relates to. a pharmaceutical or a vaccinal composition, comprising as active substance at least one substance selected from the group comprising: a protein or a polypeptide as defined above, a nucleic acid as defined above, a vector as defined above, or a cell as defined above; in association with a pharmaceutically acceptable vehicle.
A protein or a polypeptide according to the invention can be used for the treatment of abnormal syncitium formation and/or development, i.e. syncitium formation and/or development which does not occur under normal conditions, mediated by an above normal expression of Syncitin 2, by competing for Syncitin 2 receptor sites on cells. A protein or a polypeptide according to the invention could also be used to target compounds, in particular therapeutic compounds to cells which cany receptors for Syncitin 2.
Furthermore, a protein or a polypeptide according to the invention can be used for the immunosuppressive treatment of patients, such as patients afflicted with allergy, autoimmune disease or graft rejection.
Possibly, a protein according to the invention has anti-cancerous prophylactic properties and can be used for the manufacture of a vaccinal composition. As HERV-FRD is liable to be involved in cancer development due to its immunosuppressive activity which can induce immune tumor escape and due to its expression in tumors, administration of a protein according to the invention to a patient, could help preventing the development of tumors expressing this protein thanks to immunological reactions elicited in response to said administration.
In particular, proteins or polypeptides devoid of immunosuppressive activity according to the invention, such as the protein conesponding to SEQ ID NO: 65, are particularly useful since they have an antigenic activity similar to that of Syncitin 2 without the drawback of its immunosuppressive activity, they can therefore easily elicit an immune response against tumors expressing HERV-FRD. Vaccinal compositions comprising such proteins or polypeptides devoid of immunosuppressive activity are therefore particularly useful in anti- tumor prevention and/or therapy.
A nucleic acid according to the invention and a vector according to the invention can be used in gene therapy to compensate for a lower than normal expression of a fusogenic protein, in particular of Syncitin 2, notably in the placenta. Alternatively, such nucleic acids and vectors can be used to transfect tumor cells so as to induce tumor cell fusion and j consequently tumor destruction.
A cell according to the invention can be used to cure tissues which should undergo cell fusion but for which this function is impaired, or to promote the formation of syncitia in tumors.
According to a particular embodiment, the present invention relates to a vaccinal composition as defined above, comprising as active substance a protein or a polypeptide as defined above, in association with a pharmaceutically acceptable vehicle.
The present invention also relates to a pharmaceutical composition, comprising as active substance at least one substance selected from the group comprising: an antibody as defined above, an antisense sequence hybridizing to SEQ ID NO: 1, a RNAi comprising a sequence hybridizing to SEQ ID NO: 1, or an aptamer directed against a protein conesponding to SEQ ID NO: 2, in association with a pharmaceutically acceptable vehicle.
An antibody according to the invention can be used to prevent the binding of Syncitin 2 to its receptor on cells, thus preventing syncitium formation and/or development. Likely, an antisens sequence according to the invention is meant to impair the translation a Syncitin 2 encoding mRNA thus impairing its expression and as a consequence preventing syncitium formation and/or development.
Similarly, a RNAi (interference RNA) according to the invention prevents the expression of Syncitin 2, and as a consequence prevents syncitium formation and/or development.
An aptamer according to the invention is a nucleic acid, in particular a ribonucleic acid, the folding of which allows its binding to the Syncitin 2 protein so as to prevent the Syncitin 2 protein from promoting the formation and/or the develomment of syncitia.
The present invention also relates to the use of at least one substance selected from the group comprising: a protein or a polypeptide as defined above, a nucleic acid as defined above, a vector as defined above, or a cell as defined above; for the manufacture of a drug useful for the prevention and/or the treatment: - of cancers or,
- of pathologies involving a cellular fusogenicity disorder or a syncitium morphogenesis disorder, such as a placental morphogenesis disorder or,
- of an immune system disorder, in particular an immune system disorder requiring an immunosuppressive treatment, such as allergy, autoimmune disease or graft rejection.
Drugs according to the invention are useful for treating cancers by promoting the formation of syncitia by cancerous cells, which leads to cellular death. As mentioned before, the killing of tumor cells by syncitia formation promoted by fusogenic proteins is notably described in Bateman et al, (2002) Cancer Research 15: 6566-6578.
Drugs according to the invention can also be used to compensate for the absence of a functional Syncitin 2 in tissues in which it is normally present, such absence leading to a fusogenicity disorder or a syncitium morphogenesis disorder, in which the physiologic formation of a syncitium is impaired or prevented. In the case of placental morphogenesis, an impaired or deficient syncitium formation results in infertility.
Finally, drugs according to the invention could be used as anti-tumor vaccines, whereby the administration of said drugs to an individual could lead to an immunological reaction directed against said drugs, thus controlling and/or destroying tumor which express said the Syncitin 2 protein.
The present invention also relates to a method for detecting the Syncitin 2 protein or for measuring the concentration ofthe Syncitin 2 protein in a biological sample, characterized in that it comprises a step of contacting said biological sample with an antibody as defined above.
Such methods are useful for the diagnosis of pathologies in which the expression of Syncitin 2 is modified. Such methods are also useful for assessing transfection efficiency in gene therapy assays in which nucleic acids according to the invention are introduced into cells.
According to a prefened embodiment of the invention, the biological sample is a placental sample.
The present invention also relates to a method for detecting the Syncitin 2 mRNA or for measuring the concentration of the expression of the Syncitin 2 mRNA in a biological sample, characterized in that it comprises a step of contacting said biological sample with at least one nucleic acid as defined above.
The Syncitin 2 mRNA expression detection or measure methods which can be used with nucleic acids according to the invention notably comprise Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), Nuceic Acid Based Sequence Amplification
(NASBA), in situ hybridization and Northern blot. Such methods are well known to the man i skilled in the art.
Such methods are useful for the diagnosis of pathologies in which the expression of Syncitin 2 is modified. Such methods are also useful for assessing transfection efficiency in gene therapy assays in which nucleic acids according to the invention are introduced into cells.
According to a prefened embodiment of the invention, the biological sample is a placental sample.
According to a prefened embodiment of the invention, in the above defined detection method, the nucleic acids conespond to SEQ ID NO: 3 and SEQ ID NO: 4. Advantageously, nucleic acids conesponding to SEQ ID NO: 3 and 4 can be used as primers for the detection or for the assessment of the concentration of the Syncitin 2 mRNA by RT-PCR, in particular by real-time quantitative RT-PCR using the following procedure:
RNA is first extracted from biological samples in which the Syncitin 2 mRNA concentration is to be assessed, according to methods well known to the man skilled in the art. RNA concentration is then quantified spectrophotometrically. Five micrograms of each RNA sample are submitted to DNAse treatment to eliminate DNA contaminants. One microgram of RNA from each sample is reverse transcribed using a virus Reverse Transcriptase, notably in presence of a ribonuclease inhibitor, deoxynucleotides, MgCl2, KCl, and random hexamers. The complementary DNAs thus obtained are then diluted in nuclease-free water. Real-Time quantitative PCR is achieved using a complementary DNA equivalent of 20 ng of total RNA notably in presence of a thermostable polymerase, the primers according to the invention, deoxynucleotides and MgCl2. The amplification is performed using a 2 min step at 50°C, a 10 min denaturation step at 95°C, followed by 40 cycles of 15 s denaturation at 95°C, 1 min primer annealing and polymerization step at 60°C. To normalize for differences in the amount of total RNA added to the reaction, amplification of 18S total ribosomal RNA was performed as an endogenous control. The relative expression in each sample is calculated with respect to a standard calibration curve (e.g. dilution series of genomic DNA).
A method for the in vitro diagnosis of pathologies linked to the level of expression of Syncitin 2 in a tissue, comprising the following steps:
- taking a tissue sample from an individual,
- measuring, in said sample, the concentration Syncitin 2 mRNA, or the concentration of the Syncitin 2 protein.
Advantageously, measure and detection methods as described above can be used in the
\ in vitro diagnosis method according to the invention.
The present invention also relates to a method for the screening of drugs liable to modify the fusogenic activity of a polypeptide or a protein as defined above, characterized in that a drug to screen is contacted with cells expressing said polypeptide or protein, and the presence or the absence of formation of a syncitium by said cells is observed.
Drugs which lead to the absence of formation of a syncitium can be used to block abnormal syncitium formation and/or development, such as in trophoblast invasion which occurs in choriocarcinoma. Drugs which lead to the formation of a syncitium can be used to promote the formation and/or the development of syncitium, for instance in cases where there is an absence of formation and/or an underdevelopment of functional syncitia.
Description of the figures
Figure 1. Structural organization and characteristic features of the 16 identified HERV envelopes. Hydrophobicity profiles and characteristic domains of the 16 HERV envelope proteins (the 6 HERV-K HML2 envelopes being almost identical are represented by a unique protein) and ofthe Moloney murine leukemia virus envelope. The black rectangles delineate the open reading frames, and the gray rectangles at the end of R and Fc2 envelope represent the short reading frames present downstream of the stop codon. Stripped boxes conespond to hydrophobic regions associated with the fusion peptide and the transmembrane region, respectively ; the « CWLC » motifs (consensus C-X-X-C) and the proteolytic cleavage sites (consensus R/K-X-R/K-R) are represented with pale and dark gray vertical bars respectively, and their sequence are indicated in the right part of the figure; the putative immunosuppressive domain is represented with a gray box.
Figure 2. SDS-PAGE analysis of the radiolabelled proteins produced upon direct in vitro transcription / translation assays of the amplification products of the coding retroviral envelope genes obtained from the conesponding BAC clones.
Arrowheads point to the translation products ofthe expected size for each envelope gene. Bands of higher molecular weight are observed for envF(c)2, most probably associated with the presence of a frameshift signal at the env gene 3' end.
Figure 3 A and Figure 3B. Envelope-mediated cell-cell fusion. (Figure 3 A) Construction of envelope-expressing vectors and rationale of the fusion assay. Each ofthe 16 envelope genes was PCR-amplified from BAC DNA and cloned into the phCMV expression vector. The env genes inserted in-between the β-globin intron and pA sequences are schematized with the putative cleavage site between the surface (SU) and the transmembrane (TM) envelope subdomains. Cells were transfected with the env-expressing vectors and stained with May- Grϋnwald and Giemsa solutions 12 h (for the G355-5 cells) or 36 h (for the other cell types) after transfection. Fusion indices were calculated as indicated in Materials and Methods. (Figure 3B) Syncytia formation by HERV envelope glycoproteins in various cell types. Cells were transfected with vectors expressing the HERV-FRD envelope (ezϊvFRD), the HERV-W envelope (envW), or an 'empty' vector (none). Figure 4. Primary sequence, hydrophobicity profile, and predicted features of the HERV- FRD envelope. The SU and TM moities of the envelope are delineated, with the canonical RVRR cleavage site between the two subunits underlined (consensus: R/K-X-R/K-R); in the TM subunit, the hydrophobic fusion peptide and transmembrane domains are shaded in light gray, and the putative immunosuppressive domain (ISU) in dark grey; in the SU subunit, the canonical CWLC domain involved in SU-TM interaction, is underlined.
Figure 5. Northern blot analysis of HERV-FRD env expression in human tissues. Poly(A)+ RNAs (Ambion, Human Northern Blot 2) were probed with an antisense-strand HERV-FRD env riboprobe. Exposure time 12 h.
Figure 6A and Figure 6B. Conservation of the HERV-FRD env locus and open reading frame upon primate evolution. (Figure 6A) Slot-blot of genomic DNA from simian, prosimian, cat and mouse species, probed with a full-length HERV-FRD env fragment. The infened date of insertion of HERV-FRD is indicated with an anow on the primate phylogenetic tree on the left. NWM: New World Monkey. (Figure 6B) In vitro transcription- translation assay of the human HERV-FRD env gene and of the orthologous genes from the indicated simian species. Env genes were PCR-amplified as schematized, submitted to in vitro transcription/translation ('control' is without DNA template), run on a polyacrylamide gel and autoradio graphed. The anow points the bands ofthe expected size.
Figure 7. Fusion activity of the orthologous primate ERV-FRD envelope glycoproteins. The indicated target cells were transfected as indicated in Figure 3A with vectors expressing the human or simian orthologous ERV-FRD envelopes, and fusion indices were determined as j indicated in Table 2 (means± standard deviations; n = 5).
Figure 8A and Figure 8B. Infection assays using retroviral particles pseudotyped with the HERV-FRD and control envelopes. (Figure 8A) Rationale of the assay. To determine whether the HERV-FRD envelope can confer infectivity on MLV, HIV or SIV Env-defective pseudoparticles, conesponding pseudotype viruses were produced by cotransfecting 7.5 x 105 293T cells with 0.55 μg ofthe phCMV-HERV-FRD vector expressing the HERV-FRD envelope (or pcDNA3 for the negative -none- control, and phCMVampho for the amphotropic MLV envelope positive control), 1.75 μg of a vector encoding the retroviral proteins (except the envelope) of MLV (phCMVintron) HIV (pCMVΔR8.91) or SIV (pSIV3+), and 1.75 μg of the conesponding defective retroviral vectors marked with a β-galactosidase-reporter gene " (pMFGsnls/αcZ; pHR'CMV/ cZ; R9SA), using calcium phosphate precipitation (Invitrogen). 36 h post-transfection, viral supernatants were collected and filtered through 0.45-μm-pore-size membranes. Target cells (murine 3T3, feline G355-5, or human TE671, HeLa and 293T cells) were seeded in 24-well plates at a density of 104 cells per well and incubated overnight at 37°C. 5-500 μl of virus samples containing 4 μg of Polybrene per ml were added to the cells and centrifuged for spinoculation at 1,200 x g for 2 h 30 min at 25°C (10). After removal of the supernatants, the cells were incubated in regular medium for 60 h at 37°C. Viral titers were then measured upon by X-Gal staining of the cells and expressed as lacZ Colony Forming Unit (CFU) per milliliter of viral supernatant. (Figure 8B) hifectivity of SlV-based retroviral particles pseudotyped with the HERV-FRD envelope (or with no protein in the cSIV-none' control), as assayed using human 293T cells as target cells and X-gal staining, following the protocole described in (Figure 8A).
Figure 9. Infection / cell-cell fusion, activities and host range of the HERV-FRD and simian orthologous envelopes. Upper panel: Infection of feline (G355.5), human (293T and HeLa) and murine (3T3) cells by STV-based particles pseudotyped with the indicated ERV-FRD envelopes. Same experimental conditions as in Figure 8A, with negative and positive control values as in Table 1. NWM: New World Monkey (Callithrix jacchus marmoset). Lower panel: Cell-cell fusion assay for the ERV-FRD envelopes and cells as in the upper panel. The G355-5 and HeLa cells were transfected using Lipofectamine (Invitrogen, 2 μg of DNA for 5xl05 cells), and the 293T and TE671 cells using calcium phosphate precipitation (Invitrogen, 5 μg of DNA for 5xl05 cells). Fusion activities were measured 12 to 36 h post-transfection ofthe conesponding expression vectors. To visualize syncytia, cells were fixed in methanol and stained by adding May-Grϋnwald and Giemsa solutions (Sigma) according to the manufacturer's instructions. The fusion index, which represents the percentage of fusion events in a cell population is defined as [(N-S)/T] x 100, where N is the number of nuclei in the syncytia, S is the number of syncytia, and T is the total number of nuclei counted.
Figure 10A and Figure 10B. Comparison of the simian ERV-FRD envelopes and identification of a unique point mutation responsible for the gibbon envelope loss-of- function. (Figure 10 A) Aligned primary sequences ofthe HERV-FRD and simian orthologous envelopes. Abbreviations are: Hu:homo sapiens; Cpz: chimpanzee; Go: gorilla; Oo: orangutan; Gib: gibbon; Mcq: macaque; Nwm: New World Monkey. Accession numbers are AL136139 for the human gene, and AJ577595 to AJ577600 for the simian genes. The RVRR canonical motif for SU-TM cleavage is darkened, and the predicted transmembrane hydrophobic domain is boxed. Aminoacids differing between the human and gibbon proteins are indicated with an asterisk, among which those unique to the gibbon sequence are grayed. The two aminoacids in the TM moiety of the gibbon protein that were mutated and assayed for reversion to the infectious phenotype are indicated with an arrow. (Figure 10B) Infection of feline (G355-5) and human (293T) cells by SIV-based particles pseudotyped with the wild type (wt) and mutant (F490->L or T532->N) gibbon FRD envelopes, with the human FRD envelope as a control. The indicated aminoacid changes in the gibbon envelope were performed by a three-fragment ligation, using PCR fragments generated with oligonucleotides containing the gibbon-to-human single-base mutations (TTT->CTT and AAT->ACT for aminoacid positions 490 and 532, respectively), and subsequent sequencing of the resulting constructs. Infection assays were performed as described in Figure 8A. The viral titers are average from two independent experiments.
Examples
Example 1
Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins
Materials and Methods
Computer sequence analyses
Homology searches were performed using the BLASTN program at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/BLAST), screening the finished (nr) and unfinished (htgs) databases with consensus envelope genes for each family. Hydropathy of the envelope proteins was calculated by the Kyte-Doolittle method implemented by the DNA Strider program (Marck, C. 1988. 'DNA Strider': a 'C program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers. Nucleic Acids Res. 16:1829- 36). Alignments were performed with the CLUSTALW multialignment program at Infobiogen (http://www.infobiogen.fr). Chromosomal localizations ofthe coding env genes were performed at the Ensembl web site (http://www.ensembl.org/Homo sapiens).
In vitro transcription /translation assay
Amplification of the coding env genes for in vitro transcription / translation assays was performed with the Expand Long Template PCR System (Roche, Indianapolis, IN). PCRs were carried out for 35 cycles (1 min at 94°C, 30 s at 58°C, 2 min at 68°C), using 1 ng of BAC DNA. Primers were as follows: envHT7.3
(GCTAATACGACTCACTATAGGAACAGACCACCATGCACCACAGTATCAACCTTA C) (SEQ ID NO: 5) and AR2B1 (TTCTGTTTCAGCTACAACTCTGT) (SEQ ID NO: 6) for envHl; envHT7.3 and flRB2 (AGCAATAGTTTGTTAAATTC) (SEQ ID NO: 7) for envH2; envHT7.2
(GCTAATACGACTCACTATAGGAACAGACCACCATGAGGGCACCCTCCAATACTT C) (SEQ ID NO: 8) and ARB3 (ACCCCATGTTCTAGTCTTCC) (SEQ ID NO: 9) for envH3; envKT7
(GCTAATACGACTCACTATAGGAACAGACCACCATGGAGATGCAAAGAAAAGCA) (SEQ ID NO: 10) and LTRenvsK (GTGAACAAAGGTCTTTGCATCATAG) (SEQ ID NO: 11) for envKl, envK3, envK5 and envK6; envKT7 and 3'fl51C12 (GAATTAGGCTTTCGGGACTTGAA) (SEQ ID NO: 12) for envK2; envKT7 and KLTR3' (C/TTTAAC/G/AG/AAGCATGCTGC/AC) (SEQ ID NO: 13) for envK4, envTT7.2 (GCTAATACGACTCACTATAGGAACAGACCACCATGTTGGATTCATCACTCCCA) (SEQ ID NO: 14) and envTflanq2 (CTGAAGGGAGTTCCTCCTAGG) (SEQ ID NO: 15) for envT, enyWT7
(GCTAATACGACTCACTATAGGAACAGACCACCATGGCCCTCCCTTATCAT) (SEQ ID NO: 16) and envW64flR2 (ACAGCCAAGCAGGTACAG) (SEQ ID NO: 17) for envW, envFRDT7.2
(GCTAATACGACTCACTATAGGAACAGACCACCATGCTCCTGCTGGTTCTCATTC) (SEQ ID NO: 18) and envFRDfl3' (CTGCAGCAGACTCCATCCTTG) (SEQ ID NO: 19) for envFRD, enverv3T7
(GCTAATACGACTCACTATAGGAACAGACCACCATGACTAAAACCCTGTTGTATC A) (SEQ ID NO: 20) and enverv3AS (GTTAATACTTAGTTAGGGCC) (SEQ ID NO: 21) for envR, HS89F2T7
(GCTAATACGACTCACTATAGGAACAGACCACCATGGATCCACTACACACGATTG A) (SEQ ID NO: 22) and HS89R3fl (TGTTTTGGGACACCACGAAT) (SEQ ID NO: 23) for envR(b), envF(c)2T7
(GCTAATACGACTCACTATAGGAACAGACCACCATGAATTCTCCATGTGAC) (SEQ ID NO: 24) and envF(c)2flR3 (GACACTTAATAGTTGCGACA) (SEQ ID NO: 25) for envF(c)2, envF(c)lT7
(GCTAATACGACTCACTATAGGAACAGACCACCATGGCCAGACCTTCCCCACTAT GC) (SEQ ID NO: 26) and envF(c)lfl3' (GCCTTGGCAACTAAACCATTC) (SEQ ID NO: 27) for envF(c)l. T7 promoter-containing PCR products were ethanol precipitated and 200 ng of the amplification products were used in the TNT Coupled Reticulocyte Lysate System (Promega Corp., Madison, WI) according to the manufacturer instructions, with ( H) methionine (ICN
Biomedicals Inc., Irvine, CA) for protein labeling. After elecfrophoresis of the translation products, the SDS-polyacrylamide gels were impregnated in Amplify (Amersham
Biosciences, Piscataway, NJ), rinsed with water, dried and autoradiographed.
Tissue samples, RNA calibration and reverse transcription
Human BAC clones containing the identified coding envelope genes were purchased from BACPAC Resources (Oakland, CA). RNA from various human tissues were purchased from Clontech (Palo Alto, CA), Stratagene (La Jolla, CA) and Ambion (Austin, TX). Quality ofthe RNA was assessed on a RNA LabChip (Agilent 2100 Bioanalyzer), and RNA concentration was quantified spectrophotometrically. Five micrograms of each RNA sample were submitted to DNAse treatment (DNA-free, Ambion) to eliminate DNA contaminants. One microgram of RNA from each sample was reverse transcribed in a 20 μl volume reaction using 50U Moloney murine leukemia virus Reverse Transcriptase, 20U ribouclease inhibitor (Applied Biosystems, Foster City, CA), 1 mmol L dA/T/G/C (Amersham-Pharmacia Biotech, Upsala, Sweden), 5 mmol L MgCl2, 10 mmol/L Tris-HCl (ρH8.3), 10 mmol/L KCl, and 50 pmol/L of random hexamers (Applied Biosystems). The complementary DNAs were then diluted 1/25 in nuclease-free H2O (Promega Corp.).
Real-Time quantitative PCR
Oligonucleotides were designed using the computer program Oligo (MedProbe, Oslo, Norway). The special requirements were a Tm of 60° and an amplicon length comprised between 80 and 350 bp. Oligonucleotides were purchased from MWG (Ebersberg, Germany). Real-Time quantitative PCR was achieved using a complementary DNA equivalent of 20 ng of total RNA. The reaction was performed in 25 μl using SYBR Green PCR Core Reagents (Applied Biosystems, Foster City, CA) according to the manufacturer's instructions. PCR was developed with the ABI PRISM 7000 Sequence Detection System (Applied Biosystems). Amplification was performed using a 2 min. step at 50°C then a 10 min. denaturation step at 95 °C, followed by 40 cycles of 15 s denaturation at 95 °C, 1 min. primer annealing and polymerization step at 60°C. To normalize for differences in the amount of total RNA added to the reaction, amplification of 18S total ribosomal RNA was performed as an endogenous control (less than a factor of 3.5 variation). Primers and probe from 18S RNA were purchased from Applied Biosystems. The relative expression in each sample was calculated with respect to a standard calibration curve (the dilution series of genomic DNA). Each sample was analyzed at least twice.
The control plasmid (p 11 env) containing the 11 envelope amplicons obtained with the primers listed in Table 3 was constracted by first cloning each amplicon into the pGEMT vector, and then by successive three-fragment ligations using fragments from these 11 plasmids and from construct intermediates. A confrol series of pllenv plasmid dilutions ranging from 1 ng to 0.008 ng was amplified with each primer set to measure their relative yield (less than a factor of 2 variation). A control tube containing 1 ng ofthe pllenv plasmid was included in each Real-Time PCR assay as a reference. Table 3 : Sequence of the primers used to detect the expression of the coding envelopes by quantitative RT-PCR analysis
Gene Primers sequence (5 '-3') SEQ ID envHl F : TTCACTCCATCCTTGGCTAT SEQ ID NO : 28
R : CGTCGAGTATCTACGAGCAAT SEQ ID NO : 29 envHl F : ACTACACACATCACTGAAACAAA SEQ ID NO : 30
R : GGATGGAGTGAAATACAGGAC SEQ ID NO : 31 envΑ3 F : CCCTCCTCCACATTTATTTG SEQ ID NO : 32
R : GTTGGGCTTTGGAGATGG SEQ ID NO : 33 envK F : CACAACTAAAGAAGCTGACG SEQ ID NO : 34
R : CATAGGCCCAGTTGGTATAG SEQ ID NO : 35 envT F : CCAGGATTTGATGTTGGG SEQ ID NO : 36
R : GGGGTGAGGTTAAGGAGATGG SEQ ID NO : 37 envW F : CCCCATCGTATAGGAGTCTT SEQ ID NO : 38
R : CCCCATCAGACATACCAGTT SEQ ID NO : 39 eravFRD F : GCCTGCAAATAGTCTTCTTT SEQ ID NO : 3
R : ATAGGGGCTATTCCCATTAG SEQ ID NO : 4 eravR F : CCATGGGAAGCAAGGGAACT SEQ ID NO : 40
R : CTTTCCCCAGCGAGCAATAC SEQ ID NO : 41 envR(b) F : GGACAGTGCCGACATACTAT SEQ ID NO : 42
R : TAGAGTGCAGCATCCTAACC SEQ ID NO : 43 envF(c)2 F : ATGGAGGACTATATGAGCACAA SEQ ID NO : 44
R : ATTAAAGTTAACCACGAGAAGC SEQ ID NO : 45 envF(c)l F : GGGCCACTAAGTTACTAGGTC SEQ ID NO : 46
R : AGTTAGGAGGGAGTTACTGGG SEQ ID NO : 47
Screening of human databases for coding envelope genes
The rationale of the screening procedure to identify the coding envelopes in the human genome is summarized below. '
Briefly, the Repbase database (final control search with Update 8.2.1, Oct. 2002) (Jurka, J. 2000. Repbase update, a database an an electronic journal of repetitive elements. Trends Genet. 16:418-420) in which each family is represented by a « consensus » element, built from an alignment of all the proviruses belonging to the same family (i.e. copies which cluster together in phylogenetic trees) was used. It was implemented by RT- and TM-based searches as in (refs. Benit, L., P. Dessen, and T. Heidmann. 2001. Identification, phylogeny, and evolution of retroviral elements based on their envelope genes. J. Virol. 75:11709-11719 and Tristem, M. 2000. Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening ofthe human genome mapping project database. J. Virol. 74:3715-3730) which revealed two additional families (namely the F(c)l and F(c)2 families).
Overall, approximately 100 HERV families were identified. For each family, the envelope gene was tentatively delineated, with the pol gene (which was easily positioned due to its high conservation among retroviral elements) at its 5' end, and with the retroviral LTR at its 3' end. When the distance between the pol gene and LTR was higher than 1.4 kb (the average length of an envelope gene being 1.9 kb), the envelope gene was considered as potentially complete and the HERV family retained. The resulting list of the 34 conesponding HERV families is given in Table 1.
Table 1: HERV families containing full-length envelope genes
Family name1 Repbase identifier Class Total Number of Number of number of elements with elements with elements2 full-length env coding env genes genes
HERV-H HERVH I 1000 43 3
HERV-IP HERVIP10FH I 60 38 0
HERV-9 HERV9 I 1000 37 0
HERV-K HML-2 HERVK II 50 35 6
HERV-K HML-8 HERVK11 II 100 31 0
HERV-K HML-5 HERVK22 II 15 25 0
HERV-E HERVE I 150 22 0
HERV-T HERVS71 I 100 19 1
HERV-S HERV18 III 60 19 0
HERV-Z69907 MER66 I 100 18 0
HERV-ADP HERVP71A I 50 17 0
HERV-K HML-6 HERVK3 II 100 17 0
HERV-P HUERS-P3 I 100 13 0
HERV-W HERV17 I 100 13 1
HERV-F HERVFH19 I 50 11 0
HERV-U3 HERV-L66 III 30 10 0
HERV-K HML-7 HERVK11D II 20 10 0
MER57(A) I 150 10 0
RRHERV-I HERV15 I 30 10 0
HERV-U2 PRIMA41 III 100 10 0
HERV-I / FTD HERVI I 50 8 0
PRIMA4 I 100 8 0
HERV-FRD MER50 I 100 8 1
HERV-K HML-10 (C4) HERVK14 II 20 7 0
HERV-K HML-3 HERVK9 II 150 6 0
HERV-R / erv3 HERV3 I 100 6 1
HERV-R(b) PABL B I 10 6 1
MER70 III 100 6 0
HERV-XA34 HERVFH21 I 30 5 0
HERV-F(c)2 - I 15 5 1
HERV-U4 MER83 I 10 4 0
HERV30 I 40 1 0
HERV-K HML-4 HERVK13 II 20 1 0
HERV-F(c)l - I 2 1 1 total -4,000 476 f 16 refers to names given in original publications, most ofthe time following the PBS-related nomenclature
(reviewed in Tristem, 2000 and Benit et al., 2001). 2 estimates based on the number of hits obtained in blast searches with the consensus provirus against human databases.
For each family, a BLAST query was then performed on human genome databases using the envelope gene as a probe. Overall, it yielded 476 potentially complete envelope genes (see Table 1 for their distribution among the HERV families). The coding status of each identified env gene was finally assessed, and only those with an open reading frame beginning at the first Met codon of the consensus envelope gene and uninterrupted over >90% of this gene were retained. Among the 476 envelope genes that were individually analyzed, only 16 genes were found to potentially encode envelope proteins.
These 16 genes are listed and described in Table 2 and Figure 1.
Table 2 : The 16 coding envelope genes ofthe human genome.
Gene name Chrom. Accession Position of uie Bibliographic References localizatio number envelope in name sequence entry" envRl 2q24.3 AJ289709 (6313-8067) + envH ρ62, de Parseval et al, 2001;
H19 Lindeskog et al, 1999 envΗl 3q26 AJ289710 (5393-7084) + envH/p60 de Parseval et al, 2001 envH3 2q24.1 AJ289711 (5204-6871) + envH/p59 de Parseval et al, 2001 envKl 12ql4.1 AC074261 (93508-95604) + - SEQ ID NO: 48 envK2 7p22.1 AC072054 (30365-32464) - HML-2.HOM, Mayer et al, 1999; (38869-40968) -b K(C7), Tδnjes et al, 1999; HERV-K108 Barbulescu e^ α/., 1999 envK3 19ql2 Y17833 (5581-7680) + HERV-K (C19) Tδnjes et al, 1999 envKA 6ql4.1 AF164615 (6412-8508) + HERV-K109 Barbulescu eϊ α/., 1999 envK5 19pl3.11 AY037928 (6451-8550) + HERV-K113 Turner et al, 2001 envK6 8p23.1 AY037929 (6442-8541) + HERV-K115 Turner et al, 2001 envT 19pl3.11 AC078899 (154738-156618) + - SEQ ID NO; 50 envW 7q21.2 AC000064 (35879-37495) + syncytin Blond et al, 1999 ewvFRD 6p24.1 AL136139 (21355-22972) - - SEQ ID NO: 1 envR 7ql l.21 AC073210 (54963-56978) - erv3 Cohen et al, 1985 eflvR(b) 3p24.3 AC093488 (78681-80225) + - SEQ ID NO: 52 envF(c)2 7q36.2 AC016222 (85216-86963) + - SEQ ID NO: 54 e«vF(c)l Xq21.33 AL354685 (46744-48717) - - SEQ ID NO: 56
+ and - designate orientation in the sequence entry b the HML-2.HOM / K(C7) / HERV-K108 locus is organized as a tandem repeat in some individuals, with 100% nt identity for two the envelope genes.
Ten of these genes had previously been identified (Barbulescu, M., G. Turner, M. I. j
Seaman, A. S. Deinard, K. K. Kidd, and J. Lenz. 1999. Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. Cun. Biol. 9:861-868, Blond, J.-L., F. Beseme, L. Duret, O. Bouton, F. Bedin, H. Penon, B. Mandrand, and F. Mallet. 1999. Molecular characterization and placental expression of HERV-W, a new human endogenous retrovirus family. J. Virol. 73:1175-1185, Cohen, M., M. Powers, C. O'Connell, and N. Kato. 1985. The nucleotide sequence of the env gene from the human provirus erv3 and isolation and characterizatio of an erv3-specific cDNA. Virology. 147:449-458, de Parseval, N., J. F. Casella, L. Gressin, and T. Heidmann. 2001. Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates. Virology. 279:558-569, Lindeskog, M., D. Mager, and J. Blomberg. 1999. Isolation of a human endogenous retroviral HERV-H element with an open env reading frame. Virology. 258:441-450, Mayer, J., M. Sauter, A. Racz, D. Scherer, N. Mueller- Lantzsch, and E. Meese. 1999. An almost-intact human endogenous retrovirus K on human chromosome 7. Nature Genet. 21:257-258, Tδnjes, R. R., F. Czauderna, and R. Kurth. 1999. Genome-wide screening, cloning, chromosomal assignment, and expression of full-length human endogenous retrovirus type K. J. Virol. 73:9187-9195, Turner, G., M. Barbulescu, M. Su, M. I. Jensen-Seaman, K. K. Kidd, and J. Lenz. 2001. Insertional polymorphisms of full-length endogenous retroviruses in humans. Cun. Biol. 11:1531-1535), and six new genes emerged from this screen, including genes from the FRD, T, R(b), F(c)l and F(c)2 families, and one supplementary gene from the HERV-K (HML-2) family. The chromosomal localization was determined or confirmed using the Ensembl web site and the conesponding accession numbers. Noteworthy, one of these genes, namely envK2, can be found in duplicate in some individuals since the conesponding provirus is organized as a tandem repeat (Reus, K., J. Mayer, M. Sauter, D. Scherer, N. Muller-Lantzsch, and E. Meese. 2001. Genomic organization of the human endogenous retrovirus HERV-K(HML-2.HOM) (ERVK6) on chromosome 7. Genomics. 72:314-320). The two env sequences being 100% identical at the nucleotide level, both will be further refened to as the e«vK2 gene. As can be observed in Figure 1 which describes the 16 putative envelopes in comparison with the Moloney leukemia virus envelope, the overall length of he proteins is variable, with a minimum of 514 aa for EnvR(b) and maximum of 699 aa for EnvK. This size variability is also found among exogenous retroviral envelopes since, for example, HTLV-1 and HIV-1 envelopes are 488 and 861 aa long, respectively.
To ascertain the existence of the open reading frames infereed from the nucleotide sequences, an in vitro transcription-translation assay was performed using human BAC clones containing the identified coding envelope genes. The 16 BACs were obtained from BACPAC Resources (Oakland, CA), except for the HI, H2 and H3-containing BACs that had been cloned previously (de Parseval, N, J. F. Casella, L. Gressin, and T. Heidmann. 2001. Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates. Virology. 279:558-569). The in vitro transcription-translation assay was performed directly on the env gene PCR products (generated using a forward T7-containing primer at the env 5' end and a reverse primer downstream of the stop codon). In all cases, translation products ofthe size expected from the sequences in the database were obtained (indicated with anowheads in Figure 2). For some envelopes, additional bands of lower molecular weight were observed, compatible with initiation at internal sites, and interestingly in one case (i.e. F(c)2) additional bands at higher molecular weight were detected, most probably associated with the presence at the gene 3' end of a frameshift signal (Benit, L., A. Calteau, and T. Heidmann. in press. Characterization of the low copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes. Virology).
The predicted hydrophobic profiles of the 16 proteins represented in Figure 1 allow the identification of characteristic domains of these envelopes, namely the fusion peptide, located just downstream ofthe proteolytic cleavage site between the SUrface (SU) and TransMembrane (TM) moieties of the envelopes, and the transmembrane domain of the TM subunit which permits the anchorage of the envelope in the membrane. Noteworthy, this analysis revealed that one envelope (EnvR) seems to be devoid of a fusion peptide, and that two envelopes (EnvR and EnvF(c)2) disclose a premature stop codon just upstream of their transmembrane hydrophobic domain. Two other domains are delineated in Figure 1. which are characteristic features of the envelopes belonging to the C-type and D-type retroviruses : the CWLC domain, involved in the interaction between the SU and the TM moieties (Pinter, A., R. Kopelman, Z. Li, S. C. Kayman, and D. A. Sanders. 1997. Localization of the labile disulfide bond between SU and TM of the murine leukemia virus envelope protein complex to a highly conserved CWLC motif in SU that resembles the active-site sequence of thiol-disulfide exchange enzymes. J. Virol. 71:8073-8077), and the CKS17-like immunosuppressive domain (Cianciolo, G. J., T. Copeland, S. Orozlan, and R. Snyderman. 1985. Inhibition of lymphocyte proliferation by a synthetic peptide homologous to retroviral envelope protein. Science. 230:453-455). Noteworthy, as B-type, lenti-, and spuma- retroviruses envelopes, the 6 EnvK lack these two latter domains.
Transcriptome of the coding envelope genes : strategy
To get insight into the expression profile of these genes in a quantitative manner, the Inventors devised a Real-Time RT-PCR strategy which uses specific primers designed in such a way that only envelope genes with an open reading frame should be amplified among all the envelope genes of a given family. To do so, for each HERV family comprising a member with a coding element, env nucleotide sequences were aligned with the CLUSTALW program and primers were designed within domains of maximal divergence between the coding copy and the other copies. Primers for Sybr Green amplification were devised with their 3 '-ends forced at nucleotide positions with, again, maximum divergence between the coding sequence and the others. For the HERV-K (HML-2) family which contains six coding env genes, this strategy could not be applied due to the too high sequence conservation between copies. In this case, specific primers were devised that matched all six coding genes, tentatively excluding most other HERV-K (HML-2) envelope genes. The complete list of devised primers is given in Table
3.
To determine whether the resulting primers fulfilled the requirements for both efficiency and specificity, a first series of assays was performed by PCR amplification of human genomic DNA. As expected, in all cases a single band was observed, thus excluding non-specific amplifications or amplifications of elements of unusual size (data not shown). Then, PCR products for each couple of primers were cloned into a pGEM-T vector and at least 6 clones per amplicon were sequenced for each envelope (26 clones for the HERV-K (HML-2) family, see below), hi all cases, the 6 clones for a given envelope were identical and unambiguously corresponded to the coding sequence, being different from all the other aligned sequences within each HERV family. For the HERV-K (HML-2) family, 26 clones were sequenced, among which 21 had an identical sequence conesponding to the sequence of the 6 coding envelopes, and 5 which conesponded to two other HERV-K (HML-2) envelope genes. Despite this parasitic amplification of non coding envelopes, the HERV-K (HML-2) coding envelope primer set was retained since it allowed the amplification of at least all the coding envelopes.
A second series of assays was then performed to determine the yield of each couple of primers to normalize env expression levels. To do so, a single plasmid (see Materials and Methods) which contained the complete set of 11 amplicons (the 6 envK. (HML-2) being amplified by the same primer set) was constructed. This plasmid, used as a « control » matrix for each couple of primers, actually allowed a refined normalization for possible differences in the yield ofthe various primers, and was used in each Real-Time amplification below. j
Transcriptome of the coding Envelope genes : survey of human tissues
A systematic screening of the expression level of the 16 coding env genes present in the human genome was achieved with the primers listed above, on a series of 19 healthy human tissues (Table 4). Table 4: Transcript levels ofthe 16 coding retroviral envelope genes ofthe human genome in a panel of 19 healthy human tissues.
Figure imgf000030_0001
The values are determined by real-time quantitative PCR. Each value is expressed as the mean standard deviation relative to the value for a reference control plasmid assayed in each real-time PCR experiment after correction for total RNA content in each tissue extract (using the 18S transcript as an internal control). PBL, peripheral blood lymphocytes.
Briefly, RNA were submitted to DNAse treatment and reverse transcribed using MLV RT, and a first Real-Time quantitative PCR was performed using primers for rRNA 18S to normalize for differences in the amount of total RNA added to the reaction (less than a 3.5-fold variation among samples). Real-Time PCR was then performed for each couple of specific primer. Control PCRs performed on RNA without the RT step never resulted in any amplification, as expected. The expression levels represented in Table 4 disclose several interesting features.
Firstly, there is an enormous variation in the level of expression (up to 4 log) among the different tissues for a given gene as well as among the different env genes. Secondly, and at a more refined level, it appears that all genes are transcribed at a significant level in the testis, still with variations (over a 100-fold) depending on the gene tested. Thirdly, the placenta is the organ where maximal expression can be observed, for the three R, W, and FRD genes, but the other env genes are very poorly or even not expressed in this organ. Fourthly, thyroid discloses a specific and high level expression ofthe envT gene, not observed for the other env genes in this organ. Fifthly, there is no expression of coding env genes in heart and liver, except for envR (the lowest level of expression for this gene).
Finally, two groups of coding envelope genes can be infened from these transcriptional data: the envelope genes which disclose a severe tissue-specificity together with an overall low expression level, namely the 3 envH, envR(b), envF(c)l and envF(c)2, and the envelope genes which are transcribed in the majority of the tissues, namely the 6 envK, envT, envW, envFRD and envR. This latter gene is singular as its level of expression is extremely high in all tissues tested, with actually the highest value among all coding env genes (with the exception of the thyroid, for en T).
A limited number of retroviral coding envelope genes
The extensive survey of the human genome performed here reveals that among the > 10,000 retroviral elements clustered into approximately 100 families, only 16 possess a coding retroviral envelope gene (Table 1 and Figure 1). The most important contributor to the coding envelope genes is the HERV-K (HML-2) family, since it comprises 6 coding envelopes out ofthe 35 full-length envelope copies.
The status ofthe HERV-K (HML-2) family is unique among the coding env-containing families in several respects. Although elements of this family first entered the primate genome more than 30 million years ago (36), new proviral copies have been generated in the recent past. Actually, the entry date in the human genome of 4 out of the 6 HERV-K (HML-2) proviruses with a coding env gene has been estimated to be less than 5 million years ago (ref. 2 for K2, K3, K4, and data not shown for Kl). In addition, the latter two proviruses are polymorphic in humans with allele frequencies of 0.04 and 0.19 (ref. 41 for K5 and K6). Furthermore, the 6 HERV-K (HML-2) proviruses with coding env have open reading frames in other genes (all 6 have ORFs in 'their gag genes, 4 in their re? genes and 4 in their pol genes, resulting in three completely coding HERV-K (HML-2) proviruses), and among the 29 other env gene-containing proviruses of this family, 10 additional retroviral coding genes can be found.
In comparison with the HERV-K (HML-2) family, the other env gene-containing families can be considered as « old families », with no human-specific integrations. The entry date in the primate genome ofthe coding env gene-containing proviruses vary from 10 million years (for the HERV-Hp62 provirus, (15) to more than 45 million years (for the the coding env- containing HERV-R(b) provirus, data not shown). Furthermore, no entirely coding gene besides the env genes have been found so far among those families.
Transcriptional status ofthe coding envelope genes
The Inventors have devised an efficient method to detect the expression of specific genes belonging to large multigenic families with high homology between their members. It allowed the quantitative and specific monitoring of the expression level of these endogenous retroviral genes, a task which would be impossible using the Northern blot or classical RT-PCR methods which detect the overall expression ofthe complete set of elements among each family.
The first important outcome in the observed transcriptional pattern is that all genes are transcribed, at least in the testis. Despite the low (although unambiguous) transcriptional level of some of the env genes in this organ (e.g. e/wR(b), erøvF(c)2 and the three envH genes), it indicates that all promoters are active. The fact that testis is an organ in which all coding envelopes are transcribed is not a totally unexpected result since germline expression is a common feature of transposable elements in other species, including mice and drosophila (refs. 17 and 39 for the mouse, reviewed in refs. 11 and 18 for drosophila). In these species, expression in the germ line is associated with a high transpositional activity which may result in stably inherited mutations and most probably plays a role in the generation of genetic diversity in the course of evolution.
For the placenta, expression of the coding env genes is much more heterogeneous than in the testis, with an extremely high expression level detected in this organ for three envelope genes, i. e. for the newly identified envFRD gene, and for envR ana envW (for the latter two, high level expression had previously been observed at the protein level, using antibodies, refs. 8 and 42). Conversely, for five coding envelope genes (namely the three envH, envF(c)2 and ercvF(c)l) expression is undetectable. Several studies on HERV transcription have been performed by Northern blot analyses (reviewed in ref. 25) which disclosed a preferential expression of all HERV families in the placenta (except for the HERV-K family). It was put forward that a release of retroelements expression might take place in this organ, without deleterious consequences for the individual due to the « provisional » status of this organ. The above mentionned results of the incention suggest that such a « generalized » expression is likely not to stem from all HERV members among each family but rather results from the activation of a limited number of proviral copies (possibly non coding), for instance via position effects (e. g. ref. 17).
Finally, the high level expression of the newly identified envT detected in the thyroid is intriguing because it is one of the rare coding env gene highly expressed in a « permanent » healthy tissue and it is highly expressed only in this organ. This expression might be relevant to the hormone-producing status of the thyroid gland (and this interpretation might similarly hold for envR in the adrenal gland) and to specific sequences in the HERV LTR or in the vicinity of the proviral insertion site.
Biological relevance of env expression in human tissues
Detection of an active transcription of the coding envelope genes in healthy tissues together with the probable positive selective pressure responsible for the conservation of open reading frames throughout million years raises the question of a putative role of these genes in normal cell physiology.
The envelope proteins of exogenous counterparts of HERVs possess several functions besides their primary role as key molecules for viral entry: most of them elicit immunosuppressive effects and some of them have the capacity to create cell-cell fusion. Consequently, the high level expression of three endogenous coding env genes observed in the placenta (namely envR, envW and the newly identified envFRD) could be implicated in two major physiological processes of this organ : fusion of the cytotrophoblast cells to form the syncytiotrophoblast layer, and local immunosuppression at the materno-foetal barrier.
Along the first line, it has been shown that the envW gene product is a highly fusogenic protein (Blond, J. L., D. Lavillette, V. Cheynet, O. Bouton, G. Oriol, S. Chapel-Fernandes, B. Mandrand, F. Mallet, and F.-L. Cosset. 2000. An envelope glycoprotein of the human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J. Virol. 74:3321-3329). Furthermore, inhibition of envΨ expression in primary cultures of human villous cytotrophoblast leads to a decrease in trophoblast fusion and differentiation, suggesting a role in syncytiotrophoblast layer formation (Frendo, J. L., D. Olivier, V. Cheynet, J. L. Blond, O. Bouton, M. Vidaud, M. Rabreau, D. Evain-Brion, and F. Mallet. 2003. Direct Involvement of HERV-W Env Glycoprotein in Human Trophoblast Cell Fusion and Differentiation. Mol. Cell. Biol. 23:3566-3574). Interestingly, the protein encoded by envFRD (also highly expressed in the placenta) might have a similar role, as it can as well generate cell-cell fusion (Example 2). In the case of envR, on the contrary, it had been previously ruled out its possible implication in fundamental processes of placenta formation by the discovery of a premature stop mutation present in 16% of Caucasians in the heterozygous state, and in 1% in the homozygous state (de Parseval, N, and T. Heidmann. 1998. Physiological knock-out ofthe envelope gene of the single copy ERV-3 human endogenous retrovirus in a fraction ofthe Caucasian population. J. Virol. 72:3442-3445).
Another property of retroviral envelopes is to inhibit infection by retroviruses sharing the same receptor - i. e. receptor interference, reviewed in refs. Best, S., P. R. Le Tissier, and J. P. Stoye. 1997. Endogenous retroviruses and the evolution of resistance to retroviral infection. Trends Microbiol. 5:313-318 and Rosenberg, N, andP. Jolicoeur 1997. Retroviral Pathogenesis, p. 475-586. In J. M. Coffm, Hughes, C. L., Varmus, H. E. (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, New York -. It is therefore plausible, though again difficult to demonstrate, that some of the identified endogenous envelopes, as demonstrated in the mouse for the Fv4 locus (Ikeda, H., and H. Sugimura. 1989. Fv-4 resistance gene: a truncated endogenous murine leukemia virus with ecotropic interference properties. J. Virol. 63:5405- 5412), protect cells against infections by exogenous retroviruses. Interestingly, it has been demonstrated that EnvW interacts with the type-D mammalian retrovirus receptor (Blond, J. L., D. Lavillette, V. Cheynet, 0. Bouton, G. Oriol, S. Chapel-Fernandes, B. Mandrand, F. Mallet, and F.-L. Cosset. 2000. An envelope glycoprotein of the human endogenous retrovirus HERV- W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J. Virol. 74:3321-3329), and this envelope could therefore play a protective role at the placental barrier.
HERV-encoded proteins have also been tentatively involved in several human j pathologies including cancer, immune disorders and neurological diseases, (reviewed in refs.
Lower, R., J. Lower, and R. Kurth. 1996. The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. Proc. Natl. Acad. Sci. USA. 93:5177-
5184 and Nakagawa, K., and L. C. Harrison. 1996. The potential roles of endogenous retroviruses in autoimmunity. Immun. Rev. 152:193-236). By analogy with animal models, it is particularly tempting to implicate endogenous refroviral envelopes in tumorigenesis as a result of a transforming (Alberti, A., C. Murgia, S. L. Liu, M. Mura, C. Cousens, M. Sharp, A. D.
Miller, and M. Palmarim. 2002. Envelope-induced cell transformation by ovine betaretroviruses.
J Virol. 76:5387-94, Palmarini, M., and H. Fan . 2001. Refroviras-induced ovine pulmonary adenocarcinoma, an animal model for lung cancer. J. Nat. Cancer Inst. 93:1603-1614) or immunosuppressive (Blaise, S., M. Mangeney, and T. Heidmann. 2001. The envelope of Mason- Pfizer monkey virus has immunosuppressive properties. J. Gen. Virol. 82:1597-600, Mangeney, M., N. de Parseval, G. Thomas, and T. Heidmann. 2001. The full-length envelope of an HERV- H human endogenous retrovirus has immunosuppressive properties. J. Gen. Virol. 82:2515- 2518, Mangeney, M., and T. Heidmann. 1998. Tumor cells expressing a retroviral envelope escape immune rejection in vivo. Proc. Natl. Acad. Sci. USA. 95:14920-14925) effect. Numerous studies report on expressed endogenous retroviral sequences in pathological tissues, but in most cases the techniques used (Northern blot or RT-PCR using degenerate primers) did not allow the specific detection of coding sequences. Accordingly, the significance of these expressions remains elusive, and an association with diseases is only speculative. With the help ofthe primers devised in this study, a systematic and quantitative evaluation of the transcription levels of coding envelopes in pathological versus healthy tissues should now be possible.
In conclusion, the present survey of coding env genes of the human genome provides a comprehensive list of candidate genes for the possible involvement of HERVs in human physiology and physiopathology. Furthermore, it shown herein that all of the identified genes can be expressed at least in some tissues, and the invention provide tools to specifically evaluate their transcriptional status in physiological and pathological conditions. The identified genes should allow further studies of their function via classical genetic approaches (identification of susceptibility loci, search for polymorphisms among the human population as previously performed for the HERV-R locus, ref. de Parseval, N., and T. Heidmann. 1998. Physiological knock-out of the envelope gene of the single copy ERV-3 human endogenous retrovirus in a fraction of the Caucasian population. J. Virol. 72:3442-3445), whereas the limited number of unraveled coding sequences downsizes an a priori insoluble multigenic analysis to a simpler one.
Example 2
Genome-wide screening for Human Endogenous Retrovirus envelopes with fusogenic properties identifies syncytin-2, a new gene with conserved function upon primate evolution
Materials and Methods
Cell lines.The human TE671 rhabdomyosarcoma cells (ATCC CRL8805), 293T embryonal kidney cells (ATCC CRL11268) and HeLa epithelioid carcinoma cells (ATCC CCL2), the Cos- 7 African green monkey kidney cells (ECACC 87021302), the G355-5 feline astrocyte cells (ATCC CRL2033), and the NIH3T3 mouse fibroblasts were grown in Dulbeco's modified Eagle's medium (DMEM) supplemented with 10 % fetal calf serum; the CHO Chinese hamster ovary cells (ATCC-CCL61) were grown in F12K nutrient medium (Gibco) supplemented with 7 % fetal calf serum. All cell culture media were supplemented with streptomycin (100 μg / mL) and penicillin (100 U / mL).
DNAs. Human BACs were obtained from BAC PAC Resources (Oakland) and from the UK HGMP Resource Centre (Cambridge, UK). The sources of the genomic DNAs are given in (de Parseval, N., Casella, J. F., Gressin, L. & Heidmann, T. (2001) Virology 279, 558-569) and (Benit, L., Lallemand, J.-B., Casella, J.-F., Philippe, H. & Heidmann, T. (1999) J. Virol. 73, 3301-3308) for Human, Chimpanzee (Pan troglodytes), Gorilla (Gorilla gorilla), Orangutan (Pongo pygmaeus), Gibbon (Hylobates Lar Moloch), Rhesus macaque (Macaca cynomolgus), New world monkeys (Saguinus midas and Cebus capucinus) and prosimian (Eulemur fulvus).The Marmoset new world monkey (Callithrix jacchus) DNA was from ECACC (85011419). Mouse (Mus musculus) and Cat (Felis cαttus) DNAs were extracted from spleen tissue samples.
Envelope expression vectors. The FBA-RlessSALF expression vector (Lavillette, D., Maurice, M., Roche, C, Russell, S, J., Sitbon, M. & Cosset, F.-L. (1998) J. Virol. 72, 9955-9965) encoding the A-Rless hyperfusogenic mutant amphotropic MLV envelope glycoprotein and the phCMV-G expression plasmid (GenBank accession number AJ318514) were gifts from F-L Cosset (ENS, Lyon, France). The HERV-W envelope expression vector (phCMV-EnvpH74) was a gift from F. Mallet (ENS, Lyon, France). The fifteen other endogenous envelope expression vectors were constracted as follows. Full-length envelope of each provirus was PCR- amplified from the corresponding BAC DNA using a proofreading DNA polymerase and appropriate primers (sequences available upon request). PCR were carried out for only 15 cycles (1 min at 94 °C, 1 min at 60 °C, 4 min at 72 °C), in 50 μl, using 100 ng of BAC DNA, 48 pmol of each primer, 200 μM of each dNTP, 2.5 μl PfuTuτbo Hotstart polymerase and IX Pfu reaction buffer (Stratagene). Each PCR product was then cloned into the phCMV-G vector opened with EcoRI and blunt-ended by Kleenow treatment except for the HΕRV- Fc2 envelope, which was cloned into phCMV-G restricted with EcoRI and Bsu36l and blunt-ended.
Cell-cell fusion assay. Cells were transfected using Lipofectamine (Invitrogen, 2 μg of DNA for 5xl05 cells), except for 293T and TΕ671 cells which were transfected using calcium phosphate precipitation (Invitrogen, 5 μg of DNA for 5x105 cells). Fusion activity of envelope glycoproteins was measured 12 to 36 h after transfection of the conesponding expression vectors. To visualize syncytia, cells were fixed in methanol and stained by adding May- Grϋnwald and Giemsa solutions (Sigma) according to the manufacturer's instructions. The fusion index, which represents the percentage of fusion events in a cell population is defined as [(N-S)/T] x 100, where N is the number of nuclei in the syncytia, S is the number of syncytia, and T is the total number of nuclei counted.
Cloning of the HERV-FRD envelope gene from simians. The envelope genes orthologous to the human HERV-FRD gene were PCR-amplified from simian (and human as a control) genomic DNAs. PCR were carried out for 25 cycles (10 sec at 93 °C, 30 sec at 56 °C, 4 min at 68 °C), in 50 μl, using 100 ng of genomic DNA, 48 pmol of each primer, 350 μM of each dNTP, 0.75 μl Expand long template enzyme mix and IX reaction buffer (Roche). TzoI-containing primers were ATCACCTCGAGCACCATGGGCCTGCTCCTGCTGGTTCTCATTC (SEQ ID NO: 58) as forward primer and ATCACCTCGAGGCTTCAGTACAGGTGGATA (SEQ ID NO: 59) as reverse primer. Each PCR product was then Xhol restricted and cloned into the phCMV-G vector opened with Xhol. Sequencing of the simian envelope genes was performed on the bulk of the PCR products before cloning (MWG-Biotech). Sequences have been deposited in the EMBL nucleotide sequence database under accession numbers AJ577595 to AJ577600 for the chimpanzee,- gorilla, orangutang, gibbon, macaque and marmoset envelope, respectively.
In vitro transcription-translation. In vitro transcription-translation assays were performed using the Promega TNT coupled reticulocyte lysate system, following the manufacturer's instructions. DNA templates were obtained by PCR with a forward primer designed with a T7 promoter (GCTAATACGACTCACTATAGGAACAGACCACCATGGGTCTGCTCCTGCTG CTTC (SEQ ID NO: 60) for Marmoset and
GCTAATACGACTCACTATGGAACAGACCACCATGCTCCTG CTGGTTCTCATTC (SEQ ID NO: 61) for all other species) and a reverse primer (ATCACCTCGAGG CTTCAGTACAGGTGGATA (SEQ ID NO: 62) for Marmoset and TTTGAGCAAGGGTGATTCAT (SEQ ID NO: 63) for all other species). [35S] methionine was from ICN. Posttranslational analyses were performed by SDS-polyacrylamide gel electrophoresis, with the gels exposed to X-ray films (Fuji) for 6 h.
DNA slot-blot. DNAs (3 μg) from each species were loaded on Hybond N+ membranes (Amersham) using a slot blot apparatus (Hoefer). Blots were hybridized overnight at 65 °C under standard conditions (24), using a 32P-labelled full-length FRD env gene (1679 bp PCR- fragment) as a probe. Membranes were then washed at 65 °C, once with 2X SSC-0.1 % SDS for 15 min and once with IX SSC-0.1 % SDS for 15 min. Labelling was detected using a Phosphorhnager (FLA-3000 scanner).
Northern-blot analysis and RNA probe. The full-length FRD env gene obtained by PCR as described above was cloned in the antisense orientation under the T7 promoter into the pBlueScript (Stratagene) vector restricted with EcoRV. The construct was linearized by Xhol digestion and an antisense riboprobe was synthesized using the Strip-EZ RNA probe system from Ambion. A human northern blot (first choice poly(A)+ Human northern blot 2, Ambion) was used according to the manufacturer instructions, with prehybridization at 68 °C in the UltraHyb buffer for 1 h, riboprobe addition and overnight hybridization at 68 °C. The membrane was washed at 68 °C, twice with the NorthernMax low stringency buffer and once with the NorthernMax high stringency buffer (Ambion), and then exposed to X-ray film (Kodak) at -80 °C for 12 h.
Rationale of the assay for human endogenous retrovirus envelopes with fusogenic properties
An assay for fusogenicity ofthe sixteen cloned envelopes genes identified in Example 1 was. performed. This assay relies on the fransfection of cells expected to cany a receptor for the conesponding envelope, with the expression vectors for the envelope proteins. Accordingly, fusion assays were performed for all sixteen envelope genes upon transfection of a large series of cells, including feline, murine, simian and human cells. In the latter case, different cell lines were used, namely Hela cells, 293T embryonic kidney cells, and TE671 cells which have been previously used as they possess the receptors for several retrovirus groups (Porter, C. D., Collins, M. K, Tailor, C. S., Parkar, M. H., Cosset, F. -L., Weiss, R. A. & Takeuchi, Y. (1996) Hum. Gene. Ther. 1, 913-919). In a standard assay 5x105 cells were fransfected with 2-5 μg of the Env-expression vector, and fusion was tested by screening the transfected cell culture for ultinucleated giant cells -or syncytia- 12-36 h after transfection. Controls included the highly fusogenic A-Rless envelope from the amphotropic MLV (Rein, A., M ro, J., Haynes, J. G., Ernst, S. M. & Nagashima, K. (1994) J. Virol 68, 1773-1781), and an 'empty' vector.
Identification of a new fusogenic HERV envelope
As illustrated in Figure 3 and Table 5. among all the coding env genes, only two induced syncytia formation, namely the HERV-W and the HERV-FRD genes, the other genes resulting in no effect. The result obtained with HERV-W is confirmatory, as it had been previously demonstrated in (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329, Mi, S., Lee, X., Li, X., Veldman, G. M., Finnerty, H., Racie, L., LaVallie, E., Tang, X. Y., Edouard, P., Howes, S., Keith, J. C. J. & McCoy, J. M. (2000) Nature 403, 785-788). Yet, an original outcome of the present invetion is the sorting out of a new envelope gene with fusogenic properties -the HERV-FRD env gene- and the evidence that these two genes most probably constitute the sole reservoir of fusogenic human endogenous retroviral envelopes.
Table 5. Assay for fusogenicity of the 16 coding endogenous envelopes genes of the human genome.
Gene name Chrom. Accession fusion assay1 localization number envHl 2q24.3 AJ289709 envH2 3q26 AJ289710 envH3 2q24.1 AJ2897U envKl 12ql4.1 AC074261 envK2 7p22.1 AF164614 envK3 19ql2 Y17833 envK4 6ql4.1 AF164615 envK5 19pl3.11 AY037928 envK6 8p23.1 AY037929 envT 19pl3.11 AC078899 envW 7q21.2 AC000064 + envFRD 6p24.1 AL136139 + envR 7qll.21 AC073210 envR(b) 3p24.3 AC018389 envF(c)2 7q36.2 AGO 16222 envF(c)l Xq21.33 AL354685
Fusion assay was performed with the following target cells : NIH3T3, CHO, G355-5, Cos-7, TE671, 293T and HeLa. (-) indicates a negative result in all cell types ; (+) indicates a positive result in at least one cell type.
The properties ofthe HERV-FRD env gene was analyzed further and compared to that of HERV-W.
. Firstly, as illusfrated in Table 6, it can be observed that the syncytia-forming activity j of both envelopes, although of quite related extent when using the syncytia forming index defined in Materials and Methods, do not coincide for a given cell-type: for instance, the HERV-FRD Env is highly fusogenic in feline cells where that of HERV-W has no activity, and within human cells where the HERV-W Env is fusogenic, that of HERV-FRD is not fusogenic in all cell types, with only limited effect in Hela cells. Such differences can be simply accounted for by taking into consideration that retroviral envelope-mediated cell- fusion is dependent on the presence of an appropriate receptor on the cell surface, which may be different for different envelope proteins, as currently observed for most exogenous infectious animal retroviruses (reviewed in ref. Hunter, E. (1997) in Retroviruses, eds. Coffin, J. M., Hughes, S. H. & Varmus, H. E. (Cold Spring Harbor Laboratory Press, New York), pp. 71-119 and Overbaugh, J., Miller, A. D. & Eiden, M. V. (2001) Microbiol. Mol. Biol. Rev. 65, 371-389). In this respect, it has been previously demonstrated that the receptor for the HERV- W envelope protein is the receptor for the D-type retroviruses (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329; Lavillette, D., Marin, M., Ruggieri, A., Mallet, F., Cosset, F. L. & Kabat, D. (2002) J. Virol. 76, 6442-6452). Clearly, the receptor for the HERV-FRD envelope is distinct, as the cell specificity for fusion for both envelopes is different. This was further confirmed by performing an interference assay using the panel of cells derived in (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel- Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol 1A, 3321-3329), where no decrease in the fusogenic activity of the HERV-FRD Env could be detected, under conditions where the cells had been stably transfected with an expression vector for the envelope of a type-D retrovirus (RD114, not shown).
Table 6. Fusion host range of the HERV-FRD envelope
Species Target Fusion index cells
HERV-FRD HERV-W A-Rless none
Mouse NIH3T3 1.0 ± 0.9 0.2 ± 0.5 41 ± 17 0.4 ± 0.3
Hamster CHO 1.8 ± 0.6 1.3 ± 0.8 1.8 ± 0.4 1.0 + 0.5
Cat G355-5 90 ± 2 2.2 ± 3.2 83 ± 3 0.7 + 0.8
Monkey Cos-7 20 ± 4 62 ± 3 19 ± 4 13 + 3
Human TE671 66 ± 6 56 ± 10 39 ± 8 3.1 ± 1.8
293T 81 ± 7 90 ± 4 9 ± 3 0.3 ± 0.6
HeLa 1.8 ± 0.7 65 ± 9 23 ± 6 1.0 ± 0.4 a Target cells were transfected with expression vectors for the HERV- FRD envelope, the HERV-W envelope, the hyperfusogeni mutant amphotropic MLV envelope (A-Rless) or no protein (none) as a negative control, and fusion indices were determined as indicated in Materials and Methods (means ± standard deviations; n=5).
Consistent with its fusogenic property, analysis ofthe aminoacid sequence ofthe FRD envelope together with its hydrophobic profile (Figure 4) discloses the characteristic features of retroviral envelopes (reviewed in Hunter, E. (1997) in Retroviruses, eds. Coffin, J. M., Hughes, S. H. & Varmus, H. E. (Cold Spring Harbor Laboratory Press, New York), pp. 71- 119), with a canonical cleavage site (consensus: R/K-X-R/K-R; (Coffin, J. M. (1986) Cell 46, 1-4) between the SUrface (SU) and TransMembrane (TM) moities of the protein, and the presence of hydrophobic domains conesponding to the fusion peptide and the TM domain. A 'CWLC domain, involved in the interaction between the SU and TM moities in retroviral envelopes (Pinter, A., Kopelman, R., Li, Z., Kayman, S. C. & Sanders, D. A. (1997) J Virol 71, 8073-8077), and an 'immunosuppressive' domain (Cianciolo, G. J., Copeland, T., Orozlan, S. & Snyderman, R. (1985) Science 230, 453-455) can also be identified in the SU and TM moieties, respectively.
Finally, a Northern blot analysis was performed with a membrane containing polyA"1" RNA from a panel of human tissues that were hybridized with a riboprobe for the HERV- FRD envelope. As can be observed in Figure 5, a strong band is observed in the placenta, and actually almost exclusively in this organ, at the expected position for a spliced subgenomic retroviral transcript. A real-time RT-PCR analysis of the HERV-FRD env gene transcripts further disclosed high level expression in cytotrophoblast cells isolated from the placenta, not observed in the conesponding fibroblast cells.
Conservation of the FRD locus and fusogenicity upon primate evolution
The FRD family of endogenous retroviruses consists of approximately 50 provirus copies per haploid genome (Tristem, M. (2000) J. Virol. 74, 3715-3730; Seifarfh, W., Skladny, H., Krieg-Schneider, F., Reichert, A., Hehlmann, R. & Leib-Mosch, C. (1995) J. Virol. 69, 6408-6416). This family is most probably a very ancient family whose members entered the primate genome after the divergence between prosimians and simians: this is demonstrated in the zoo-slot in Figure 6A. where hybridization can be detected using an envelope probe and genomic DNAs from humans to New World Monkeys, with no signal for prosimians nor rodents (nor other mammals, not shown). Taking into consideration that conservation of the HERV-FRD envelope gene with an open reading frame might not be fortuitous but rather be the result of positive selection for a still unknown function, the status of the orthologous locus in the course of primate evolution was analyzed using a PCR approach with a 'flanking' primer located 3' to the proviral insertion, and an 'internal' proviral primer 5' to the env gene. Consistent with the zoo-blot analysis, PCR amplification was found positive for all simians, resulting in DNA fragments ofthe expected size.
The identified putative envelope genes were characterized further, along three lines: firstly, the PCR products were sequenced for an unambiguous identification of the env genes and the determination of their level of divergence in the course of primate evolution; secondly, an in vitro transcription/translation assay was performed to determine whether the genes are fully coding; and thirdly a fusion assay was performed as above, to determine if env gene function has been preserved.
As illustrated in Table 7. sequencing of the PCR products disclosed very high sequence conservation among the primate ERV-FRD env genes, with values in the 95-100 % range from human to macaque, and still 88 % identity between human and New World Monkey, which have diverged at least 40 millions years ago. No stop codon could be found in the sequences, a result consistent with the in vitro transcription/translation assay performed directly on the PCR products (Figure 6B), which demonstrates full-length products for all genes.
Table 7. Percentage identity of amino-acid sequences of envFRD in simians a
Human Chimpanzee Gorilla Orangutang Gibbon Macaque NWM
Human _
Chimpanzee 99.6
Gorilla 99.1 99.1
Orangutang 96.7 96.7 96.8
Gibbon 97.2 97.2 97.4 97.0
Macaque 95.2 95.2 95.4 95.7 96.5
NWM 88.1 88.1 88.0 87.9 88.5 87.9 Orthologous envFRD genes were PCR-amplifϊed and sequenced. Alignments were performed with the LALIGN program. Sequences are deposited in the EMBL nucleotide sequence database (see Materials and Methods).
To assay for the possible conservation of the fusogenic property of the identified genes, the PCR env fragments were cloned into the phCMV expression vector and tested in the syncytia-forming assay, as above. For each env gene, at least six clones were assayed to circumvent possible mutations introduced by the PCR amplification procedure (a feature with no consequence on both the sequencing and the transcription/translation assay above, directly performed on the bulk of the PCR product), using both the highly fusogenic feline G355.5 cells, and human cells (see Figure 7). Remarkably, as illustrated in the figure, fusion of the transduced feline cells could be observed for all env genes (with in each case at least four out of six cloned PCR-fragments positive, a result consistent with the expected rate of mutation of the DNA polymerase used for the conesponding genomic amplifications), with no significant difference in the extent of fusogenicity from human to New World Monkey.
A similar conclusion holds using human cells for the fusion assay, as expected, but with an exception for the most distantly related env gene (the New World Monkey gene), which is not positive in human cells although clearly fusogenic when assayed in feline cells.
This unexpected result is most probably relevant to subtle differences in the envelope aminoacid sequence which, together with expected differences among the human and feline receptors, result in the impairment of a productive interaction with the former. Such differences might be of interest for a future identification of the aminoacids involved in the fusion process.
The present investigation has unraveled a new fusogenic protein of retroviral origin that is encoded in primate genomes. This envelope protein promotes cell-cell fusion in a specific manner as it depends on the cell type used, with positive effects in both feline and human cells. Interestingly, analysis ofthe cell types prone to fusion discloses differences with the other fusogenic envelope identified so far, i.e. the HERV-W envelope (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329; Mi, S., Lee, X., Li, X., Veldman, G. M., Finnerty, H., Racie, L., LaVallie, E., Tang, X. Y., Edouard, P., Howes, S., Keith, J. C. J. & McCoy, J. M. (2000) Nature 403, 785-788), indicating differences in receptor usage. In the case of the HERV-W envelope, interference assays had led to the identification of the corresponding receptor as being that for D-type retroviruses (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel-Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329; Lavillette, D., Marin, M., Ruggieri, A., Mallet, F., Cosset, F. L. & Kabat, D. (2002) J. Virol. 16, 6442-6452). Similar assays demonstrate that this receptor is not that for the HERV-FRD envelope, and preliminary experiments suggest that it is none of the identified receptors for the present-day infectious retroviruses. Specific search for the HERV-FRD receptor will therefore be necessary to identify the cell membrane protein involved in the observed cell-cell fusion. Following the proposed nomenclature for the HERV-W envelope gene, that was named syncytin in relation with its ability to make syncytia via cell-cell fusion (Mi, S., Lee, X., Li, X., Veldman, G. M., Finnerty, H., Racie, L., LaVallie, E., Tang, X. Y., Edouard, P., Howes, S., Keith, J. C. J. & McCoy, J. M. (2000) Nature 403, 785-788), it seems appropriate to name the fully coding HERV-FRD envelope gene the syncytin-2 gene, and accordingly to rename the syncytin gene as syncytin-1 in future studies.
An important issue of the present investigation is the discovery that the identified envelope gene has been conserved in primate evolution in a functional state over >40 millions years, as the conesponding locus is present from New World Monkeys to humans as a full- length coding gene, for which the Inventors further demonstrate that the fusogenic function is conserved in all primates tested. Conservation ofthe fusogenic function is a strong hint for a functional role of the gene in the physiology of the host, and suggests a selective process by which the retroviral gene function has been diverted by the host to its own benefit. Similar diversions have already been described for 'parasitic' genes, with examples of retroviral promoters which confer novel tissue specificities to nearby cellular genes (Wilkinson, D. A., Mager, D. L. & Leong, J.-A. C. (1994) in The Retroviridae, ed. Levy, J. A. (Plenum Press, New York), Vol. 3, pp. 465-535; Samuelson, L. C, Philips, R. S. & Swanberg, L. J. (1996) Mol. Biol Evol. 13, 767-779; Schulte, A. M., Lai, S., Kurtz, A., Czubayko, F. & Riegel, A. T. (1996) Proc. Natl. Acad. Sci. USA 93, 14759-14764), and examples of coding sequences of retroviral origin which, in the mouse, confer resistance to infections by exogenous retroviruses (reviewed in ref. Best, S., Le Tissier, P. R. & Stoye, J. P. (1997) Trends Microbiol 5, 313-318).
Among the numerous functions that have been suggested for a possible physiological role of HERV envelopes, the fusogenic function has been frequently hypothesized as being plausibly involved in placenta formation, via the fusion of the cytotrophoblast cells into the syncytiotrophoblast (Blond, J. L., Lavillette, D., Cheynet, V., Bouton, O., Oriol, G., Chapel- Fernandes, S., Mandrand, B., Mallet, F. & Cosset, F.-L. (2000) J. Virol. 1A, 3321-3329; Mi, S., Lee, X., Li, X., Veldman, G. M., Finnerty, H., Racie, L., LaVallie, E., Tang, X. Y., Edouard, P., Howes, S., Keith, J. C. J. & McCoy, J. M. (2000) Nature 403, 785-788; Frendo, J. -L., Olivier, D., Cheynet, V., Blond, J. -L., Bouton, O., Vidaud, M., Rabreau, M., Evain- brion, D. & Mallet, F. (2003) Mol. Cell Biol. 23, 3566-3574). This hypothesis is consistent with the identified fusogenic activities of the HERV-W and -FRD envelope genes and their observed expression in the placenta -and cytotrophoblast cells. A possible approach to assay the model in humans would be a genetic one, with the finding of possible 'natural' mutants among the human population that could be associated with a pathological situation.
Indeed, it had previously been shown, for the first envelope gene that had been unambiguously demonstrated to be highly expressed in the placenta - namely the HERV-R env gene- that it could not be involved in placenta formation, due to the occunence of a severe polymorphism (a premature stop codon) found in 10 % of Caucasians in the heterozygote state, and in 1% in the homozygote state, and not resulting in any placenta- related phenotype (de Parseval, N. & Heidmann, T. (1998) J. Virol 72, 3442-3445). It was thereafter argued that this defect could be complemented by other genes with the same function, an interpretation which indeed could not be rejected. In fact, as a consequence of its exhaustivity, the present invention now provides the required genetic tools to unambiguously address the issue: there are two identified HERV envelope genes with fusogenic properties in the human genome, and these two genes are expressed in the placenta. A concomitant search for polymorphisms of these two genes among the human population, and in a more refined manner among groups disclosing abnormalities in placenta formation such as pre-eclampsia, Down's syndrome, or uncontrolled trophoblast invasion as observed in choriocarcinoma (Fox, H. (1997) in Pathology of the placenta, ed. Fox, H. (W. B. Saunders, Philadelphia), pp. 151- 175; Frendo, J. L., Vidaud, M., Guibourdenche, L, Luton, D., Muller, F., Belief, D., Giovagrandi, Y., Tanade, A., Porquet, D., Blot, P. & Evain-Brion, D. (2000) J. Clin. Endocrinol Metab. 85, 3700-3707; Baergen, R. N. (1997) Gen. Diagn. Pathol. 143, 127-141) should now provide hints for the possible involvement of these genes in placenta physiology.
Finally, it is noteworthy that the identified HERV-FRD envelope gene canies a domain -the immunosuppressive domain- which could play a physiological role in protecting the fetus against the maternal immune system, and as such have also participated in the 'positive selection' ofthe syncytin-2 gene in the course of primate evolution.
Example 3
Identification of an envelope protein from the FRD family of Human Endogenous
Retroviruses (HERV-FRD) conferring infectivity and functional conservation among simians
It had previously been demonstrated that the HERV-W envelope gene is functional, since pseudotypes generated with HIV-l virions are infectious (An, D. S., Y.-M. Xie, and I. S. Y. Chen. 2001. Envelope gene ofthe human endogenous retroviras HERV-W encodes a functional retrovirus envelope. J. Virol. 75:3488-3489; Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002. The envelope glycoprotein of human endogenous retroviras type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442- 6452).
In this Example, it is shown that HERV-FRD envelope can also confer infectivity to pseudotypes generated with lentiviral virions.
To do so, the HERV-FRD envelope gene was cloned into a hCMV promoter-driven expression vector to be used in a previously described infection assay (Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002. The envelope glycoprotein of human endogenous retroviras type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442-6452), as schematized in Figure 8A.
Briefly, human 293T cells are co-transfected with an expression vector for the retroviral proteins -except the envelope- from type-C (MLV) or lenti (HIV-1 and SIV) virases, a conesponding lacZ gene-marked defective retroviral vector, and an expression vector for the env gene to be tested (or an empty vector as a negative control and a vector for the amphotropic MLV envelope as a positive control). Then, the pseudotype virions are assayed for infectivity after recovery of the transfected cell supernatant 36 h post-transfection, transfer of the supernatant onto target test cells and centrifugation of the plates (i.e. spinoculation, see Ref. Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002. The envelope glycoprotein of human endogenous retrovirus type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442-6452) and, after an additional 60 h period, counting the lacZ positive test cell colonies by an in situ histochemical staining for β- galactosidase activity. The results of such an assay are given in Figure 8B and Table 8. for the various viral cores (MLV, SIV and HIV-1) and target cells tested, which included murine, feline, and human cells. It can be clearly observed that the HERV-FRD envelope, when expressed on lentiviral particles, confers infectivity to the virions, with evidence for viral titers on feline (G355-5) and human (TE671 and 293T) cells in the 100-500 cm per ml range. Interestingly, the murine 3T3 cells and the human HeLa cells are refractory to infection (although they are positive for the confrol amphotropic MLV envelope), a result consistent with the absence of any detectable syncytia formation in a fusion assay carried out with these cells (see below). It can also be noted that the MLV core is much less efficient -if any- than the lentiviral cores, as similarly observed for the HERV-W envelope (An, D. S., Y.-M. Xie, and I. S. Y. Chen. 2001. Envelope gene of the human endogenous retrovirus HERV-W encodes a functional retrovirus envelope. J. Virol. 75:3488-3489; Blond, J.-L., D. Lavillette, V. Cheynet, O. Bouton, G. Oriol, S. Chapel-Fernandes, B. Mandrand, F. Mallet, and F.-L. Cosset. 2000. An envelope glycoprotein ofthe human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J. Virol. 74:3321- 3329; Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002. The envelope glycoprotein of human endogenous retrovirus type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442-6452). Finally, since some envelopes are sensitive to shearing, viral titers were also measured in the absence ofthe spinoculation step: in all cases, its omission (not shown) resulted in a 5-20 fold reduction of the titers in Table 8 (and similarly for the simian FRD envelopes assayed in Figure 9).
In view of the results of Examples 1 and 2. the Inventors assayed whether the simian orthologous env genes also confer infectivity to SIV-pseudotype virions. The results of an experiment similar to that carried out in Figure 8A for the human gene are given in Figure 9, which discloses the following features: i) all simian ERV-FRD envelopes (with one exception, see below) confer infectivity to the pseudotype virions, with closely related viral titers (up to 2000 cfu/ml) and target cell specificity, thus demonstrating conservation over >40 millions years of the ERV-FRD envelope function, but ii) there is one exception to this rule for the gibbon envelope which is negative for all the target cells tested. Interestingly, this negative result is not due to a severe defect in the gibbon envelope, since the protein is still capable of promoting cell- cell fusion, as illusfrated in the lower panel ofthe Figure by an experiment carried out in parallel using the same expression vectors and cells : the results show that for all simian envelopes (except the gibbon envelope) there is a good conelation, as expected, between infectivity and cell-cell fusion, and that the gibbon envelope is clearly positive for cell-cell fusion, with the same cell specificity as. the other simian envelopes. These features, which de facto uncouple the processes of cell-cell fusion and viral entry, could be accounted for by either intrinsic differences in the molecular requirements for the two processes, or by differences, possibly, in the envelope viral load and/or stability (see discussion in Refs. Aguilar, H. C, W. F. Anderson, and P. M. Cannon. 2003. Cytoplasmic tail of Moloney murine leukemia virus envelope protein influences the conformation of the extracellular domain: implications for mechanism of action of the R Peptide. J. Virol. 77:1281-1291; Lavillette, D., M. Marin, A. Ruggieri, F. Mallet, F. L. Cosset, and D. Kabat. 2002. The envelope glycoprotein of human endogenous retroviras type W uses a divergent family of amino acid transporters/cell surface receptors. J. Virol. 76:6442-6452; Lavillette, D., M. Maurice, C. Roche, S. J. Russell, M. Sitbon, and F.-L. Cosset. 1998. A proline-rich motif downstream of the receptor binding domain modulates conformation and fusogenicity of murine refroviral envelopes. J. Virol. 72:9955-9965). At the sequence level, it is noteworthy that the gibbon envelope discloses strong conservation with the other simian FRD envelopes, as it is 97 % identical to the human sequence, i.e. it is closer than the infection- positive marmoset New World Monkey envelope which is only 88 % identical to the human sequence (Figure lOA . Actually, comparison of the gibbon and human sequences reveals only four mutations which are gibbon-specific, two within the SU and two within the TM subunits (grayed in Figure lOA). Preliminary experiments using a chimeric construct with the human SU domain fused to the gibbon TM moiety strongly suggested that mutations in the TM subunit were responsible for the loss of infectivity ofthe gibbon envelope, as infectivity ofthe chimeric envelope remained low (not shown). Two constructs with reversion of the identified TM point mutations were therefore tested for infectivity, one with the F to L reversion at position 490 and one with the T to N reversion at position 532. As illustrated in Figure 10B. the T to N reversion fully restored infectivity to the gibbon envelope, with no effect ofthe F to L mutation -located in the hydrophobic transmembrane domain of the TM subunit. Due to its specific location in the cytoplasmic tail of the envelope protein, it is likely that the N to T mutation alters some of the functions and interactions associated, in infectious retroviruses, with this specific domain and involved in the loading, stability, and conformational transition of the Env proteins (e.g. Brody, B. A., S. S. Rhee, and E. Hunter. 1994. Postassembly cleavage of a refroviral glycoprotein cytoplasmic domain removes a necessary incorporation signal and activates fusion activity. J. Virol. 68:4620-4627, Rein, A., J. Mino, J. G. Haynes, S. M. Ernst, and K. Nagashima. 1994. Function of the cytoplasmic domain of a retroviral transmembrane protein: pl5E-p2E cleavage activates the membrane fusion capability of the murine leukemia virus Env protein. J. Virol. 68:1773-1781, Yu, X., X. Yuan, M. F. McLane, T. H. Lee, and M. Essex. 1993. Mutations in the cytoplasmic domain of human immunodeficiency virus type 1 transmembrane protein impair the incorporation of Env proteins into mature virions. J. Virol. 67:213-221; references in Ref. Aguilar, H. C, W. F. Anderson, and P. M. Cannon. 2003. Cytoplasmic tail of Moloney murine leukemia .virus envelope protein influences the conformation of the extracellular domain: implications for mechanism of action of the R Peptide. J. Virol. 77:1281-1291). In this respect, the gibbon envelope together with the other presently characterized simian envelopes can be considered as 'natural mutants' and be of use to study the refine molecular processes associated with envelope function and virus entry.
Whatever the underlying molecular events, the present functional characterization of the ERV-FRD envelopes is strongly suggestive of an 'ancestral' infection event by a functional retrovirus and its subsequent 'endogenization', with some of the envelope functions retained in evolution. Close examination of the primate FRD envelope sequences indeed reveals a prevalence of synonymous versus nonsynonymous substitutions (ratios for all pairwise comparisons >3, using the SNAP.pl program at the www .hiv-web . lanl . gov site), thus suggesting positive selection for a physiological function -which remains to be unraveled.
Table 8. Infection assay of the HERV-FRD envelope a
Core Env Viral titer (CFU/ι mL)
NIH3T3 G355-5 TE671 HeLa 293T
MLV FRD 0 0 1.9 x 10' 0 2.0 x 10'
None 0 0 0 0 6
Ampho 4 x l05 2 x l06 4 l06 l x lO6 1.1 lO6
HIV FRD 1 l lO2 2.1 x lO1 0 8.8 x 10'
None 0 0 0 0 6
Ampho 2 x lO5 1.4 x lO6 l lO5 1.2 x lO4 6 x l04
srv FRD 0 3.6 x 102 2.3 x 102 4 3.4 x lO2
None 0 5 0 ' f o 6 Ampho 5 x lO5 1.2 x lO6 6.8 x lO5 4.3 x 105 8 x l05 experimental conditions as in Figure 8A; the retroviral particles (core) pseudotyped with the HERV-FRD envelope (FRD), no protein (none) or the amphotropic MLV envelope (Ampho), and the target test cells are indicated ; viral titers are each the means from two independent experiments. Example 4
Characterization of the immunosuppressive activity of the HERV-FRD envelope (Syncitin 2) and ofthe HERV-W envelope (Syncitin 1)
The assay for measuring the immunosuppressive activity was performed following the general procedure described in Mangeney & Heidmann, PNAS 1998 and Mangeney et al, J. Gen. Virol 2001.
Materials and Methods
Mice and Cell Lines
The cell line used in the assay was MCA205(methylcholanthrene-induced murine fibrosarcoma cells (Shu and Rosemberg, 1985). Cells were cultured in DMEM supplemented with 1.0% fetal calf serum, streptomycin (100μg/ml) and penicillin (lOOunits/ml).
In order to test the immunosuppressive effect of the envelope proteins, C57BL/6 and BALB/c mice, 8-12 wk-old, obtained from Janvier (Laval, France) were used.
Constructions pDFG-envHERV-FRD expression vector was constracted as follows. The full-length
HERV-FRD envelope gene was PCR-amplified from the conesponding BAC DNA
(accession number RP4761I2) obtained from BAC PAC resources (Oakland), using a proof reading DNA polymerase and with the 5' phosphate modified oligonucleotide
TCGAGCTCTTAGGTCACCATGGGC (SEQ ID NO: 66) as forward primer and the Mlul- containing oligonucleotide AACGGACGCGTCTCTGTCGTGTTCC ACTA (SEQ ID NO: j 67) as reverse primer. PCR was carried out for only 15 cycles (1 min. at 94 °C, 1 min at 60 °C,
4 min at 72 °C), in 50 μl, using 100 ng of BAC DNA, 48 pmol of each primer, 200 μM of each dNTP, 2.5 μl PfuTurbo Hotstard polymerase and IX Pfu reaction buffer (Stratagene).
The PCR product was then cloned into the pDFG-MoTMtag vector (see below) opened at the
Agel site blunt-ended by Klenow treatment and the Mlul site.
pDFG-MoTMtag was constructed by ligating pDFG-MoTM (Mangeney & Heidmann, 1998) opened with Bsu361 and Xhol and a PCR fragment (digested with the same enzymes) generated using primers 5' CGTCTTGTCTGCTGCAGCATC-3' (SEQ ID NO: 68) and 5'- CATACTCGAGTCAACGCGTAGAATCGAGACCGAGGAGAGGGTTAGGGATAGGCT TACCGTACGGCTCGTACTCTATAGGCTTC-3' (SEQ ID NO: 69) and pDFGMoTM as a template.
pDFG-envHERV-W was constracted by inserting the Agel-Dral Klenow treated fragment from pCR2.1 pH74 (Blond et al. J. Virol. (2000) Vol 74: 3321-3329) into the pDFG- MoTMTag vector digested by Agel and BsiWI and Klenow treated.
Establishment of envelope-expressing tumor Cells and in vivo assay
Retroviral expression vectors (1.75 μg) were packaged by transient cotransfection into 7.5 x 105 293T cells with 1.75 μg of CMV-gag-pol-MoMLV and 0.55 μg CMV-envAmpho, using the calcium phosphate method. Supernatants were recovered 2 days later, filtered and used for infection of 5 x 105 MCA205 tumor cells in the presence of 4 μg/ml polybrene, as described in Mangeney & Heidmann, 1988. Cells were maintained in selective medium (400 units/ml hygromycin) for 2 weeks. For in vivo assays, tumor cells were trypsinized, centrifuged and resuspended in PBS at a concentration of 1 x 107 cells/ml. 100 μl of each suspension were injected s.c. in the shaved right flank of 3 C57/BL6 and 8 to 10 BALB/c mice. Tumor establishment was determined by palpation and tumor area (in mm2) was determined by measuring perpendicular tumor diameters.
The immunosuppression index is defined as i = (Senv-Snone)/Snone, wherein Senv is the maximum area reached by a tumour expressing an envelop protein and Snone is the maximum area reached by a tumor which does not express any envelop protein (negative control).
Results
The results ofthe immunosuppression assay are presented in the following table:
Envelope Immunosuppression Index (i)
HERV-FRD (Syncitin 2) + 0,64 + 0,36
HERV-W (Synctin 1) - 0,30 ± 0,06
It appears that whereas Synctin 2 presents a strong immunosuppressive activity, Synctin 1 is devoid of such an activity. Syncitin 2 is the first HERV envelope described to date with both immunosuppressive and fusogenic activity.

Claims

1. A protein or a polypeptide, characterized in that it conesponds to an amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide conesponding to said derived sequence presents a fusogenic activity similar to that of Syncitin 2 and/or an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2, and/or an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2.
2. A protein or a polypeptide according to claim 1, characterized in that it conesponds to an amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide conesponding to said derived sequence presents a fusogenic activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2, and/or an antigenic activity similar to that of Syncitin 2.
3. A protein or a polypeptide according to claim 1, characterized in that it conesponds to an amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide conesponding to said derived sequence presents an immunosuppressive activity similar to that of Syncitin 2 and/or an antigenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents an immunosuppressive activity similar to that of Syncitin 2, and/or an antigenic activity similar to that of Syncitin 2.
4. A protein or a polypeptide according to claim 1 or 2, characterized in that it conesponds to an amino acid sequence, comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 2 (Syncitin 2), or
• a sequence derived from SEQ ID NO: 2 by insertion, deletion or substitution of at least one amino acid, provided that the protein or the polypeptide conesponding to said derived sequence presents a fusogenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 85% amino acid identity with SEQ ID NO: 2, provided that the protein or the polypeptide conesponding to said homologous sequence presents a fusogenic activity similar to that of Syncitin 2.
5. A protein or a polypeptide according to claim 2, characterized in that it conesponds to an amino acid sequence comprising or being constituted by a sequence derived from SEQ ID NO: 2 by deletion of at least the 17 contiguous amino acids from position 414 to position 430 of SEQ ID NO: 2.
6. A protein or a polypeptide according to claim 5, characterized in that it conesponds to SEQ ID NO: 64.
7. A nucleic acid, characterized in that it conesponds to a sequence encoding a protein or a polypeptide as defined in any of claims 1 to 6, and/or to its complementary sequence.
8. A nucleic acid, characterized in that it conesponds to a nucleic acid sequence comprising or being constituted by:
• a sequence conesponding to SEQ ID NO: 1, or • a sequence derived from SEQ ID NO: 1 by insertion, deletion or substitution of at least one nucleotide, provided that said derived sequence encodes a protein or a polypeptide presenting a fusogenic activity similar to that of Syncitin 2, or
• a homologous sequence presenting at least 66% nucleotide identity with SEQ ID NO: 1, provided that said homologous sequence encodes a protein or a polypeptide presenting a fusogenic activity similar to that of Syncitin 2, or
• fragments of said sequences, such as SEQ ID NO: 3 or 4; and/or to its complementary sequence.
9. A nucleic acid, characterized in that it hybridizes with a nucleic acid according to claim 7 or 8 under stringent conditions.
10. A prokaryotic or eukaryotic expression vector, characterized in that it comprises a nucleic acid according to any of claims 7 to 9 and the elements required for its expression in a host cell.
11. A prokaryotic or eukaryotic cell, characterized in that it comprises vector according to claim 10.
12. An antibody, characterized in that it is directed against a protein or a polypeptide according to any of claims 1 to 6.
13. A purified natural human protein, characterized in that: it is recognized by an antibody according to claim 12 and, it presents a fusogenic activity.
14. A pharmaceutical or a vaccinal composition, comprising as active substance at least one substance selected from the group comprising: a protein or a polypeptide according to any of claims 1 to 6 and 13, a nucleic acid according to any of claims 7 to 9, a vector according to claim 10, or a cell according to claim 11; in association with a pharmaceutically acceptable vehicle.
15. A vaccinal composition according to claim 14, comprising as active substance a protein or a polypeptide according to any of claims 1 to 6 and 13, in particular according to claim 5 or 6, in association with a pharmaceutically acceptable vehicle.
16. A pharmaceutical composition, comprising as active substance at least one substance selected from the group comprising: an antibody according to claim 12, an antisense sequence hybridizing to SEQ ID NO: 1, a RNAi comprising a sequence hybridizing to SEQ ID NO: 1, or an aptamer directed against a protein conesponding to SEQ ID NO: 2, in association with a pharmaceutically acceptable vehicle.
17. The use of at least one substance selected from the group comprising: a protein or a polypeptide according to any of claims 1 to 6 and 13, a nucleic acid according to any of claims 7 to 9, a vector according to claim 10, or a cell according to claim 11 ; for the manufacture of a drug useful for the prevention and/or the treatment:
- of cancers or,
- of pathologies involving a cellular fusogenicity disorder or a syncitium morphogenesis disorder, such as a placental morphogenesis disorder or,
- of an immune system disorder, in particular an immune system disorder requiring an immunosuppressive treatment, such as allergy, autoimmune disease or graft rejection.
18. A method for detecting the Syncitin 2 protein or for measuring the concentration of the Syncitin 2 protein in a biological sample, characterized in that it comprises a step of contacting said biological sample with an antibody according to claim 12.
19. A method for detecting the Syncitin 2 mRNA or for measuring the concentration of the expression ofthe Syncitin 2 mRNA in a biological sample, characterized in that it comprises a step of contacting said biological sample with at least one nucleic acid according to any of claims 7 to 9.
20. A method according to claim 19, wherein the nucleic acids conespond to SEQ ID NO: 3 and SEQ ID NO: 4.
21. A method for the in vitro diagnosis of pathologies linked to the level of expression of Syncitin 2 in a tissue, comprising the following steps:
- taking a tissue sample from an individual,
- measuring, in said sample, the concentration Syncitin 2 mRNA, or the concentration of the Syncitin 2 protein.
22. A method for the screening of drags liable to modify the fusogenic activity of a polypeptide or a protein as defined in any of claims 1 to 6, characterized in that a drug to screen is contacted with cells expressing said polypeptide or protein, and the presence or the absence of fonnation of a syncitium by said cells is observed.
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