# Patent

## Title
Compositions and methods involving endogenous retrovirus proteins

## Abstract

This disclosure describes methods and compositions that involve endogenous retrovirus proteins as diagnostic markers and/or therapeutic agents. The detection of endogenous retrovirus envelope proteins on a cell surface can indicate early neoplasticity of the cell. Antibody compositions that specifically bind to cell-surface-expressed endogenous retrovirus proteins may be used in such diagnostic methods. Overexpression of the endogenous retrovirus proteins can slow cell growth and decrease cell viability.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application is the § 371 U.S. National Stage of International Application No. PCT/US2014/012964, filed 24 Jan. 2014, which claims priority to U.S. Provisional Patent Application Ser. No. 61/756,937, filed Jan. 25, 2013, each of which is incorporated herein by reference.
This application contains a Sequence Listing electronically submitted to the United States Patent and Trademark Office via EFS-Web as an ASCII text file entitled “2015-07-22_USNatlStage-SeqList_ST25_PTO.txt” having a size of 134 KB and created on Jul. 22, 2015. Due to the electronic filing of the Sequence Listing, the electronically submitted Sequence Listing serves as both the paper copy required by 37 CFR § 1.821(c) and the CRF required by §1.821(e). The information contained in the Sequence Listing is incorporated by reference herein and does not go beyond the disclosure in the Application as filed.


SUMMARY
This disclosure describes, in one aspect, a method of slowing cellular growth. Generally, the method includes increasing expression of an endogenous retrovirus envelope protein in at least one cell, wherein the cell expresses p53 and expression of the retrovirus envelope protein is controlled by p53; and exposing the cell to conditions that upregulate expression of p53.
This disclosure also describes a method of decreasing cell viability. Generally, this method includes increasing expression of an endogenous retrovirus envelope protein in at least one cell, wherein the cell expresses p53 and expression of the retrovirus envelope protein is controlled by p53; and exposing the cell to conditions that upregulate expression of p53.
In either case, in certain embodiments, the conditions that upregulate expression of p53 can include cellular stress. In some embodiments, increasing expression of an endogenous envelope protein can include overexpressing the endogenous envelope protein. In some of these embodiments, overexpressing the endogenous envelope protein can include introducing into the cell a polynucleotide that includes a coding region that encodes a functional portion of the endogenous envelope protein operably linked to a p53 response element. In some of these embodiments, the p53 response element can include the polynucleotide sequence reflected in SEQ ID NO:1. In other embodiments, the p53 response element can include at least 10 contiguous nucleotides of any one of: nucleotides 10-19 of SEQ ID NO:2, nucleotides 47-56 of SEQ ID NO:2, nucleotides 88-100 of SEQ ID NO:2, nucleotides 334-344 of SEQ ID NO:2, nucleotides 419-430 of SEQ ID NO:2, nucleotides 473-486 of SEQ ID NO:2, nucleotides 548-560 of SEQ ID NO:2, nucleotides 607-618 of SEQ ID NO:2, or nucleotides 679-690 of SEQ ID NO:2. In still other embodiments, the p53 response element can include nucleotides 169-179 of SEQ ID NO:3, nucleotides 246-255 of SEQ ID NO:3, nucleotides 337-346 of SEQ ID NO:3, nucleotides 371-380 of SEQ ID NO:3, nucleotides 460-469 of SEQ ID NO:3, nucleotides 524-533 of SEQ ID NO:3, nucleotides 588-597 of SEQ ID NO:3, nucleotides 786-795 of SEQ ID NO:3, nucleotides 800-809 of SEQ ID NO:3, nucleotides 892-901 of SEQ ID NO:3, or nucleotides 1122-1131 of SEQ ID NO:3.
In another aspect, this disclosure describes a composition that includes a polynucleotide that includes a coding region that encodes a functional portion of the endogenous envelope protein operably linked to a p53 response element. In some embodiments, the p53 response element can include the polynucleotide sequence reflected in SEQ ID NO:1. In other embodiments, the p53 response element can include at least 10 contiguous nucleotides of any one of: nucleotides 10-19 of SEQ ID NO:2, nucleotides 47-56 of SEQ ID NO:2, nucleotides 88-100 of SEQ ID NO:2, nucleotides 334-344 of SEQ ID NO:2, nucleotides 419-430 of SEQ ID NO:2, nucleotides 473-486 of SEQ ID NO:2, nucleotides 548-560 of SEQ ID NO:2, nucleotides 607-618 of SEQ ID NO:2, or nucleotides 679-690 of SEQ ID NO:2. In still other embodiments, the p53 response element can include nucleotides 169-179 of SEQ ID NO:3, nucleotides 246-255 of SEQ ID NO:3, nucleotides 337-346 of SEQ ID NO:3, nucleotides 371-380 of SEQ ID NO:3, nucleotides 460-469 of SEQ ID NO:3, nucleotides 524-533 of SEQ ID NO:3, nucleotides 588-597 of SEQ ID NO:3, nucleotides 786-795 of SEQ ID NO:3, nucleotides 800-809 of SEQ ID NO:3, nucleotides 892-901 of SEQ ID NO:3, or nucleotides 1122-1131 of SEQ ID NO:3. In any of these embodiments, the composition can further include a delivery vehicle.
In another aspect, this disclosure describes a composition that includes antibody that specifically binds to an endogenous retrovirus envelope protein. In some embodiments, the endogenous envelope protein can include HENV-R, HENV-W, HENV-V1, HENV-V2, HENV-F(c)1, HENV-F(c)2, HENV-FRD, HENV-R(b), HENV-H2, HENV-H1, HENV-H3 HENV-K (1q23.3), HENV-K1 (12q14.1), HENV-T, ABB52637, hCG2039029, or Q4KWC9. In some embodiments, the antibody can include a monoclonal antibody. In some embodiments, the antibody can include polyclonal antibodies.
In yet another aspect, this disclosure describes a method of identifying a subject as at risk of having cancer. Generally, the method includes obtaining a biological sample from a subject comprising cells from at least one tissue, analyzing the cells for expression of an endogenous retrovirus envelope protein, and identifying the subject as having or at risk of having cancer if the cells express the endogenous retrovirus envelope protein. In some embodiments, the tissue can include tissue of the ovary, colorectum, esophagus, head and neck, larynx, lung, skin, pancreas, stomach, liver, brain, bladder, breast, uterus, soft tissues, lymph nodes, prostate, bones endocrine glands, the hematopoietic system, or cervix. In particular embodiments, the tissue can include tissue of the human breast or tissue of the human prostate. In some embodiments, the endogenous retrovirus envelope protein can include HENV-R, HENV-W, HENV-V1, HENV-V2, HENV-F(c)1, HENV-FRD, HENV-R(b), HENV-H (3q26), HENV-H (2q24.3), HENV-K (1q23.3), HENV-K (12q14.1), HENV-T, ABB52637, hCG2039029, or Q4KWC9. In some embodiments, the method can further include providing the subject a treatment effective for treating cancer.
The above summary of the present invention is not intended to describe each disclosed embodiment or every implementation of the present invention. The description that follows more particularly exemplifies illustrative embodiments. In several places throughout the application, guidance is provided through lists of examples, which examples can be used in various combinations. In each instance, the recited list serves only as a representative group and should not be interpreted as an exclusive list.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Identification of hERVs transcriptionally upregulated after UV exposure in Mcf7 cells.
FIG. 2. HERV-W is upregulated in response to genotoxic stress.
FIG. 3. The 5′ LTR of HERV-W contains putative p53 response elements. Nucleotides in light shading reflect nucleotide matches with the consensus p53 response element sequence; nucleotides in dark shading indicate variation from the consensus p53 response element sequence.
FIG. 4. Mmergln-int is an endogenous retrovirus with intact gag, pol, and env coding regions.
FIG. 5. Semi-quantitative RT PCR detects the expression of Mmergln-int in p53+/+ MEFs but not in p53−/− MEFs. Two pairs of primers were made to span the transcript of Mmergln-int at the 5′ and regions of the transcript.
FIG. 6. Semi-quantitative RT PCR detects the expression of Mmergln-int in multiple adult and fetal tissues. RNA was extracted from the tissues two mice (n=2) for conversion to cDNA.
FIG. 7. Genotoxic stress upregulates the transcription of Mmergln-int. Detection of the upregulation of Mmergln-int transcript 8 hours after treatment with 50 kj/m2.
FIG. 8. Dox induces p53-independent expression of Mmergln-int.
FIG. 9. Overexpression of endogenous retrovirus results in decreased cell viability in p53+/−+MEFs. OD readings were plotted for absorbance measurements taken at 12, 36, 60 and 80 hours. Error bars represent S.D.
FIG. 10. Overexpression of Mmergln-int env is sufficient to decrease proliferation of p53+/+MEFs
FIG. 11. Identification of hERVs transcriptionally upregulated after UV exposure in LNCaP cells.
FIG. 12. The 5′ LTR of hERV-FRD contains putative p53 response elements. Nucleotides in light shading reflect nucleotide matches with the consensus p53 response element sequence; nucleotides in dark shading indicate variation from the consensus p53 response element sequence.
FIG. 13. Mmergln-int envelope can mediate cellular senescence. Transient overexpression of Mmergln-int results in decreased cell viability in wild type MEFs, which can be detected by a MTS assay.
FIG. 14. Lung carcinomas expressing endogenous retroviral envelopes exhibit early tumor latency (A) C57/B6 mice were injected with isogenic Lewis lung carcinoma (LLC1) cells harboring GFP, Mmergln-int endogenous retrovirus or Mmergln-int ENV. (B) On day 14 tumors are not detected in GFP expressing LLC1 cells but LLC1 cells expressing endogenous retrovirus or ENV localize to lungs to form tumors. (C) Kaplan Meier analysis compares lifespan of LLC1-GFP (green), LLC1-ERV (red) and LLC1-ENV (black) mice.
FIG. 15. HTLV-1-like envelopes are endogenized in the genomes of multiple vertebrate species. (A) A conserved domain database (CDD) analysis reveal that Mmergln-int ENV belongs to HTLV-1-like HR1-HR2 family of proteins. Sequences shown include HTLV-1-like HR1-HR2 domains from Gorilla gorilla gorilla (SEQ ID NOs:83 and 92); Homo sapiens (SEQ ID NOs:84, 87, 90, 91, 93, 98, 107, 108, 110, 111, 115, 116, 119, 120, and 122); Ailuropoda melanoleuca (SEQ ID NO:85); Callithrix jacchus (SEQ ID NOs:86 and 96); Pan troglodytes (SEQ ID NOs:88 and 99); Mus musculus (SEQ ID NOs:89, 95, 100, 101, 104, and 106); Trichosurus Vulpecula (SEQ ID NO:94); Monodelphis domestica (SEQ ID NOs:97, 102, and 105); Taeniopygia guttata (SEQ ID NOs:104, 113, and 117); Danio rerio (SEQ ID NO:109); Gallus gallus (SEQ ID NOs:112 and 188); Xenopus tropicalis (SEQ ID NO:114); Bos Taurus (SEQ ID NO:121); Ovis aries (SEQ ID NO:123). A consensus sequence is also shown (SEQ ID NO:124). (B) The HTLV-1-like HR1-HR2 domain was identified in human, gorilla, chimpanzee, bushtail, mouse, panda, marmoset, opossum, and zebra finch. Amino acids are highlighted to depict conservation among organisms. The degree of conservation is illustrated by calculating the conservation, quality, and consensus of the alignments.
FIG. 16. Conserved HTLV-1-like HR1-HR2 domain in 16 coding competent human retroelements.
FIG. 17. HTLV-1-like envelopes are stress responsive in humans. (A) envR, envl, and envW are transcriptionally upregulated in response to UV stress in human Mcf7 cells. (B) envW is upregulated at the protein level at 12 hours and at 24 hours after UV exposure.
FIG. 18. Highly conserved CKS-17 and CX(6)C domains in HERV and Mmergln-int ENV sequences with potential therapeutic consequences. Sequences shown include CKS-17 and CX(6)C domains from ENV-R (residues 524-593 of SEQ ID NO:75), ENV-R(b) (residues 354-427 of SEQ ID NO:76), ENV-T (residues 479-550 of SEQ ID NO:71), Mmergln-int envelope (residues 493-564 of SEQ ID NO:66), ENVF(c)-1 (residues 425-496 of SEQ ID NO:69), ENVF(c)-2 (residues 452-524 of SEQ ID NO:70), ENVW-1 (residues 356-427 of SEQ ID NO:67), ENVFRD-1 (residues 390-461 of SEQ ID NO:68), ENV-H2 (residues 430-501 of SEQ ID NO:73), ENV-H1 (residues 430-501 of SEQ ID NO:72), and ENV-H3 (residues 430-493 of SEQ ID NO:74). A consensus sequence is also shown (SEQ ID NO:125).
FIG. 19. Role of immune system in cancer and the scope of immunotherapy in treating cancer patients. (A) Different stages of tumorigenesis following an oncogenic stress. (B) Synergistic approach in boosting immunity through vaccine and inhibiting immune suppression as a therapeutic strategy for cancer patients.
FIG. 20. CKS-17 and CX(6)C conserved in human and mouse envelopes as antibody and vaccine candidates for cancer immunotherapy.



DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
This disclosure describes compositions and methods that reflect the observation that expression of endogenous retroviruses (ERVs) can decrease cell viability and/or limit cell growth. Thus, exploiting this feature of endogenous retroviruses can provide a basis for therapeutic compositions and methods for use in treating conditions of uncontrolled cell growth including, for example, neoplastic conditions such as various forms of cancer.
Endogenous retroviruses (ERVs) are polynucleotide sequences that are derived from retroviruses that have integrated into the genome of a vertebrate organism. The standard replication cycle of a retrovirus includes insertion of the retroviral DNA into the genome of the infected host cell. If the retrovirus integrates into germline cells, the integrated retrovirus may be passed on to subsequent generations, thus becoming an endogenous retrovirus.
If an endogenous retrovirus is active, it can relocate within the genome. In some cases, cancer may be caused by an endogenous retrovirus inserting into and disrupting a coding region that controls cell growth and inhibits cancer if not affected by the endogenous retrovirus. Global epigenetic changes that occur during cancer can reactivate an endogenous retrovirus so that elevated expression of the endogenous retrovirus is detectable.
The tumor suppressor p53 activates portions of the genome involved in apoptosis, senescence, and cell cycle arrest in response to cellular stress. One function of p53 is its role as a transcription factor, and the characterization of genes activated by p53 provides insight into mechanisms of tumor suppression. Although the identification of p53 target genes is common in cancer research, discerning the role of p53 in regulating non-genic regions of the genome is not.
We began by studying the role of p53 in regulating non-genic regions of the genome and discovered that p53, in addition to regulating expression of certain cancer genes, also regulates expression of non-genic regions such as, for example, endogenous retroviruses. We then discovered that endogenous retrovirus expression directly affects cell viability and can serve as a marker for elevated p53 expression.
This disclosure describes expression of endogenous retroviruses being induced by cellular stress. When induced in this manner, endogenous retrovirus expression can decrease cell viability and/or limit cell growth and, consequently, can serve as a suppressor of tumor growth.
Thus, in one aspect, this disclosure describes methods and compositions that exploit endogenous retrovirus expression in either early cellular stages (as opposed to clinical stages) of cancer or in later cellular stages of cancer (which encompass all clinical stages of cancer). In early cellular stages of cancer, in which a subject typically does not experience any symptoms or exhibit any clinical signs of cancer, endogenous retrovirus expression can be used to limit pre-cancerous cell growth. That is, during this cellular stage, expression of endogenous retroviruses is involved in natural pathways of cell death. One cause of cancer is disruption of these pathways so that cells ignore programmed cell death signals and persist. Increasing endogenous retrovirus expression at this stage can help reinforce natural programmed cell death pathways and decrease the likelihood that cells persist to become neoplastic.
In later cellular stages, endogenous retrovirus expression can serve as a tumor antigen and may, therefore, serve as a diagnostic marker of cancer or as a therapeutic target for, for example, therapeutic immunotherapy. Endogenous retrovirus expression is typically regulated by p53 so that elevated p53 expression may be reflected by elevated expression of the ERV. Moreover, endogenous retrovirus envelope polypeptides typically may be expressed on the surface of a cell expressing the ERV. Thus, the endogenous retrovirus envelope polypeptide can be a cell surface marker of elevated p53 expression inside the cell.
As used herein, the following terms shall have the indicated meanings:
“Antigen” and variations thereof refer to any material capable of raising an immune response in a subject challenged with the material. In various embodiments, an antigen may raise a cell-mediated immune response, a humoral immune response, or both. Suitable antigens may be synthetic or occur naturally and, when they occur naturally, may be endogenous (e.g., a self-antigen) or exogenous.
“At risk” refers to a subject that may or may not actually possess the described risk. Thus, for example, a subject “at risk” for developing a specified condition is a subject that possesses one or more indicia of increased risk of having or developing the specified condition compared to individuals who lack the one or more indicia, regardless of the whether the subject manifests any symptom or clinical sign of having or developing the condition. “Sign” or “clinical sign” refers to an objective physical finding relating to a particular condition capable of being found by one other than the patient. “Symptom” refers to any subjective evidence of disease or of a patient's condition.
“Coding region” refers to a nucleotide sequence that encodes a polypeptide and, when placed under the control of appropriate regulatory sequences expresses the encoded polypeptide. The boundaries of a coding region are generally determined by a translation start codon at its 5′ end and a translation stop codon at its 3′ end. A “regulatory sequence” is a nucleotide sequence that regulates expression of a coding sequence to which it is operably linked. Regulatory sequences include, for example, promoters, enhancers, transcription initiation sites, translation start sites, translation stop sites, and transcription terminators. The term “operably linked” refers to a juxtaposition of components such that they are in a relationship permitting them to function in their intended manner. A regulatory sequence is “operably linked” to a coding region when it is joined in such a way that expression of the coding region is achieved under conditions compatible with the regulatory sequence.
“Express” and variations thereof refer to the conversion of genetic information in a nucleotide sequence to a gene product. Expression of a polynucleotide sequence (e.g., a gene) may be measured and/or described with reference to (a) transcription of DNA to mRNA, (b) translation of mRNA to protein, (c) post-translational steps (e.g., modification of the primary amino acid sequence; addition of a carbohydrate, a lipid, a nucleotide, or other moiety to the protein; assembly of subunits; insertion of a membrane-associated protein into a biological membrane; and the like), or any combination of the foregoing.
“Polypeptide” and “protein refer to a sequence of amino acid residues without regard to the length of the sequence. Therefore, the terms “polypeptide” and “protein” may be used interchangeably to refer to any amino acid sequence having at least two amino acids and may refer to a full-length protein, a fragment thereof, and/or, as the case may be, a polyprotein.
“Specific” and variations thereof refer to having a differential or a non-general (i.e., non-specific) affinity, to any degree, for a particular target.
“Treat” or variations thereof refer to reducing, limiting progression, ameliorating, or resolving, to any extent, the symptoms or signs related to a condition. A “treatment” may be therapeutic or prophylactic. “Therapeutic” and variations thereof refer to a treatment that ameliorates one or more existing symptoms or clinical signs associated with a condition. “Prophylactic” and variations thereof refer to a treatment that limits, to any extent, the development and/or appearance of a symptom or clinical sign of a condition. Generally, a “therapeutic” treatment is initiated after the a condition manifests in a subject, while “prophylactic” treatment is initiated before a condition manifests in a subject.
The term “and/or” means one or all of the listed elements or a combination of any two or more of the listed elements.
The terms “comprises” and variations thereof do not have a limiting meaning where these terms appear in the description and claims.
Unless otherwise specified, “a,” “an,” “the,” and “at least one” are used interchangeably and mean one or more than one.
Also herein, the recitations of numerical ranges by endpoints include all numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.80, 4, 5, etc.).
Mmergln-int is a murine LTR retrotransposon that is expressed in multiple tissues. Initially, in studies described in more detail below, we discovered that Mmergln-int (a) contains open reading frames for common retroviral genes gag, pol, and env, (b) p53 activates Mmergln-int expression, and (c) upregulated expression of Mmergln-int env decreases cell viability in the presence of p53.
Using the Conserved Domain Database, we observed that the envelope of Mmergln-int belongs of the Ebola HIV-1-like heptad repeat 1-heptad repeat 2 superfamily (HR1-HR2 superfamily), a domain superfamily characterized by its HR1-HR2 domain. The HR1-HR2 domain is present in numerous exogenous and endogenous retroviruses. Thus, our observations using the murine Mmergln-int may be extrapolated to endogenous retrovirus envelope proteins in the HR1-HR2 superfamily. We collated the GI numbers from each subfamily of the HR1-HR2 superfamily and found a total of 70 proteins that were classified as members of the HR1-HR2 superfamily, 42 of which are found in non-viral species (Table 1). Of the 42 HR1-HR2 Domain-containing proteins found in non-viral species, 15 are found in Homo sapiens. (Table 2). Interestingly, while the H1-H2 superfamily Env proteins in humans are highly conserved, the corresponding Gag and Pol proteins are highly mutated and no longer have open reading frames. This suggests selective pressure to preserve the Env protein because it is the functional component of the endogenous retrovirus.










TABLE 1





Reference No.
Organism
Reference No.
Organism







GI: 281351230
Ailuropoda melanoleuca (giant
GI: 44887882
Homo sapiens


(Seq ID No. 85)
panda)




GI: 83722646
Atlantic salmon swim bladder
GI: 44887889
Homo sapiens



sarcoma virus ‡




GI: 120561155
Avian leukosis virus ‡
GI: 47716681
Homo sapiens


GI: 123217679
Bos taurus (cattle)
GI: 119476
HoMuLV murine leukemia virus ‡


(Seq ID No. 121)





GI: 119400
Bovine immunodeficiency virus
GI: 119464
Human T-cell lymphotrophic



R29 ‡

virus type 1 ‡


GI: 296215288
Callithrix jacchus (white-tufted-
GI: 4930066
Human T-lymphotropic virus 1 ‡


(Seq ID No. 86)
ear marmoset)




GI: 296220571
Callithrix jacchus (white-tufted-
GI: 119467
Human T-lymphotropic virus 2 ‡


(Seq ID No. 96)
ear marmoset)




GI: 148726013
Danio rerio (zebrafish)
GI: 82300752
Jaagsiekte sheep retrovirus ‡


(Seq ID No. 109)





GI: 193885318
Ebola virus ‡
GI: 82294412
Jembrana disease virus ‡


GI: 5107713
Ebola virus ‡
GI: 465412
Marburg virus ‡


GI: 82278767
Equine infectious anemia virus ‡
GI: 119482
Mason-Pfizer monkey virus ‡


GI: 82302297
Equine infectious anemia virus ‡
GI: 126294061
Monodelphis domestica (gray




(Seq ID No. 102)
short-tailed opossum)


GI: 399433
Feline endogenous virus ECE1 ‡
GI: 126331679
Monodelphis domestica (gray




(Seq ID No. 97)
short-tailed opossum)


GI: 82317606
Feline immunodeficiency virus ‡
GI: 126340267
Monodelphis domestica (gray




(Seq ID No. 105)
short-tailed opossum)


GI: 82281565
Feline immunodeficiency virus ‡
GI: 111145928
Mouse mammary tumor virus





(MMTV) ‡


GI: 119417
Feline leukemia provirus ‡
GI: 27735176
Mus musculus (house mouse)


GI: 30313561
Gallus gallus (chicken)
GI: 33667796
Mus musculus (house mouse)


(Seq ID No. 112)





GI: 45383091
Gallus gallus (chicken)
GI: 74180532
Mus musculus (house mouse)


(Seq ID No. 118)





GI: 47605605
Gorilla gorilla gorilla (western 
GI: 12854150
Mus musculus (house mouse)


(Seq ID No. 92)
lowland gorilla)




GI: 47605612
Gorilla gorilla gorilla (western 
GI: 148703999
Mus musculus (house mouse)


(Seq ID No. 83)
lowland gorilla)




GI: 119432
HIV-1 ‡
GI: 26332246
Mus musculus (house mouse)


GI: 119439
HIV-1 ‡
GI: 149412708
Ornithorhynchus anatinus





(platypus)


GI: 119595081
Homo sapiens
GI: 157779048
Ovis aries (sheep)




(Seq ID No. 123)



GI: 121944325
Homo sapiens
GI: 114645334
Pan troglodytes (chimpanzee)




(Seq ID No. 88)



GI: 145651814
Homo sapiens
GI: 24474949
Pan troglodytes verus




(Seq ID No. 99)



GI: 44887864
Homo sapiens
GI: 223627
Rous sarcoma virus ‡


GI: 44887888
Homo sapiens
999443
Simian immunodeficiency virus





(SW) ‡


GI: 47605576
Homo sapiens
2EZS A
Simian immunodeficiency virus





(SW) ‡


GI: 47605616
Homo sapiens
GI: 119494
Simian immunodeficiency virus





(SW) ‡


GI: 47716681
Homo sapiens
GI: 3891827
Simian immunodeficiency virus





(SW) ‡


GI: 80550508
Homo sapiens
GI: 224132894
Taeniopygia guttata (zebra




(Seq ID No. 103)
finch)


GI: 195963433
Homo sapiens
GI: 224147561
Taeniopygia guttata (zebra




(Seq ID No. 117)
finch)


GI: 300796687
Homo sapiens
GI: 224167236
Taeniopygia guttata (zebra




(Seq ID No. 113)
finch)


GI: 300796709
Homo sapiens
GI: 11055586
Trichosurus vulpecula (common




(Seq ID No. 94)
brushtail)


GI: 44887863
Homo sapiens
GI: 325053859
Unknown




GI: 301605491
Xenopus (Silurana) tropicalis




(Seq ID No. 114)
(western clawed frog)





‡ virus species

















TABLE 2







Envelope
Chromosomal Location
GI No.









envR
7q21.2
GI: 145651814



envW
7q21.2
GI: 195963433



envV 1
19q13.41 
GI: 300796687



envV 2
19q13.41 
GI: 300796709



envF(c)1
Xq21.33
GI: 44887863



envF(c)2
7q36.2
GI: 7770445



envFRD
6p24.1
GI: 44887864



envR(b)
3p24.3
GI: 44887882



envH2
3q26
GI: 44887888



envH1
2q24.3
GI: 44887889



envH3
2q24.1
GI: 8439399



envK
1q23.3
GI: 47605576



envK1
12q14.1
GI: 47605616



envT
19q13.11 
GI: 47716681



ABB52637
unknown
GI: 80550508



hCG2039039
unknown
GI: 119595081



Q4KWC9
unknown
GI: 121944325










Next, we stressed human cells to determine whether one can detect upregulation of these retroviral Env proteins. We designed a qPCR-based screen and determined that endogenous retroviral Env proteins are indeed upregulated at the transcript level in human cells. We designed qPCR primers to specifically recognize the intact open reading frames of the endogenous retroviral Env proteins. We detected upregulation of endogenous retrovirus Env proteins in cells from various human tissues. For example, the endogenous retrovirus Env proteins HERV-FRD, HERV-K, HERV-R, HERV-V, HERV-ENV2, and HERV-W were upregulated in a human breast cell line eight hours after UV exposure. As another example, the endogenous retrovirus Env proteins HERV-F(c)1 and HERV-FRD were upregulated in a human prostate cell line after similar UV exposure. Moreover, HERV-W was upregulated at the protein level, with an increase in protein level eight and 24 hours after UV exposure in comparison to non-treated Mcf7 cells (FIG. 2).
To find further evidence for regulation of HERV-W by p53, we looked for p53 response elements in the LTR of HERV-W. We identified nine decameric motifs with high similarity to the p53 consensus sequence. (FIG. 3, light shading reflects consensus sequence nucleotides, dark shading reflects point mutations). We did not find two motifs with a spacer of less than 13 nucleotides. However, substantial transactivation of p53 by noncanonical p53 consensus sequences that contain a single decameric motif, or “half-site” have been identified (Jordan et al., 2008. PLoS Genet 4(6):e1000104).
Thus, p53 activates the expression of endogenous retroviral Env proteins in humans. The ability of ancient retroviruses to sense cellular stress of their host may have been advantageous to the retrovirus in determining its state in the lytic and lysogenic cycle. The exaptation of retroviral Env proteins of the Ebola RSV-like HR1-HR2 domain superfamily may be beneficial to non-viral organisms also. Although many human endogenous retrovirus loci are degenerate due to the accumulation of mutations that result in truncated open reading frames that can render the gag and the pol proteins nonfunctional, the open reading frames of endogenous retrovirus envelope coding regions have remained intact. This suggests a positive selection for the endogenous retrovirus envelope proteins, which are likely to be functional. We demonstrate that expression of endogenous retroviral Env open reading frames is upregulated in the modern human genome following cellular stress. Also, because their expression is regulated by p53, the expressed Env proteins can serve as a cell surface marker for cells that overexpress p53, one hallmark of neoplasticity.
Moreover, the expression of endogenous retroviral Env protein in the modern human genome is consistent with the expression of corresponding retroviral Env protein we observed in the mouse genome. Endogenous retrovirus Env expression and p53 response elements that regulate expression of endogenous retrovirus Env proteins are similar in mouse and humans. As described in more detail below, murine endogenous retrovirus Env expression decreases cell viability. The similarities that we have observed in endogenous retrovirus Env expression in mouse cells and human cells lead us to conclude that expression of human endogenous retrovirus Env proteins decreases cell viability in a manner similar to that observed in mouse cells. Accordingly, overexpression of human endogenous retrovirus Env proteins can provide targeted cell-based therapy against neoplastic cells originating from various human tissues such as, for example, breast tissue and prostate tissue. In addition, p53 mutations are reported in cancer of the ovary, colorectum, esophagus, head and neck, larynx, lung, skin, pancreas, stomach, liver, brain, bladder, breast, uterus, soft tissues, lymph nodes, prostate, bones endocrine glands, the hematopoietic system, and cervix. Furthermore, p53 transactivation of target genes—e.g., endogenous retrovirus Env—is involved tumor suppression in these tissues. Finally, aberrant expression of endogenous retroviruses is evident in lymphoma, breast cancer, melanoma and cells of the immune system in human cancers. Therefore, overexpression of endogenous retrovirus Env proteins can provide targeted cell-based therapy against neoplastic cells originating from these other tissues.
To investigate whether p53 regulates the expression of non-genic regions of the murine genome, we performed RNA Sequencing on primary p53+/+, p53+/−, and p53−/− mouse embryonic fibroblasts (MEFs). RNA Seq identified transcription of both established p53 targets and novel p53 targets. Among the top genomic loci differentially expressed among p53+/+, p53+/−, and p53−/− MEFs, we identified transcription of genomic loci for which no references genes are annotated. Within these genomic coordinates, we identified LTR Retrotransposons, LINES, SINES, Micro Satellites, Low Complexity Repeats and DNA Repeat Elements. (Table 3).







TABLE 3







RNA Sequencing Data Analysis








Genome coordinates
Repetitive Elements





chr2: 75476500-
MMVL30-int and other LTR 


75486500
Retrotransposons, SINES and Micro Satellites


clu-4: 149442800-
LTR Retrotransposons, SINES, LINES, 


149452800
Micro Satellites and Low Complexity Repeats


chr8: 124357500-
Mmergln-int and other LTR Retrotransposon, 


124367500 
SINES, Micro Satellites, DNA Repeat elements









Using the Integrated Genome Viewer, we extracted the sequences of the regions which demonstrated loss of expression in p53−/− MEFs. We identified expression of the LTR Retrotransposons MMV30-int and Mmergln-int and SINEs of the Alu, B2 and B4 families in p53+/+ and p53−/+MEFs, and loss of expression in p53−/− MEFs.

Mutations in the genome frequently render endogenous retroviruses inactive. Therefore, we determined whether we could identify the open reading frames (ORFs) in the LTR retrotransposons MMV30-int and Mmergln-int. Using NCBI's Open Reading Frame Finder, we did not find open reading frames within the sequence of MMV30-int. We identified that the transcript of Mmergln-int, derived from chromosome 8: 124357175-124364734 (mm9), contains open reading frames with homology to retroviral gag, pro, pol, and env coding regions. In the +1 frame from basepairs 526-2139, we detected homology to the matrix protein, p15, and Gag p30, which are involved in viral assembly and pathogenicity. In the +1 frame at nucleotide position 2395-5682, we detected sequence homology to the RT ZFREV-like family of reverse transcriptases, Bel/Pao family of RNase HI, and a Rve Integrase which mediates the integration the provirus into the host genome. Finally, we detected the env coding region at nucleotide position 6514-7518, which belongs to Ebola RSV-like heptad repeat 1-heptad repeat 2 (HR1-HR2) domain superfamily. (FIG. 4). Mmergln-int can encode functional retroviral particles and is highly abundant in the mouse genome. We detect 86 genomic loci with homology to Mmergln-int throughout the murine genome, distributed across every murine chromosome with the exception of chromosome 20.
To verify that expression of Mmergln-int is p53-dependent, we performed semiquantitative reverse transcriptase PCR (RT-PCR) using cDNA generated from p53+/+ and p53−/− MEFs. Consistent with our RNA Seq data, we detected the expression of MMergln-int in p53+/+MEFs, but not in p53−/− MEFs (FIG. 5). The expression of endogenous retroviruses often may be restricted to few tissues such as the placenta. Therefore, investigated the distribution of Mmergln-int expression among multiple tissue types. We detected the transcript of Mmergln-int in all tissues examined with the highest expression being found in the placenta and lowest in the spleen. (FIG. 6).
After observing that Mmergln-int expression is lost in the absence of p53, we looked for evidence of p53 regulatory elements within the promoter region of Mmergln-int. The p53 tetramer binds a highly conserved p53 responsive element (RE). The p53 RE is defined as two decameric motifs, with a sequence of RRRCWWGYYY (SEQ ID NO:1) where R=purine, Y=pyrimidine, W=A or T. The two decameric motifs are separated by a spacer of 0 to 13 nucleotides. Since the Long Terminal Repeats (LTRs) of retroviruses serve as promoters, we searched for the presence a p53 response element within the LTR of Mmergln-int. Within the 430 by of the Mmergln-int LTR, RLTR1B, we found the sequence GGACATGCCCGGGCAAGCCC (SEQ ID NO:4) at position 103-123, which fits the sequence criteria of a p53 RE, with a spacer of 0 nt.
To test the ability of p53 to regulate the expression of Mmergln-int, we cloned the LTR into a promoterless luciferase vector and tested its ability to drive the expression of luciferase in p53+/+ and p53−/− MEFs. We detected robust expression of luciferase in p53+/+MEFs greater than or equal to our p21 promoter positive control vector. We detected negligible luciferase expression driven by p21 or the LTR in p53−/− MEFs. To determine if the Mmergln-int p53 response element is the single site of p53 regulation within the LTR, we performed site-directed mutagenesis to render the promoter non-functional. The cytosine at nt positions 4 of the decameric motif is highly conserved because it mediates DNA-protein interaction. Therefore, we generated cytosine to adenine transversion mutations at position 107, 177, or both 107 and 117. The transversion mutations and mutant p21 promoter failed to promote luciferase expression in p53+/+ and p53−/− MEFs.
The stability of p53 can be increased in response to various forms of cellular stress. To determine if enhanced p53 stability upregulates Mmergln-int expression, we treated the MEFs with UV irradiation or Doxorubicin. We observe a significant increase in luciferase expression driven by the LTR after exposure to genotoxic agents in p53+/+ MEFs. Furthermore, we detect a 2.1±0.19 fold increase of the Mmergln-int transcript post UV irradiation. (FIG. 7). To detect a physical interaction of p53 with the LTR of Mmergln-int, we performed chromatin immunoprecipitation in p53+/+ and p53−/− MEFs. The p53 antibody precipitated the LTR as well as other established p53 target genes in p53+/+ MEFs.
Next, we analyzed the functional consequences of Mmergln-int expression. With the similarities observed between Mmergln-int expression and human endogenous retrovirus Env proteins expression, Mmergln-int serves as a model for human endogenous retrovirus Env expression. Thus, one can extrapolate the functional consequences of Mmergln-int expression to be similar to the functional consequences of human endogenous retrovirus Env expression.
We developed a doxycycline-inducible system to overexpress Mmergln-int in p53+/+ and p53−/− MEFs. Upon induction with doxycycline, we detected the expression of GFP by florescence microscopy and observed a 15-fold (±4.1) and 51-fold (±9.6) increase of the Mmergln-int transcript in p53+/+ and p53−/− MEFs, respectively (FIG. 8). Thus, expression of Mmergln-int may be induced in both p53+/+ and p53−/− MEFs.
To determine cell viability, we performed a MTT assay. We detected no significant change in cell viability upon induction of GFP in either p53+/+ or p53−/− MEFs (FIGS. 9a and 9b) or induction of Mmergln-int (ERV) in p53−/− MEFs (FIG. 9d). We saw a decrease in cell viability, however, in p53+/+MEFs at 36 hours (1.5 days), 60 hours (2.5 days), and 84 hours (3.5 days) after exposure to doxycycline (FIG. 9c). No decrease in cell viability was observed in p53−/− MEFs overexpressing Mmergln-int. Thus, p53 is involved in cell death mediated by Mmergln-int, indicating that the Mmergln-int functions in a feed forward signaling mechanism that enhances p53 activity that decreases in cellular viability. Moreover, expression of Mmergln-int Env is sufficient to mediate cell death. We individually expressed the gag, pol, or env of Mmergln-int under a CMV promoter. We observe a decrease in cell viability at 3.5 days post transfection with the Mmergln-int env, but not after transfection with either gag or pol. (FIG. 10).
When inspecting the morphology of the MEFs by bright field microscopy, we observed what appeared to be syncytia. We performed immunofluorescence using an anti-β-catenin antibody to detect the cellular membrane and DAPI to stain the nuclei. Some viral envelopes of the Ebola RSV-like HR1-HR2 domain superfamily mediate cellular fusion through their HR1-HR2 domain. Cellular fusion mediated by viral envelopes can mediate cell death via apoptotic and non-apoptotic pathways.
The observation that p53−/− MEFs do not demonstrate significant changes in cell viability suggests p53 is involved in cell death pathways induced by overexpression of Mmergln-int Env. Interestingly, the HIV retroviral envelope, which is also a classified as a member of the Ebola RSV-like HR1-HR2 domain superfamily activates the p53 signaling pathway. Expression of the HIV envelope protein induces cellular fusion and subsequent mitotic catastrophe through the activation of Chk2, a upstream component of the p53 signaling pathway. Therefore, it is possible that the observed cellular fusion phenotype reflects the mechanism of cell death responsible for the decrease in cell viability. It is further possible that additional or alternative pathways amplify the p53 signaling pathway. For example, expression of the hERV-W Env protein can activate the endoplasmic reticulum (ER) stress responses and ER stress can induce apoptosis through p53 signaling.
Mmergln-int envelope can induce cellular senescence in wild type mouse embryonic fibroblasts. Overexpression of entire Mmergln-int, or its envelop (but not gag or pol) leads to decreases in cell viability in p53+/+ mouse embryonic fibroblasts (MEFs), and the transient overexpression of the env is sufficient to induce cellular senescence in p53+/+MEFs (FIG. 13).
Mmergln-int envelope can enhance tumorigenicity of transformed cells in vivo. We investigated the consequences of ectopic expression of Mmergln-int ENV in the context of already transformed cells. We expressed full length Mmergln-int ERV, Mmergln-int ENV or the GFP constructs in Lewis lung carcinoma (LLC1), a cell line isolated from a lung tumor of a C57BL mouse and which form lung cancer in mice. 2×105 cells of each genotype were inoculated into C57BL mice via tail vein injection. Tumor volume was monitored by measuring the luciferase level in live mice every seven days (FIG. 14). The moribund mice were euthanized, the tumor tissue harvested, and histopathology was performed. Expression of Mmergln-int ERV or Mmergln-int ENV significantly increased the tumor burden and reduced the tumor latency in vivo. The median survival for mice inoculated with LLC1 expressing Mmergln-int ERV or Mmergln-int ENV are 21 and 22.5 days, compared to mice inoculated with LLC1 expressing GFP having median survival of 31 days, p<0.001, FIG. 14C). Median survival is the time period at which 50% of the mice have died. This suggests that expression of Mmergln-int ENV can lead to enhanced tumorigenicity of transformed cells in vivo.
Mmergln-int envelope belongs to a conserved HTLV-1-like HR1 HR2 protein domain family shared by many vertebrates (FIG. 15). A further examination of Mmergln-int ENV protein reveals that it is classified as member of the HTLV-1-like heptad repeat 1-heptad repeat 2 (HR1-HR2) protein domain family, a group of proteins that share a motif found in the oncogenic retrovirus human T-cell leukemia virus type 1 (HTLV-1, FIG. 15A). This highly conserved domain is present in modern infectious viruses and also is found endogenized in the genomes of many vertebrate species including, for example, humans, gorilla, chimpanzee, bushtaii, mouse panda, marmoset, opossum, and zebra finch (FIG. 15B). In addition, oncogenic retroviral envelope proteins from viruses such as Jaagsiekte Sheep Retrovirus (JSRV), avian hemangioma retrovirus (AHV), and Friend spleen focus-forming virus (SFFV) have been identified. Unlike classic mechanisms of retroviral tumorigenesis (e.g., viral capture of host proto-oncogenes or capture of host gene regulation through insertational mutagenesis), some retroviral envelope proteins alone can serve as promote malignant transformation. Infection by exogenous JSRV can cause lung cancer in sheep, and cellular transformation can be mediated by the viral envelope alone. Human lung tumors examined for JSRV infection did not find evidence for the exogenous sheep virus. Endogenous sequences similar to JSRV were detected in human lung tumors, however. The human endogenous retrovirus sequences with a high degree of homology to JSRV may contribute to the development of lung cancer tumors.
We further analyzed human endogenous retroviral envelopes belonging to HTLV 1-like HR1-HR2 protein family. Up to 8% of the human genome are endogenous retroviral sequences. Most of the sequences of retroviral origin have lost their coding potential, thus relegating the status of these sequences as ‘junk DNA’. However, an analysis of the complete human genome revealed that 16 envelope sequences of retroviral origin have retained their coding potential. All 16 sequences code for retroviral envelope genes, while the gag and pol genes of endogenous retroviruses have accumulated mutations that render them inactive. This suggests a positive selection for sequences that encode the endogenous retrovirus envelope proteins. An analysis of these 16 envelope sequences using conserved domain database (CDD) shows that all of them belong to the HTLV-1 HR1-HR2 family of proteins (FIG. 16), similar to Mmergln-int envelope protein.
Human endogenous retrovirus envelope proteins are induced following DNA damage. We observe an approximately twofold upregulation of envR, envl, and envW transcripts in human p53+/+ breast carcinoma cells after UV exposure, a known agent to induce p53 (FIG. 17A). Although very few antibodies exist to detect expression of human endogenous retroviruses, we were able to confirm that protein level of envW increases at eight hours and 24 hours after UV exposure relative to non-treated cells (FIG. 17B). This suggests that these proteins are stress responsive and can be used as early markers following DNA damage.
We identified immunomodulatory domains in Mmergln-int and human endogenous retrovirus envelope proteins. To delineate the mechanism by which Mmergln-int ENV promotes tumorigenesis, we looked for putative protein domains within the ENV that may interact with established cancer signaling pathways. Using the conserved domain database we identified a distinct immunosuppressive domain residing within the ENV of the HR1-HR2 protein domain family. This well classified domain of 17 amino acid residues, referred to as a CKS-17 peptide, activates the Ras-Raf-MEK-MAPK and PI3K-AKT-mTOR signal transduction pathways. The CKS-17 peptide also can exert effects on cytokine regulation, which culminate in the inhibition of natural killer cells, macrophages, and cytotoxic T lymphocytes. Taken together, Mmergln-int ENV and homologous human endogenous retrovirus envelope proteins can enhance tumorigenesis by activating oncogenic signaling pathways and inhibiting an immune response associated with the clearance of neoplastic cells.
We also found that the human ENV proteins share a CX(6)C motif with Mmergln-int ENV, harboring conserved cysteine (C) residues separated by six amino acids (FIG. 18). The conserved cysteine residues may be involved in mediating cell fusion when these envelope proteins are expressed in response to oncogenic activation in non-cancerous cells, resulting to cellular senescence.
Understanding how cancer originates and progresses can lead to the development of better diagnostics and therapeutics. this disclosure addresses two issues regarding tumorigenesis, namely 1) the earliest molecular markers of cancer initiation, and 2) how these molecules activate oncogenic signaling pathways as well as interact with the immune system, thereby promoting expansion of neoplastic cells. Elevated expression of endogenous retrovirus proteins may allow identification of individuals at risk of developing cancer before the individuals begin to display any clinical sign or exhibit any symptoms of cancer. Therapeutically, the identification of markers of cancer initiation with immunosuppressive properties, such as human endogenous retrovirus (hERV) envelope proteins, can provide new therapeutic targets that allow for earlier medical interventions. Because the endogenous retrovirus envelope proteins have immunosuppressive activity, therapies that target these markers can be used as adjuvants that allow other immunotherapies to act without the immunosuppressive influence of the hERV envelope proteins.
The role of oncogene-induced senescence and how the immune system takes part in preventing cancer is illustrated in FIG. 19. Following an oncogenic assault (e.g., DNA damage, activation of an oncogene, etc.), the senescence program intrinsic in the cellular defense mechanism is activated. This results in cells that are affected with genotoxic stress undergoing replicative senescence, cell fusion, and ultimately being cleared by immune cells. Thus, the immune system plays an important role in the senescence barrier to cancer. Neoplasia develops, however, when some of these cells escape the immune surveillance mechanism by activating an immune suppressing mechanism. The cells that evade the immune surveillance system can lead to expansion of cancerous cells that ultimately leads to tumor formation and/or malignancy (FIG. 19A).
In one aspect, therefore, this disclosure describes a therapeutic composition that includes components that interact with human endogenous retrovirus envelope proteins. In some embodiments, the composition can include antibody that specifically binds to the CKS-17 domain of a human endogenous envelope protein. As sued herein, the term “antibody” in the absence of a preceding definite or indefinite article, is a general term that encompasses both polyclonal preparations and monoclonal antibodies. Such antibody can interfere with the cell signaling activity of the CKS-17 domain and/or reduce the immunosuppression (e.g., reduce inhibition of NK cells, macrophages, and CTLs) exerted by the endogenous retrovirus envelope protein through the CKS-17 domain. In some of these embodiments, the antibody can include a monoclonal antibody.
In other cases, the composition can include a component that interacts with the CX(6)C domain of a human endogenous envelope protein to promote cell fusion, senescence, and/or immune clearance of pre-malignant or malignant neoplastic cells. CX(6)C may play a role in activation of innate immunity. For example, the CX(6)C motif can be recognized as a pathogen-associated molecular patterns (PAMPs) by, for example, toll-like receptors (TLRs) on antigen-presenting cells (APCs). The TLRs can then induce cytokines and chemokines and trigger other events that would result into induction and activation of matured T-cells and subsequently result into immune clearance of the pre-cancerous or malignant cells. Therefore, the CX(6)C motif can serve as a prophylactic vaccine candidate, similar to the ones used against cervical cancer caused by human papillomavirus. In some embodiments, the composition can include both a monoclonal antibody that specifically binds to the CKS-17 domain and a component that interacts with the CX(6)C domain. Such a composition can inhibit the mechanism by which cancer cells suppress immunity—i.e., reduce the inhibition of T cells that otherwise attack and/or clear cancer cells from the body (FIG. 20). Such a composition also can increase activity related to the identification and clearance of neoplastic cells from the body by promoting senescence and cell clearance.
In the preceding description, particular embodiments may be described in isolation for clarity. Unless otherwise expressly specified that the features of a particular embodiment are incompatible with the features of another embodiment, certain embodiments can include a combination of compatible features described herein in connection with one or more embodiments.
For any method disclosed herein that includes discrete steps, the steps may be conducted in any feasible order. And, as appropriate, any combination of two or more steps may be conducted simultaneously.
The present invention is illustrated by the following examples. It is to be understood that the particular examples, materials, amounts, and procedures are to be interpreted broadly in accordance with the scope and spirit of the invention as set forth herein.
EXAMPLES
Cell Culture
Mouse embryonic fibroblasts (MEFs) were derived from embryos 12.5 days post-conception (dpc) with a mixed B6/129 background (The Jackson Laboratory, Bar Harbor, Me.). The embryos were homogenized and plated on 10 cm tissue culture dishes. When cells reached confluency, they were passaged on three 10 cm dishes (p1), then frozen down into three vials per plate. The p1 vials of MEFs were thawed and the cells were expanded to passage 3 for experimental use. All experiments were conducted with early passage cells (p3-p6). MEFs were cultured in DMEM supplemented with 10% FBS and penicillin-streptomycin (100 units/ml). MCF p7 cells were cultured in DMEM supplemented with 10% FBS, penicillin-streptomycin (100 units/ml) and insulin (0.01 mg/ml). In induce cellular stress, cells were exposed to UV light (50 J/m2) or doxorubicin (50 mg/ml).
MEFs were transiently transfected using the NEON transfection system (Invitrogen, Life Technologies Corp., Grand Island, N.Y.) or the FuGENE HD transfection reagent (Promega Corp., Madison, Wis.). Using the NEON transfection system, MEFs were pulsed once with a pulse voltage of 1,350 V and a pulse width of 30 ms at a density of 5×106/ml cells. To generate stable cell lines, MEFs were selected with puromycin. The expression of the tet-on constructs was induced using 50 ng/ml of doxycycline.
Generation of Constructs
Mmergln-int was PCR amplified from BAC RP23-8H9 using LA Taq DNA Polymerase (Takara Bio Inc., Shiga, Japan) and the following primers:









Mmergln-int F:



(SEQ ID NO: 5)



5′-GGTTCCAATGCGCATTTGGAGGTCCCAGCGAGAT-3′



 



Mmergln-int R:



(SEQ ID NO: 6)



5′-GGTTCCAAACTAGTTTCCCCTCTTCTTCTGTTTAGAC-3′.






Thermocycler conditions: 94° C. 1 min/94° C. 30 sec, 58° C. 1 min, 72° C. 9 min for 30 cycles/72° C. 10 min.
The gag, pol and env were PCR amplified from BAC RP23-8H9 using LA Taq DNA Polymerase (Takara Bio Inc., Shiga, Japan) and the following primers:









Pol F:



(SEQ ID NO: 7)



5′-GGTTCCAAAAGCTTATGCCTTTATTGGGGAGAGACTT-3′



 



Pol R:



(SEQ ID NO: 8)



5′-GGTTCCAAGCGGCCGCTCATTGAGTACCTCCCACGTTTG-3′



 



Env F:



(SEQ ID NO: 9)



5′-GGTTCCAAAAGCTTATGATGAGTGGACTTTGGAGAA-3′



 



Env R:



(SEQ ID NO: 10)



5′-GGTTCCAAGCGGCCGCTTAGAGGTCGGTGTCCCTTAAC-3′



 



Gag F:



(SEQ ID NO: 11)



5′-GGTTCCAAAAGCTTATGGGACAGACCGTGTCTACTC-3′



 



Gag R:



(SEQ ID NO: 12)



5′-GGTTCCAAGCGGCCGCTAGTCTTCATCTTCTCCAAGAG-3′






The following thermocycler conditions were used for to amplify the pol gene: 94° C. 1 min/94° C. 30 sec, 58° C. 1 min, 72° C. 3 min 30 sec for 30 cycles/72° C. 10 min. The gag and env genes were amplified with the following conditions: 94° C. 1 min/94° C. 30 sec, 58° C. 1 min, 72° C. 2 min for 30 cycles/72° C. 10 min. The PCR products were purified from an agarose gel using Wizard SV Gel and PCR Clean-Up System cloned into Invitrogen's pcDNA 3.1(+) expression vector.
Cell Viability
In order to determine cell viability, cells were seeded in a 96-well tissue culture dish at a concentration of 105 cells/well. Cell viability was measured using a CELLTITER 96 AQueous One Solution Cell Proliferation Assay (MTS, Promega Corp., Madison, Wis.). Measurements were taken at 12 hours, 36 hours, 60 hours, and 84 hours after plating the cells. The MTS reagent was incubated at incubation at 37° C., and the absorbance was measured with a microplate reader (Synergy Mx, BioTek Instruments, Inc., Winooski, Vt.) at 490 nm and 650 nm.
Transcriptome Analysis
RNA was isolated from cells and tissues using an RNeasy Mini kit (Qiagen Inc. USA, Valencia, Calif.) according to the manufacturer's instructions, and treated with DNase I (Invitrogen, Life Technologies Corp., Grand Island, N.Y.) before cDNA synthesis.
To detect the transcript of Mmergln cDNA was synthesized using a reverse transcription system (GOSCRIPT, Promega Corp., Madison, Wis.). Multiple PCR primers were designed to span the transcript of Mmergln-int. The primer pairs used for RT PCR are provided in Table 4.









TABLE 4






Chromosome
SEQ


Primer
location
ID NO







5′-GGACCAAGGAGACCCAGAGAAG-3′
Ch8 ex2 Fi
13


 


5′-CCCGTGTCAACTAGAAAGTC-3′
Ch8 ex2 Ri
14


 


5′-TCCGAGCCAATAACCCACAGG-3′
Ch8 ex4 Fi
15


 


5′-TTTAGCAGAGGCCCGATACC-3′
Ch8 ex4 Ri
16


 


5′-CCACGCATCCCACGTTAAGAG-3′
Ch8 ex10 Fi
17


 


5′-AGGCCACCAAGTCCACAGAG-3′
Ch8 ex10 Ri
18


 


5′-CCAATTACTTTAACCCTGGCTGC-3′
Ch8 exl4 Fi
19


 


5′-GTCGCTAGGTCTTCATTGACAG-3′
Ch8 ex14 Ri
20









cDNAs were amplified using a DNA Polymerase (GOTAQ, Promega Corp., Madison, Wis.). The following thermocycler conditions were used to amplify the transcript of Mmergln-int: 95° C. 2 min/95° C. 30 sec, 54° C. 15 sec, 72° C. 15 sec for 22 cycles/72° C. 5 min. β-actin loading control was run with the previous thermocycler conditions PCR products were run of 2% TBE agarose gels.
Real time quantitative PCR primers were designed to specifically detect to the envelope genes with a complete ORF. Primer sequences were designed using NCBI's Primer Blast or taken from de Parseval et al., 2003. J Virol 77(19):10414-10422. RNA was extracted from cells with an RNeasy Mini kit (Qiagen Inc. USA, Valencia, Calif.) according to the manufacturer's instructions. cDNA was synthesized using a reverse transcription system (GOSCRIPT, Promega Corp., Madison, Wis.). Real time quantitative PCR was performed using 25 μl of a qPCR Master Mix (GOTAQ, Promega Corp., Madison, Wis.). The reactions were run using a realplex 2.2 thermocycler (Eppendorf, Hauppauge, HY) with the following program: 50° C. 2 min, 95° C. 10 min/95° C. 15 sec, 60° C. 1 min for 45 cycles. 95° C. 15 sec, 60° C. 15 sec, then 95° C. over 20 min for melting curve analysis.
β-actin or GAPDH was used as an internal control to calculate differences in the amount of total RNA added in each individual reaction. Experiments with variation of the internal control less than a factor of 1 were considered valid. A student's T test was performed to determine statistical significance. A p-value of p=0.05 was considered significant.
The sequence of the RT PCR and qPCR primers are listed in Table 5. Primer sequences for internal controls:









human GAPDH F:



(SEQ ID NO: 21)



5′-TGCACCACCAACTGCTTAGC-3′



 



human GAPDH R:



(SEQ ID NO: 22)



5′-GGCATGGACTGTGGTCATGAG-3′



 



murine β-actin F:



(SEQ ID NO: 23)



5′-GTGGTTTTGATTCTCCTGTGTGC-3′



 



murine β-actin R:



(SEQ ID NO: 24)



5′-GCCTTGTACCCATCAGGGA-3′
















TABLE 5





GI
Name
Forward Primer (SEQ ID NO)
Reverse Primer (SEQ ID NO)







GI: 145651814
HERV-R_7q21.2
F: CCATGGGAAGCAAGGGAACT (25)
R: CTTTCCCCAGCGAGCAATAC (26)


 


GI: 195963433
HERV-W_7q21.2
F: CCCCATCGTATAGGAGTCTT (27)
R: CCCCATCAGACATACCAGTT (28)


 


GI: 300796687
HERV-V_19q13.41 ENV 1
F: TGATGGCCTCCTTGGAAACG (29)
R: CAGGTGTAGCCAGTGTAGCC (30)


 


GI: 300796709
HERV-V_19q13.41 ENV 2
F: CTCTGAGGAGGGATTCCCCA (31)
R: AGTCAAGTTAGGGTGGCAGC (32)


 


GI: 44887863
HERV-F(c)1_Xq21.33
F: GGGCCACTAAGTTACTAGGTC (33)
R: AGTTAGGAGGGAGTTACTGGG (34)


 


GI: 44887864
HERV-FRD_6p24.1
F: GCCTGCAAATAGTCTTCTTT (35)
R: ATAGGGGCTATTCCCATTAG (36)


 


GI: 44887882
HERV-R(b)_3p24.3
F: GGACAGTGCCGACATACTAT (37)
R: TAGAGTGCAGCATCCTAACC (38)


 


GI: 44887888
HERV-H_3q26
F: ACTACACACATCACTGAAACAAA (39)
R: GGATGGAGTGAAATACAGGAC (40)


 


GI: 44887889
HERV-H_2q24.3
F: TTCACTCCATCCTTGGCTAT (41)
R: CGTCGAGTATCTACGAGCAAT (42)


 


GI: 47605576
HERV-K_1q23.3
F: CACAACTAAAGAAGCTGACG (43)
R: CATAGGCCCAGTTGGTATAG (44)


 


GI: 47716681
HERV-T_19q13.11
F: CCAGGATTTGATGTTGGG (45)
R: GGGGTGAGGTTAAGGAGATGG (46)









Promoter Assay

The LTR of Mmergln-int PCR amplified from BAC RP 23-2D22 cloned into the promoterless pGL3 basic vector with the following primers:









LTR F:



(SEQ ID NO: 47)



5′-GGTTCCAACTCGAGTGAAAGGAAATA-3′



 



LTR R:



(SEQ ID NO: 48)



5′-GGTTCCAAAAGCTTTGAAAGAACTCA-3′.






The p21 and p21 mutant constructs are described in [Genes Dev. 1995 Apr. 15; 9(8):935-44.] Mutations to the Mmergln-LTR were generated using QuikChange II Site-Directed Mutagenesis Kit. A deletion was made at bases 104-123 with the following primers:









del104-123 F:



(SEQ ID NO: 49)



5′-ATAGCAGAACAGACCAATCGCCTCCCTAGCTC-3′



 



del104-123 R:



(SEQ ID NO: 50)



5′-GAGCTAGGGAGGCGATTGGTCTGTTCTGCTAT-3′.






A single cytosine to adenine transversion mutations were made with the following primers:









c107a F:



(SEQ ID NO: 51)



5′-AGAACAGACCAGGAAATGCCCGGGCAAGC-3′



 



c107a R:



(SEQ ID NO: 52)



5′-GCTTGCCCGGGCATTTCCTGGTCTGTTCT-3′



 



c117a F:



(SEQ ID NO: 53)



5′-GACATGCCCGGGAAAGCCCATCGCC-3′



 



c117a R:



(SEQ ID NO: 54)



5′-GGCGATGGGCTTTCCCGGGCATGTC-3′.






Two cytosine to adenine transversion mutations were made with primers:









c107a c117a F:



(SEQ ID NO: 55)



5′-ACAGACCAGGAAATGCCCGGGAAAGCCCATCGC-3′



 



c107a c117a R:



(SEQ ID NO: 56)



5′-GCGATGGGCTTTCCCGGGCATTTCCTGGTCTGT-3′.






To generate the single base substitutions, the following thermocycler conditions were used: 95° C. 30 sec/95° C. 30 sec, 55° C. 1 min, 68° C. 5 min 30 sec for 16 cycles to generate the deletion; and 95° C. 30 sec/95° C. 30 sec, 55° C. 1 min, 68° C. 5 min 30 sec for 18 cycles to generate the double base substitutions. p53+/+ and p53−/− MEFs were plated in 48-well tissue culture plates at a density of 3×104 per well. MEFs were co-transfected with the 50 ng/well of the pRL-TK Renilla reporter vector (Promega Corp., Madison, Wis.) and 200 ng/well of the pGL3 basic experimental constructs. Cells were lysed and luciferase activity was measured 48 hours post transfection using DUAL-LUCIFERASE reporter assay system (Promega Corp., Madison, Wis.) according to manufacturer's instructions.
Western Blots
Protein was harvested with SDS sample buffer, run on 10% SDS-polyacrylamide gels, and transferred to a PVDF membrane overnight at 20 V. The membranes were blocked with 5% milk in TBS-T, incubated with the primary antibodies and secondary antibodies diluted in 5% milk in TBS-T. Protein was visualized using GeneMate Chemiluminescent HRP substrate (BioExpress, Kaysville, Utah). Anti-hERVantibody (ab71115, Abcam PLC, Cambridge, Mass.) was used at a concentration of 1:1,000 to detect Syncytin 1 and anti-HERV-FRD (ab90733) was used at a concentration of 1:100 to detect Syncytin 2 protein levels. For a loading control GAPDH rabbit mAb (#2118, Cell Signaling Technology, Inc., Danvers, Mass.) was used at a concentration of 1:2,000.
ChIP
Chromatin immunoprecipitation was performed using a Magna ChIP A kit (Millipore Corp., Billerica, Mass.) was used according to p53 (1C12) Mouse mAb (#2524, Cell Signaling Technology, Inc., Danvers, Mass.).
Primers to detect LTR:









ChIP LTR Fi



(SEQ ID NO: 57)



5′-GCTGAGAACATAGCAGAACAGACC-3′



 



ChIP LTR Ri



(SEQ ID NO: 58)



5′-GCACCCAAGAATCACGAATAGAAC-3′



 



ChIP LTR Rii



(SEQ ID NO: 59)



5′-AACAGGAGACAGTGGATTCGACC-3′






Primers used as positive control:









Mdm2-F chip:



(SEQ ID NO: 60)



5′-GGTGCCTGGTCCCGGACTCGCCGGG-3′



 



Mdm2-R chip:



(SEQ ID NO: 61)



5′-CCGAGAGGGTCCCCCAGGGGTGTCC-3′



 



p21-F chip:



(SEQ ID NO: 62)



5′-CCTTTCTATCAGCCCCAGAGGATACC-3′



 



p21-R chip:



(SEQ ID NO: 63)



5′-GGGACGTCCTTAATTATCTGGGGTC-3′



 



Bax-F chip:



(SEQ ID NO: 64)



5′-GATGTTGTAGCCACCGCGTACAGCC-3′



 



Bax-R chip:



(SEQ ID NO: 65)



5′-TTCATGGTAGAGAGCACTAAGGAGG-3′






Immunofluorescence and Microscopy

Immunofluorescence was performed according to Spector, D. L. and H. C. Smith. 1986. Exp. Cell Res. 163, 87-94. Imaging was performed on a DeltaVision Elite live cell microscope (Applied Precision, Issaqua, Wash.) using the 40× objective.
Bioinfomatics
mRNA Expression Analysis
mRNA transcript levels were detected by hybridization to Illumina bead arrays (Illumina, Inc., San Diego, Calif.). Each dataset was separately assessed for signal quality, quantile normalized and then probe sets mapping to the same gene were averaged.
RNA Seq
The RNA integrity was verified by quantification using a RIBOGREEN assay (Invitrogen, Life Technologies Corp., Grand Island, N.Y.) and an Agilent RNA 6000 Nano chip (Agilent Technologies, Inc., Santa Clara, Calif.). Samples with an RNA Integrity Number (RIN) of 8 or above were used for mRNA seq library preparation. To prepare the library, mRNA was purified and fragmented. Next, cDNA was generated, end repair was performed, the 3′ ends were adenylated and the DNA fragments were ligated to adaptors. Ligation products were purified from an gel. The library was quantified and validated using an Agilent High Sensitivity chip (Agilent Technologies, Inc., Santa Clara, Calif.), PICOGREEN (Invitrogen, Life Technologies Corp., Grand Island, N.Y.) assay and KAPA qPCR (KAPA Biosystems, Inc., Wilmington, Mass.).
The characterization of repetitive elements was performed using the Table Browser function of the UCSC Genome Browser, and the classification of the repetitive elements was determined using BLAT and the Repeat Masker function (Jurka et al., 2005. Cytogentic and Genome Research 110:462-467). Identification of sequences of homology of to Mmergln-int were identified using the BLAT feature of the UCSC Genome Browser. Open reading frames were determined using NCBI's Open Reading Frame Finder. NCBI's Conserved Domain Database was used to identify species containing protein domains of the Ebola HIV-1-like HR1-HR2 Superfamily.
Mmergln-Int ENV Enhances Tumorigenicity In Vivo
LLC1 cells (ATCC# CRL-1642) were transfected with vectors containing GFP, ERV, and ENV transgenes as described earlier using the NEON transfection system (Invitrogen, Life Technologies Corp., Grand Island, N.Y.) or the FuGENE HD transfection reagent (Promega Corp., Madison, Wis.). Using the NEON transfection system, LLC1 cells were pulsed once with a pulse voltage of 1,350 V and a pulse width of 30 ms at a density of 5×106/ml cells. To generate stable cell lines, LLC1 cells were selected with puromycin.
The ERV and ENV constructs were generated as described above. The Mmergln-int F (SEQ ID NO:5) and Mmergln-int R (SEQ ID NO:6) primers were used with thermocycler conditions 94° C. 1 min/94° C. 30 sec, 58° C. 1 min, 72° C. 9 min for 30 cycles/72° C. 10 min to generate the ERV construct. The ENV construct was generated using the Env F (SEQ ID NO:9) and Env R (SEQ ID NO:10), and thermocycler conditions 94° C. 1 min/94° C. 30 sec, 58° C. 1 min, 72° C. 2 min for 30 cycles/72° C. 10 min. The GFP construct was obtained from Addgene, Cambridge, Mass.). The cells containing the designated transgenes were selected by using puromycin.
2×105 cells of each genotype were inoculated in C57BL mice (The Jackson Laboratory, Bar Harbor, Me.) via tail vein injection. 15 mice per stable cell line were used.
Tumor growth was monitored by bio luminescence using IVIS spectrum in vivo imaging system (Xenogen Corp., Alameda, Calif.), after delivering 100 μl of 28.5 mg/ml luciferin (Gold Biotechnology, Inc., St. Louis, Mo.) in mice by intraperitoneal injection.
For survival curves, statistical analyses (Kaplan Meier) were performed by using Prism 4 (GraphPad Software), and p values were calculated by the log-rank test. All other p values were calculated using Student's t test (unpaired, two-tailed, p<0.05 was considered significant).
Results are shown in FIG. 14.
Structural Analysis
The structural analysis of the envelope protein was carried out by using the open source Conserved Domain (CD) Search software tool available at ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi using the following amino acid sequence of Mmergln-int envelope (SEQ ID NO:66):







MMSGLWRRLLILLSCACFVGAIPKDFNPHSPVQQTWEVLNEEGRAVWTIA


 


EVHPLWTWWPDLFPDICKLAIGAPPGWDLEGYSDIQRAPLTPPPYVEKHL


 


RDPWGGCSNQRDRSMLRTHPFYVCPGPHQSQSLNPTCGGKADFFCKSWGC


 


ETSGTARWKPSSSWDYIRVTANYSLASYVPGGFDLDECTDWCHPLRVTFT


 


EPGKRALGWTRGYTWGLRIYKERYDEGLLFTIRLKIETPYNPLGPPTKFT


 


PLTHTITQPTPVIADPLNMAAITQPPTPQVPLTITPTIPSRQRMFNLVRG


 


AFYALNRTDPSATEDCWLCLSSGPPYYEGIAFNGDFNRISSHTSCSWGTG


 


QKLTLTEVSVRNPGLCIGTPPSTHKHLCGQIQSMSRTEANYYLVPSPVGW


 


WACNTGLTPCVSTKVFNSSHDFCVMIQLLPHVYYHPASSLEESYAGRRSK


 


REPTTLTLAAFMGIGMAVGVGTGVSALIEGRQGIQSLRDAVNEDLAAIEK


 


SIDALKKSLTSLSEVVLQNRRGLDLLFLKEGGLCAALKEECCFYADHTGI


 


VRDSMQKLREKLERRKPERDAQRGWFESWFESRPSWITSLISAVAGPILM


 


ICLALVFSPCIINRGMAFIQSKIDTVKLMVLQRQYQPIVQVDEELGDTNL






Results are shown in FIG. 15.
Similar structural analyses, using the same open source software, were performed using the following amino acid sequences of other envelope proteins.
ENVW-1 (SEQ ID NO:67)







MALPYHIFLFTVLLPSFTLTAPPPCRCMTSSSPYQEFLWRMQRPGNIDAP


 


SYRSLSKGTPTFTAHTHMPRNCYHSATLCMHANTHYWTGKMINPSCPGGL


 


GVTVCWTYFTQTGMSDGGGVQDQAREKHVKEVISQLTRVHGTSSPYKGLD


 


LSKLHETLRTHTRLVSLFNTTLTGLHEVSAQNPTNCWICLPLNFRPYVSI


 


PVPEQWNNFSTEINTTSVLVGPLVSNLEITHTSNLTCVKFSNTTYTTNSQ


 


CIRWVTPPTQIVCLPSGIFFVCGTSAYRCLNGSSESMCFLSFLVPPMTIY


 


TEQDLYSYVISKPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQFYYKL


 


SQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFL


 


GEECCYYVNQSGIVTEKVKEIRDRIQRRAEELRNTGPWGLLSQWMPWILP


 


FLGPLAAIILLLLFGPCIFNLLVNFVSSRIEAVKLQMEPKMQSKTKIYRR


 


PLDRPASPRSDVNDIKGTPPEEISAAQPLLRPNSAGSS






ENVFRD-1 (SEQ ID NO:68)








MGLLLLVLILTPSLAAYRHPDFPLLEKAQQLLQSTGSPYSTNCWLCTSSS


 


TETPGTAYPASPREWTSIEAELHISYRWDPNLKGLMRPANSLLSTVKQDF


 


PDIRQKPPIFGPIFTNINLMGIAPICVMAKRKNGTNVGTLPSTVCNVTFT


 


VDSNQQTYQTYTHNQFRHQPRFPKPPNITFPQGTLLDKSSRFCQGRPSSC


 


STRNFWFRPADYNQCLQISNLSSTAEWVLLDQTRNSLFWENKTKGANQSQ


 


TPCVQVLAGMTIATSYLGISAVSEFFGTSLTPLFHFHISTCLKTQGAFYI


 


CGQSIHQCLPSNWTGTCTIGYVTPDIFIAPGNLSLPIPIYGNSPLPRVRR


 


AIHFIPLLAGLGILAGTGTGIAGITKASLTYSQLSKEIANNIDTMAKALT


 


TMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVNQSGKVQD


 


NIRQLLNQASSLRERATQGWLNWEGTWKWFSWVLPLTGPLVSLLLLLLFG


 


PCLLNLITQFVSSRLQAIKLQTNLSAGRHPRNIQESPF






ENVF(c)-1 (SEQ ID NO:69)








MARPSPLCLLLLLTLLTPIVPSNSLLTEPPFRWRFYLHETWTQGNRLSTV


 


TLATVDCQPHGCQAQVTFNFTSFKSVLRGWSNPTICFVYDQTHSNCRDYW


 


VDTNGGCPYAYCRMHVTQLHTAKKLQHTYRLTSDGRTTYFLTIPDPWDSR


 


WVSGVTGRLYRWPTDSYPVGKLRIFLTYIRVIPQVLSNLKDQADNIKHQE


 


EVINTLVQSHPKADMVTYDDKAEAGPFSWITLVRHGARLVNMAGLVNLSH


 


CFLCTALSQPPLVAVPLPQAFNTSGNHTAHPSGVFSEQVPLFRDPLQPQF


 


PFCYTTPNSSWCNQTYSGSLSNLSAPAGGYFWCNFTLTKHLNISSNNTLS


 


RNLCLPISLVPRLTLYSEAELSSLVNPPMRQKRAVFPPLVIGVSLTSSLV


 


ASGLGTGAIVHFISSSQDLSIKLQMAIEASAESLASLQRQITSVAKVAMQ


 


NRRALDLLTADKGGTCMFLGEECCYYINESGLVETSLLTLDKIRDGLHRP


 


SSTPNYGGGWWQSPLTTWIIPFISPILIICLLLLIAPCVLKFIKNRISEV


 


SRVTVNQMLLHPYSRLPTSEDHYDDALTQQEAAR






ENVF(c)-2 (SEQ ID NO:70)








MNSPCDRLQQFIQVLLEESWSFPSFANTLHWPENLLSYIDELVWQGSLQN


 


FHQHEVRFDKPPLLPLTGFSSLTENWSSRQAVSSRLVATAASPPAGCQAP


 


IAFLGLKFSSLGPARKNPALCFLYDQSNSKCNTSWVKENVGCPWHWCNIH


 


EALIRTEKGSDPMFYVNTSTGGRDGFNGFNLQISDPWDPRWASGVDGGLY


 


EHKTFMYPVAKIRIARTLKTTVTGLSDLASSIQSAEKELTSQLQPAADQA


 


KSSRFSWLTLISEGAQLLQSTGVQNLSHCFLCAALRRPPLVAVPLPTPFN


 


YTINSSTPIPPVPKGQVPLFSDPIRHKFPFCYSTPNASWCNQTRMLTSTP


 


APPRGYFWCNSTLTKVLNSTGNHTLCLPISLIPGLTLYSQDELSHLLAWT


 


EPRPQNKSKWAIFLPLVLGISLASSLVASGLGKGALTHSIQTSQDLSTHL


 


QLAIEASAESLDSLQRQITTVAQVAAQNRQALDLLMAEKGRTCLFLQEEC


 


CYYLNESGVVENSLQTLKKKKSSKRS






ENV-T (SEQ ID NO:71)








MGPEAWVRPLKTAPKPGEAIRLILFIYLSCFFLPVMSSEPSYSFLLTSFT


 


TGRVFANTTWRAGTSKEVSFAVDLCVLFPEPARTHEEQHNLPVIGAGSVD


 


LAAGFGHSGSQTGCGSSKGAEKGLQNVDFYLCPGNHPDASCRDTYQFFCP


 


DWTCVTLATYSGGSTRSSTLSISRVPHPKLCTRKNCNPLTITVHDPNAAQ


 


WYYGMSWGLRLYIPGFDVGTMFTIQKKILVSWSSPKPIGPLTDLGDPIFQ


 


KHPDKVDLTVPLPFLVPRPQLQQQHLQPSLMSILGGVHHLLNLTQPKLAQ


 


DCWLCLKAKPPYYVGLGVEATLKRGPLSCHTRPRALTIGDVSGNASCLIS


 


TGYNLSASPFQATCNQSLLTSISTSVSYQAPNNTWLACTSGLTRCINGTE


 


PGPLLCVLVHVLPQVYVYSGPEGRQLIAPPELHPRLHQAVPLLVPLLAGL


 


SIAGSAAIGTAALVQGETGLISLSQQVDADFSNLQSAIDILHSQVESLAE


 


VVLQNCRCLDLLFLSQGGLCAALGESCCFYANQSGVIKGTVKKVRENLDR


 


HQQERENNIPWYQSMFNWNPWLTTLITGLAGPLLILLLSLIFGPCILNSF


 


LNFIKQRIASVKLTYLKTQYDTLVNN






ENV-H1 (SEQ ID NO:72)








MIFAGKAPSNTSTLMKFYSLLLYSLLFSFPFLCHPLPLPSYLHHTINLTH


 


SLLAASNPSLVNNCWLCISLSSSAYTAVPAVQTDWATSPISLHLRTSFNS


 


PHLYPPEELIYFLDRSSKTSPDISHQQAAALLRTYLKNLSPYINSTPPIF


 


GPLTTQTTIPVAAPLCISWQRPTGIPLGNLSPSRCSFTLHLRSPTTNINE


 


TIGAFQLHITDKPSINTDKLKNISSNYCLGRHLPCISLHPWLSSPCSSDS


 


PPRPSSCLLIPSPENNSERLLVDTRRFLIHHENRTFPSTQLPHQSPLQPL


 


TAAALAGSLGVWVQDTPFSTPSHLFTLHLQFCLAQGLFFLCGSSTYMCLP


 


ANWTGTCTLVFLTPKIQFANGTEELPVPLMTPTQQKRVIPLIPLMVGLGL


 


SASTVALGTGIAGISTSVMTFRSLSNDFSASITDISQTLSVLQAQVDSLA


 


AVVLQNRRGLDLLTAEKGGLCIFLNEECCFYLNQSGLVYDNIKKLKDRAQ


 


KLANQASNYAEPPWALSNWMSWVLPIVSPLIPIFLLLLFGPCIFRLVSQF


 


IQNRIQAITNHSIRQMFLLTSPQYHPLPQDLPSA






ENV-H2 (SEQ ID NO:73)








MIFAGRASSNTSTLMKFYSLLLYSLLFSFPILCHPLPLPSYLHHTINLTH


 


SLLAVSNPSLAKNCWLCISLPSSAYPAVPALQTDWGTSPVSPHLRTSFNS


 


PHLYPPEKLIYFLDRSSKTSPDISHQQAAALLCTYLKNLSPYINSTPPTF


 


GPLTTQTTIPVAAPLCISRQRPTGIPLGNLSPSRCSFTLHLRSPTTHITE


 


TNGAFQLHITDKPSINTDKLKNVSSNYCLGRHLSCISLHPWLFSPCSSDS


 


PPRPSSCLLIPSPKNNSESLLVDAQRFLIYHENRTSPSTQLPHQSPLQPL


 


TAAPLGGSLRVWVQDTPFSTPSHLFTLHLQFCLVQSLFFLCGSSTYMCLP


 


ANWTGTCTLVFLTSKIQFANGTEELPVPLMTPTRQKRVIPLIPLMVGLGL


 


SASTVALGTGIAGISTSVTTFRILSNDFSASITDISQTLSGLQAQVDSSA


 


AVVLQNRQGLDLLTAEKGGLCIFLNEESYFYLNQSGLVYDNIKKLKDKAQ


 


NLANQASNYAEPPWPLSNWMSWVLPILSPLIPIFLLLFFRPCIFHLVSQF


 


IQNHIQAITDHSI






ENV-H3 (SEQ ID NO:74)








MILAGRAPSNTSTLMKFYSLLLYSLLFSFPFLYHPLPLPSYLHHTINLTH


 


SLPAASNPSLANNCWLCISLSSSAYIAVPTLQTDRATSPVSLHLRTSFNS


 


PHLYPPEELIYFLDRSSKTSPDISHQPAAALLHIYLKNLSPYINSTPPIF


 


GPLTTQTTIPVAAPLCISRQRPTGIPLGNISPSRCSFTLHLQSPTTHVTE


 


TIGVFQLHIIDKPSINTDKLKNVSSNYCLGRHLPYISLHPWLPSPCSSDS


 


PPRPSSCLLTPSPQNNSERLLVDTQRFLIHHENRTSSSMQLAHQSPLQPL


 


TAAALAGSLGVWVQDTPFSTPSHPFSLHLQFCLTQGLFFLCGSSTYMCLP


 


ANWTGTCTLVFLTPKIQFANGTKELPVPLMTLTPQKRVIPLIPLMVGLGL


 


SASTIALSTGIAGISTSVTTFRSPSNDFSASITDISQTLSVLQAQVDSLA


 


AVVLQNRRGLGLSILLNEECCFYLNQSGLVYENIKKLKDRAQKLANQASN


 


YAESPWALSNWMSWVLPILSPLIPIFLLLLFGPCIFHLVSQFIQNRIQAI


 


TNHSI






ENV-R (SEQ ID NO:75)








MLGMNMLLITLFLLLPLSMLKGEPWEGCLHCTHTTWSGNIMTKTLLYHTY


 


YECAGTCLGTCTHNQTTYSVCDPGRGQPYVCYDPKSSPGTWFEIHVGSKE


 


GDLLNQTKVFPSGKDVVSLYFDVCQIVSMGSLFPVIFSSMEYYSSCHKNR


 


YAHPACSTDSPVTTCWDCTTWSTNQQSLGPIMLTKIPLEPDCKTSTCNSV


 


NLTILEPDQPIWTTGLKAPLGARVSGEEIGPGAYVYLYIIKKTRTRSTQQ


 


FRVFESFYEHVNQKLPEPPPLASNLFAQLAENIASSLHVASCYVCGGMNM


 


GDQWPWEARELMPQDNFTLTASSLEPAPSSQSIWFLKTSIIGKFCIARWG


 


KAFTDPVGELTCLGQQYYNETLGKTLWRGKSNNSESPHPSPFSRFPSLNH


 


SWYQLEAPNTWQAPSGLYWICGPQAYRQLPAKWSGACVLGTIRPSFFLMP


 


LKQGEALGYPIYDETKRKSKRGITIGDWKDNEWPPERIIQYYGPATWAED


 


GMWGYRTPVYMLNRIIRLQAVLEIITNETAGALNLLAQQATKMRNVIYQN


 


RLALDYLLAQEEGVCGKFNLTNCCLELDDEGKVIKEITAKIQKLAHIPVQ


 


TWKG






ENV-R(b) (SEQ ID NO:76)








MDPLHTIEKVPARRNIHDRGHQGHRMGDGTPGRPKISVQQMTRFSLIIFF


 


LSAPFVVNASTSNVFLQWAHSYADGLQQGDPCWVCGSLPVTNTMELPWWV


 


SPLQGKDWVFFQSFIGDLKQWTGAQMTGVTRKNISEWPINKTLNEPGHDK


 


PFSVNETRDKVIAFAIPLLDTKVFVQTSRPQNTQYRNGFLQIWDGFIWLT


 


ATKGHLSQIAPLCWEQRNHSLDNWPNTTRVMGWIPPGQCRHTILLQQRDL


 


FATDWSQQPGLNWYAPNGTQWLCSPNLWPWLPSGWLGCCTLGIPWAQGRW


 


VKTMEVYPYLPHVVNQGTRAIVHRNDHLPTIFMPSVGLGTVIQHIEALAN


 


FTQRALNDSLQSISLMNAEVYYMHEDILQNRMALDILTAAEGGTCALIKT


 


ECCVYIPNNSRNISLALEDTCRQIQVISSSALSLHDWIASQFSGRPSWWQ


 


KILIVLATLWSVGIALCCGLYFCRMFSQHIPQTHSIIFQQELPLSPPSQE


 


HYQSQRDIFHSNAP






ENV-K1 (SEQ ID NO:77)








MHPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEQMKLPSTKKAEPPTWA


 


QLKKLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAANY


 


TNWAYVPFPPLIRAVTWMDNPIEVYVNDSVWVHGPIDDRCPAKPEEEGMM


 


INISIGYHYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTYNMVSGMS


 


LRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSV


 


VILQNNEFGTIIDWAPRGQFYHNCSGQTQSCPSAQVSPAVDSDLTESLDK


 


HKHKKLQSFYPWEWGEKGISTPRPKIISPVSGPEHPELWRLTVASHHIRI


 


WSGNQTLETRDRKPFYTVDLNSSLTVPLQSCVKPPYMLVVGNIVIKPDSQ


 


TITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPSIHI


 


LTEVLKGVLNRSKRFIFTLIAVIMGLIAVTAMAAVAGVALHSFVQSVNFV


 


NDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQC


 


DWNTSDFCITPQIYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEAS


 


KAHLNLVPGTEAIAGVADGLANLNPVTWVKTIGSTTIINLILILVCLFCL


 


LLVCRFTQQLRRDSYHRERAMMTMVVLSKRKGGNVGKSKRDQIVTVSV






ENV-K2 (SEQ ID NO:78)








MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTW


 


AQLKKLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAAN


 


YTYWAYVPFPPLIRAVTWMDNPTEVYVNDSVWVPGPIDDRCPAKPEEEGM


 


MINISIGYHYPPICLGRAPGCLMPAVQNWLVEVPTVSPICRFTYHMVSGM


 


SLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANS


 


AVILQNNEFGTIIDWAPRGQFYHNCSGQTQSCPSAQVSPAVDSDLTESLD


 


KHKHKKLQSFYPWEWGEKGISTPRPKIVSPVSGPEHPELWRLTVASHHIR


 


IWSGNQTLETRDRKPFYTIDLNSSLTVPLQSCVKPPYMLVVGNIVIKPDS


 


QTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPSVH


 


ILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNF


 


VNDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQ


 


CDWNTSDFCITPQIYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEA


 


SKAHLNLVPGTEAIAGVADGLANLNPVTWVKTIGSTTIINLILILVCLFC


 


LLLVCRCTQQLRRDSDHRERAMMTMAVLSKRKGGNVGKSKRDQIVTVSV






ENV-K3 (SEQ ID NO:79)








MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTW


 


AQLKKLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAAN


 


YTYWAYVPFPPLIRAVTWMDNPIEVYVNDSVWVPGPTDDHCPAKPEEEGM


 


MINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTYHMVSGM


 


SLRPRVNYLQDFSYQRSFKFRPKGKPCPKEIPKESKNTEVLVWEECVANS


 


AVILQNNEFGTIIDWAPRGQFYHNCSGQTQSCPSAQVSPAVDSDLTESLD


 


KHKHKKLQSFYPWEWGEKGISTPRPKIISPVSGPEHPELWRLTVASHHIR


 


IWSGNQTLETRDRKPFYTVDLNSSVTVPLQSCIKPPYMLVVGNIVIKPDS


 


QTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWETSPSIH


 


TLTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNF


 


VNDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQ


 


CDWNTSDFSITPQIYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEA


 


SKAHLNLVPGTEAIAGVADGLANLNPVTWVKTIGSTTIINLILILVCLFC


 


LLLVCRCTQQLRRDSDHRERAMMTMAVLSKRKGGNVGKSKRDQIVTVSV






ENV-K4 (SEQ ID NO:80)








MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTW


 


AQLKKLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAAN


 


YTNWAYVPFPPLIRAVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGM


 


MINISIGYRYPICLGRAPGCLMPAVQNWLVEVPIVSPICRFTYHMVSGMS


 


LRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSA


 


VILQNNEFGTIIDWTPQGQFYHNCSGQTQSCPSAQVSPAVDSDLTESLDK


 


HKHKKLQSFYPWEWGEKGISTPRPKIISPVSGPEHPELWRLTVASHHIRI


 


WSGNQTLETRDRKPFYTVDLNSSLTLPLQSCVKPPYMLVVGNIVIKPDSQ


 


TITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPSIHI


 


LTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNFV


 


NDGQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQC


 


DWNTSDFCITPQIYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEAS


 


KAHLNLVPGTEAIAGVADGLANLNPVTWVKTIGSTTIINLILILVCLFCL


 


LLVCRCTQQLRRDSDHRERAMMTMAVLSKRKGGNVGKSKRDQIVTVSV






ENV-K5 (SEQ ID NO:81)








MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTW


 


AQLKKLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAAN


 


YTYWAYVPFPPLIRAVTWMDNPIEIYVNDSVWVPGPTDDCCPAKPEEEGM


 


MINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTYHMVSGM


 


SLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANS


 


AVILQNNEFGTLIDWAPRGQFYHNCSGQTQSCPSAQVSPAVDSDLTESLD


 


KHKHKKLQSFYPWEWGEKGISTARPKIISPVSGPEHPELWRLTVASHHIR


 


IWSGNQTLETRDRKPFYTIDLNSSLTVPLQSCVKPPYMLVVGNIVIKPDS


 


QTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPSVH


 


ILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNF


 


VNDWQNNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQ


 


CDWNTSDFCITPQIYNESEHHWDMVRCHLQGREDNLTLDISKLKEQIFEA


 


SKAHLNLVPGTEAIAGVADGLANLNTVTWVKTIGSTTIINLILILVCLFC


 


LLLVYRCTQQLRRDSDHRERAMMTMVVLSKRKGGNVGKSKRDQIVTVSV






ENV-K6 (SEQ ID NO:82)








MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTW


 


AQLKKLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAVAN


 


YTNWAYVPFPPLIRAVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGM


 


MINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTYHMVSGM


 


SLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANS


 


AVILQNNEFGTIIDWAPRGQFYHNCSGQTQSCPSAQVSPAVDSDLTESLD


 


KHKHKKLQSFYPWEWGEKRISTPRPKIVSPVSGPEHPELWRLTVASHHIR


 


IWSGNQTLETRDRKPFYTVDLNSSLTLPLQSCVKPPYMLVVGNIVIKPDS


 


QTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPSVH


 


ILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNF


 


VNDGQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQ


 


CDWNTSDFCITPQIYNDSEHHWDMVRRHLQGREDNLTLDISKLKEQIFEA


 


SKAHLNLVPGTEAIAGVADGLANLNPVTWVKTIGSTTIINLILILVCLFC


 


LLLVCRCTQQLRRDSDHRERAMMTMAVLSKRKGGNVGKSKRDQIVTVSV






Results are shown in FIG. 16.
An alignment analysis of ENV-R (SEQ ID NO:75), ENV-R(b) (SEQ ID NO:76), ENV-T (SEQ ID NO:71), Mmergln-int envelope (SEQ ID NO:66), ENVF(c)-1 (SEQ ID NO:69), ENVF(c)-2 (SEQ ID NO:70), ENVW-1 (SEQ ID NO:67), ENVFRD-1 (SEQ ID NO:68), ENV-H2 (SEQ ID NO:73), ENV-H1 (SEQ ID NO:72), and ENV-H3 (SEQ ID NO:74) was performed using the open source software tool Clustal Omega (European Molecular Biology Laboratory, Cambridge, United Kingdom, www.ebi.ac.uk/Tools/msa/clustalo/). The alignment is presented using Jalview software (www.jalview.org/).
Results are shown in FIG. 18.
LISTING OF EXEMPLARY EMBODIMENTS
Embodiment 1
A method of slowing cellular growth, the method comprising:
increasing expression of an endogenous retrovirus envelope protein in at least one cell, wherein the cell expresses p53 and expression of the retrovirus envelope protein is controlled by p53; and exposing the cell to conditions that upregulate expression of p53.
Embodiment 2
A method of decreasing cell viability, the method comprising:
increasing expression of an endogenous retrovirus envelope protein in at least one cell, wherein the cell expresses p53 and expression of the retrovirus envelope protein is controlled by p53; and
exposing the cell to conditions that upregulate expression of p53.
Embodiment 3
The method of Embodiment 1 or Embodiment 2 wherein the conditions that upregulate expression of p53 comprise cellular stress.
Embodiment 4
The method of any preceding Embodiment wherein increasing expression of an endogenous envelope protein comprises overexpressing the endogenous envelope protein.
Embodiment 5
The method of Embodiment 4 wherein overexpressing the endogenous envelope protein comprises introducing into the cell a polynucleotide that comprises a coding region that encodes a functional portion of the endogenous envelope protein operably linked to a p53 response element.
Embodiment 6
The method of Embodiment 5 wherein the p53 response element comprises the polynucleotide sequence reflected in SEQ ID NO:1.
Embodiment 7
The method of Embodiment 5 wherein the p53 response element comprises at least 10 contiguous nucleotides of any one of: nucleotides 10-19 of SEQ ID NO:2, nucleotides 47-56 of SEQ ID NO:2, nucleotides 88-100 of SEQ ID NO:2, nucleotides 334-344 of SEQ ID NO:2, nucleotides 419-430 of SEQ ID NO:2, nucleotides 473-486 of SEQ ID NO:2, nucleotides 548-560 of SEQ ID NO:2, nucleotides 607-618 of SEQ ID NO:2, or nucleotides 679-690 of SEQ ID NO:2.
Embodiment 8
The method of Embodiment 5 wherein the p53 response element comprises nucleotides 169-179 of SEQ ID NO:3, nucleotides 246-255 of SEQ ID NO:3, nucleotides 337-346 of SEQ ID NO:3, nucleotides 371-380 of SEQ ID NO:3, nucleotides 460-469 of SEQ ID NO:3, nucleotides 524-533 of SEQ ID NO:3, nucleotides 588-597 of SEQ ID NO:3, nucleotides 786-795 of SEQ ID NO:3, nucleotides 800-809 of SEQ ID NO:3, nucleotides 892-901 of SEQ ID NO:3, or nucleotides 1122-1131 of SEQ ID NO:3.
Embodiment 9
The method of any preceding Embodiment wherein the subject is a mammal.
Embodiment 10
The method of Embodiment 9 wherein the mammal is a human.
Embodiment 11
A composition comprising a polynucleotide that comprises a coding region that encodes a functional portion of the endogenous envelope protein operably linked to a p53 response element.
Embodiment 12
The composition of Embodiment 11 wherein the p53 response element comprises the polynucleotide sequence reflected in SEQ ID NO:1.
Embodiment 13
The composition of Embodiment 11 wherein the p53 response element comprises at least 10 contiguous nucleotides of any one of: nucleotides 10-19 of SEQ ID NO:2, nucleotides 47-56 of SEQ ID NO:2, nucleotides 88-100 of SEQ ID NO:2, nucleotides 334-344 of SEQ ID NO:2, nucleotides 419-430 of SEQ ID NO:2, nucleotides 473-486 of SEQ ID NO:2, nucleotides 548-560 of SEQ ID NO:2, nucleotides 607-618 of SEQ ID NO:2, or nucleotides 679-690 of SEQ ID NO:2.
Embodiment 14
The composition of Embodiment 11 wherein the p53 response element comprises nucleotides 169-179 of SEQ ID NO:3, nucleotides 246-255 of SEQ ID NO:3, nucleotides 337-346 of SEQ ID NO:3, nucleotides 371-380 of SEQ ID NO:3, nucleotides 460-469 of SEQ ID NO:3, nucleotides 524-533 of SEQ ID NO:3, nucleotides 588-597 of SEQ ID NO:3, nucleotides 786-795 of SEQ ID NO:3, nucleotides 800-809 of SEQ ID NO:3, nucleotides 892-901 of SEQ ID NO:3, or nucleotides 1122-1131 of SEQ ID NO:3.
Embodiment 15
The composition of any one of Embodiments 11-14 further comprising a delivery vehicle.
Embodiment 16
A composition comprising antibody that specifically binds to an endogenous retrovirus envelope protein.
Embodiment 17
The composition of Embodiment 16 wherein the endogenous retrovirus envelope protein comprises HENV-R, HENV-W, HENV-V1, HENV-V2, HENV-F(c)1, HENV-FRD, HENV-R(b), HENV-H (3q26), HENV-H (2q24.3), HENV-K (1q23.3), HENV-K (12q14.1), HENV-T, ABB52637, hCG2039029, or Q4KWC9.
Embodiment 18
The composition of Embodiment 16 or Embodiment 17 wherein the antibody comprises a monoclonal antibody.
Embodiment 19
The composition of Embodiment 16 or Embodiment 17 wherein the antibody comprises polyclonal antibodies.
Embodiment 20
A method comprising:
obtaining a biological sample from a subject comprising cells from at least one tissue;
analyzing the cells for expression of an endogenous retrovirus envelope protein; and
identifying the subject as having or at risk of having cancer if the cells express the endogenous retrovirus envelope protein.
Embodiment 21
The method of Embodiment 20 wherein the tissue comprises human breast tissue or human prostate tissue.
Embodiment 22
The method of Embodiment 20 or Embodiment 21 wherein the endogenous retrovirus envelope protein comprises HENV-R, HENV-W, HENV-V1, HENV-V2, HENV-F(c)1, HENV-FRD, HENV-R(b), HENV-H (3q26), HENV-H (2q24.3), HENV-K (1q23.3), HENV-K (12q14.1), HENV-T, ABB52637, hCG2039029, or Q4KWC9.
Embodiment 23
The method of any one of Embodiments 20-22 further comprises providing to the subject a treatment effective for treating cancer.
Embodiment 24
The method of Embodiment 20 further comprising administering to the subject a pharmaceutical composition effective for treating cancer.
Embodiment 25
The method of Embodiment 24 wherein the pharmaceutical composition comprises a monoclonal antibody that specifically binds a tumor-associated antigen.
Embodiment 26
The method of Embodiment 24 or Embodiment 25 wherein the pharmaceutical composition comprises antibody that specifically binds to an endogenous retrovirus envelope protein.
Embodiment 27
The method of Embodiment 26 wherein the monoclonal antibody binds to the CKS-17 domain of the endogenous retrovirus envelope protein.
Embodiment 28
The method of any one of Embodiments 24-27 wherein the pharmaceutical composition comprises a compound that specifically binds to the CX(6)C domain of an endogenous retrovirus envelope protein.
Embodiment 29
A composition comprising:
antibody that specifically binds to the CKS-17 domain of the endogenous retrovirus envelope protein; and a pharmaceutically acceptable carrier.
Embodiment 30
The composition of Embodiment 29 wherein the antibody comprises a monoclonal antibody.
Embodiment 31
The composition of Embodiment 29 or Embodiment 30 further comprising a compound that specifically binds to the CX(6)C domain of the endogenous retrovirus envelope protein.
Embodiment 32
A composition comprising:
a compound that specifically binds to the CX(6)C domain of an endogenous retrovirus envelope protein; and a pharmaceutically acceptable carrier.
Embodiment 33
The composition of any one of Embodiments 29-32 further comprising antibody that specifically binds to a tumor-associated antigen.
The complete disclosure of all patents, patent applications, and publications, and electronically available material (including, for instance, nucleotide sequence submissions in, e.g., GenBank and RefSeq, and amino acid sequence submissions in, e.g., SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq) cited herein are incorporated by reference in their entirety. In the event that any inconsistency exists between the disclosure of the present application and the disclosure(s) of any document incorporated herein by reference, the disclosure of the present application shall govern. The foregoing detailed description and examples have been given for clarity of understanding only. No unnecessary limitations are to be understood therefrom. The invention is not limited to the exact details shown and described, for variations obvious to one skilled in the art will be included within the invention defined by the claims.
Unless otherwise indicated, all numbers expressing quantities of components, molecular weights, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about.” Accordingly, unless otherwise indicated to the contrary, the numerical parameters set forth in the specification and claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.
Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. All numerical values, however, inherently contain a range necessarily resulting from the standard deviation found in their respective testing measurements.
All headings are for the convenience of the reader and should not be used to limit the meaning of the text that follows the heading, unless so specified.

## Claims

1. A method of slowing cellular growth, the method comprising: overexpressing an endogenous HR1-HR2 superfamily retrovirus envelope protein in at least one cell, wherein the cell expresses p53 and expression of the retrovirus envelope protein is controlled by p53; and exposing the cell to conditions that upregulate expression of p53.

2. A method of decreasing cell viability, the method comprising: overexpressing an endogenous HR1-HR2 superfamily retrovirus envelope protein in at least one cell, wherein the cell expresses p53 and expression of the retrovirus envelope protein is controlled by p53; and exposing the cell to conditions that upregulate expression of p53.

3. The method of claim 1, wherein the conditions that upregulate expression of p53 comprise cellular stress.

4. The method of claim 1, wherein overexpressing the HR1-HR2 superfamily retrovirus endogenous envelope protein comprises introducing into the cell a polynucleotide that comprises a coding region that encodes a functional portion of the endogenous HR1-HR2 superfamily retrovirus envelope protein operably linked to a p53 response element.

5. The method of claim 1, wherein the subject is a mammal.

6. The method of claim 5, wherein the mammal is a human.

7. The method of claim 2, wherein the conditions that upregulate expression of p53 comprise cellular stress.

8. The method of claim 2, wherein overexpressing the HR1-HR2 superfamily retrovirus endogenous envelope protein comprises introducing into the cell a polynucleotide that comprises a coding region that encodes a functional portion of the HR1-HR2 superfamily retrovirus endogenous envelope protein operably linked to a p53 response element.

9. The method of claim 2, wherein the subject is a mammal.

10. The method of claim 9, wherein the mammal is a human.