WO2007038757A2 - Methods and compositions for non-invasive assessment of gene expression - Google Patents

Abstract

The present invention provides methods and compositions relating to assays for detection of RNA transcription, transcription factor activity, apoptosis and other cellular activities. For example, in some aspects the present invention provides methods of extracellularly detecting a reporter RNA wherein the reporter RNA is extracellular released in an encapsidated particle from a target cell comprising a packaging polypeptide, wherein the encapsidated particle comprises the packaging polypeptide, and wherein the reporter RNA is intracellularly transcribed in the target cell. In other aspects, the present invention provides a host cell that extracellularly releases a reporter RNA in an encapsidated particle comprising a packaging protein, wherein the reporter RNA is intracellularly transcribed.

Description

METHODS AND COMPOSITIONS FOR

NON-INVASIVE ASSESSMENT OF GENE EXPRESSION

1. RELATED APPLICATIONS

[0001] This application claims the benefit of U.S . Provisional Application No.

60/721,844, filed September 28, 2005, which is incorporated by reference herein in its entirety for all purposes.

2. FIELD OF THE INVENTION

[0002] The present invention provides methods and compositions relating to assays for gene expression, apoptosis, and transcription factor activity.

3. BACKGROUND OF THE INVENTION

[0003] Analyzing gene expression is central to the understanding of cell functions and activities. Research tools and diagnostic assays employ a variety of techniques to identify gene expression in response to the activation of intracellular signaling pathways. For example, Northern blotting, array hybridization, in volume hybridization, polymerase chain reaction (PCR) and the like, are used to obtain a "read out", of the intracellular gene transcript (RNA) expressed in response to gene activation. However, a common shortcoming is that such techniques typically require lysing or breaking open the cells in order to isolate the RNA. Thus, cells are evaluated for gene expression only at one time point. Further, manipulations to obtain RNA require precautionary steps to avoid RNA loss due to the ubiquitous RNA-degrading enzymes.

[0004] Technologies that are non-invasive to the cells can be employed to evaluate gene expression. Typically, non-invasive technology makes use of "reporter" gene constructs that express polypeptides with a extracellularly detectable activity such as fluorescence or catalysis of a light producing reaction. The use of non-invasive technology to evaluate gene expression is also limited, however. For example, only a small number of convenient reporter polypeptides available. Moreover, within a cell, only a few reporter gene constructs can be assessed in parallel using such reporter polypeptides. Furthermore, the cell expressing the reporter polypeptide must also be readily available to imaging devices for detection of the reporter polypeptide. [0005] In view of the foregoing, gene expression detection systems are sought that are non-invasive, amenable to repeated testing in a single cell, and adaptable to identifying expression of a large number of genes in parallel in a single cell.

4. SUMMARY OF THE INVENTION

[0006] The present invention provides methods and compositions for the non-invasive assessment of gene expression in cells. As will be understood from the detailed description, the methods provided are useful for detecting, in some embodiments, quantitatively detecting, transcription factor activities or transcription of RNA in living cells in vitro, or in biological systems, such as in an animal.

[0007] Thus, in one aspect, the present invention provides methods of detecting expression of a reporter RNA in a target cell, comprising: detecting an extracellular reporter RNA, wherein the reporter RNA is released extracellularly in an encapsidated particle from a target cell, wherein the encapsidated particle comprises a packaging polypeptide, and wherein the target cell comprises the packaging polypeptide and a reporter-coding nucleic acid that expresses the reporter RNA when transcribed.

[0008] In some embodiments, the detection of the extracellular reporter RNA is determinative of a transcription activity to initiate, increase or repress transcription of a reporter RNA.

[0009] In some embodiments, the modulation of transcriptional activity can be by a trans-acting protein.

[0010] In certain embodiments, the detection of the extracellular reporter RNA is determinative of a transcription factor binding to a cis-regulatory element in the target cell. [0011] In some embodiments the target cell is a fungal cell, e.g., yeast, an animal cell or plant cell.

[0012] The packaging polypeptide can be directly introduced into the target cell or expressed from a packaging polypeptide-coding nucleic acid construct. In some embodiments, the packaging polypeptide is Rous sarcoma virus (RSV) packaging polypeptide, murine leukemia virus (MLV) packaging polypeptide, human immunodeficiency virus (HIV) packaging polypeptide, equine immunodeficiency virus (EIV) packaging polypeptide, influenza virus packaging polypeptide, Sindbis virus packaging polypeptide, vesicular stomatitis packaging polypeptide, Moloney murine leukemia virus (MoMLV) packaging polypeptide, Moloney murine sarcoma virus (MoMSV) packaging polypeptide, or substantially identical packaging polypeptide thereof. [0013] In certain embodiments, a packaging signal in the reporter RNA can be used to assist in complex formation of the reporter RNA with a packaging polypeptide thereby leading to increased extracellular release of encapsidated particles. Typically, a packaging polypeptide recognizes specific packaging signals. In some embodiments, the packaging signal is specific for RSV packaging polypeptide, MLV packaging polypeptide, HIV packaging polypeptide, EIV packaging polypeptide, influenza virus packaging polypeptide,

Sindbis virus packaging polypeptide, vesicular stomatitis packaging polypeptide, MoMLV packaging polypeptide, or MoMSV packaging polypeptide.

[0014] hi certain embodiments, the reporter RNA is a nonviral RNA. The reporter

RNA can be native to the target cell or heterologous to the target cell.

[0015] Typically, the target cell further comprises a cis regulatory element operably linked to the reporter-coding nucleic acid. In certain embodiments, the cis-regulatory element comprises a gene regulatory sequence, a promoter, an enhancer or an RNA stability determinant.

[0016] In some embodiments, the cis-regulatory element comprises a NF-/cB response element, peroxisome proliferator-activated receptor response element (PPRE),

TGFα inducible response element (TGFce), glucocorticoid receptor response element

(GRE), interferon inducible response element (ISRE), cAMP response element (CRE), aryl hydrocarbon receptor response element (AhRE), estrogen receptor response element (ERE), liver X receptor response element (LXRE), p53 response element (p53), BMP inducible response element (BRE), hypoxia-inducible factor \a (HIF-Io;) or SV40 immediately early promoter from simian virus (SV40).

[0017] hi certain embodiments, a reporter construct comprising the cis-regulatory element operably linked to the reporter-coding nucleic acid sequence is introduced into the target cell. The reporter construct can be, for example, stably integrated into the target cell

DNA or extrachromosomally located.

[0018] hi certain embodiments, a plurality of non-identical reporter RNAs are extracellularly detected wherein the plurality of non-identical reporter RNAs are released extracellularly from the target cell in encapsidated particles, and wherein the plurality of non-identical reporter RNAs are transcribed in the target cell.

[0019] hi certain embodiments, extracellular reporter RNA is detected at two or more points in time. This facilitates the detection of a change in reporter RNA transcribed in the target cell with time, and, in addition, can used to asses responses of the target to test stimuli. [0020] In another embodiment, extracellular reporter RNA is detected wherein the reporter RNA is transcribed in a target cell contacted with a test stimulus and the amounts of extracellular reporter RNA detected is compared to detected amounts of extracellular reporter RNA transcribed in a control cell not contacted the test stimulus. [0021] It will also be apparent that, in certain embodiments of the methods provided herein, the target cell, or target cell population, can be in cell culture or in an animal. [0022] For example, in some embodiments where a target cell population is in an animal, the extracellularly released reporter RNA is detected in a sample from the animal. Samples from the animal can include a bodily fluid, such as, for example, blood, sera, plasma, urine, spit, tears, sweat, milk, synovial fluid, cerebrospinal fluid, amniotic fluid, and the like.

[0023] Where target cell populations are in different animals, the reporter RNA (or, in some embodiments, plurality of reporters) are detected in samples from the animals and the amounts of detected reported RNAs between animals compared. This can useful, for example, to non-invasively assess differences in transcriptional activities arising in an animal afflicted with disease or other pathological states as compared to a healthy animal, or, as another example, to assess differences in transcriptional activities arising in a genetically-modified (e.g., transgenic, gene knockout, and the like) animal as compared to a wildtype animal.

[0024] In another aspect the present invention provides methods of detecting apoptosis in a target cell, the method comprising detecting a first reporter RNA in a subcellular and/or extracellular fraction; and detecting the second reporter RNA in the subcellular and/or extracellular fraction, wherein the target cell comprises 1) a first reporter- coding nucleic acid that expresses the first reporter RNA, 2) a second reporter-coding nucleic acid that express the second reporter RNA, and 3) a packaging polypeptide, wherein the first reporter RNA lacks a packaging signal and the second reporter RNA comprises a packaging signal, and wherein apoptosis in the target cell is detected when an increase in the ratio of the detected amount of first reporter RNA to the detected amount of second reporter RNA expressed in the target is present when compared to the ratio of the detected amount of first reporter RNA to the detected amount of second reporter RNA expressed in a non-apoptotic control cell.

[0025] In some embodiments for detecting apoptosis, the target cell, or more usually, a target cell population is in animal, and the extracellularly released reporter RNAs are detected in a sample from the animal. The methods of detecting apoptosis provided herein can be employed, for example, to non-invasively determine that a transplanted or grafted organ or tissue is not appropriately being accepted in one animal as compared to another animal were the transplant or graft has been successful.

[0026] In another aspect, the present invention provides host cells comprising a packaging nucleic acid sequence encoding a packaging polypeptide, wherein the host cell extracellularly releases an encapsidated particle comprising the packaging polypeptide and a reporter RNA, wherein the reporter RNA is transcribed in the host cell. Typically, the reporter RNA is a nonviral RNA, more typically, the reporter RNA is heterologous to the host cell.

[0027] In certain embodiments, the present invention provides host cells expressing a plurality of reporter RNAs that can be extracellularly detected.

[0028] Host cells as provided herein, are useful, for example, to detect changes in intracellular transcriptional activities in response to test stimuli and thus find applications, for example, in drug screening, profiling intracellular responses to biological samples from organisms to determine differences in health or other physiological states.

[0029] In certain embodiments, the host cell is located in an animal.

5. BRIEF DESCRIPTION OF THE FIGURES

[0030] Figure 1 provides schematics of exemplary NF-κB-inducible reporter constructs.

[0031] Figure 2 provides results of SEAP reporter RNAs detected intracellularly

(Figure 2A) and extracellularly (Figure 2B) demonstrating that the expression of MoMLV

Gag-pol packaging polypeptide increases the efficacy of extracellular release of reporter

RNA from target cells.

[0032] Figure 3 provides results of reporter RNAs detected intracellularly

(Figure 3A) and extracellularly (Figure 3B) in target cells in the absence (-) and presence

(+) of TNFα demonstrating that the increase of intracellular reporter RNA in response to

TNFα is faithfully detected extracellularly.

[0033] Figure 4 provides an illustration of the plurality of reporter constructs discussed in the working examples.

[0034] Figure 5 provides a representation of results of extracellular reporter RNAs detected in response to treatment with IL- 1/3 and with forskolin of target cells comprising a plurality of non-identical reporter RNAs.

[0035] Figure 6 provides the sequence of SEQ ID NO: 1.

[0036] Figure 7 provides the sequence of SEQ ID NO: 2.

[0037] Figure 8 provides the sequences of SEQ ID NOS : 3-5. [0038] Figure 9 provides the sequence of SEQ ID NO: 6.

[0039] Figure 10 provides the sequences of SEQ ID NOS : 7-11.

[0040] Figure 11 provides the sequences of SEQ ID NOS : 12- 16.

[0041] Figure 12 provides the sequences of SEQ ID NOS : 17-20.

[0042] Figure 13 provides schematics of exemplary reporter constructs used in an embodiment of the methods provided herein to detect apoptosis.

[0043] Figure 14 provides a comparison of results from an application of an embodiments of the methods and compositions provided herein to detect apoptosis to results of an assay commonly employed in the art to detect apoptosis.

[0044] Figure 15 provides the sequence of SEQ E⁾ NO: 21.

[0045] Figure 16 provides the sequence of SEQ ID NO: 22.

6. TERMINOLOGY

[0046] The term "coding nucleic acid," as used herein, refers to a nucleic acid that can be transcribed, that is, a nucleic acid from which a RNA is expressed. The resulting transcript may or may not code for a polypeptide.

[0047] As used herein, the term "heterologous" in reference to a polynucleotide, gene, DNA, RNA, and the like (collectively "nucleic acid") refers to an identifiable nucleic acid segment (or segments) wherein the segment is in association with, e.g., operably linked to, a nucleic acid molecule with which it is not normally associated in nature. For example, a heterologous nucleic acid can be one that is present in a construct in a target cell in which it is not normally present, expressed and/or active. In another example, a heterologous nucleic acid is one that is normally present, expressed or active in a target cell, but is present in association with a nucleic acid with which it is not normally associated, e.g., is a cis-regulatory element normally present within a target cell but which in this situation is operably linked to a reporter-coding nucleic acid with which it is not normally associated. Allelic variations or naturally-occurring mutational events do not give rise to a heterologous nucleic acid as defined herein, hi contrast to a "heterologous" nucleic acid, a "native" nucleic acid is one that is normally present, expressed or active in a target cell and which is associated with the nucleic acid molecule or molecules, e.g., regulatory elements, with which it is normally associated in nature. For example, a native nucleic acid is a nucleic acid present at the genomic position within a target cell that the nucleic acid would normally be present in nature.

[0048] The terms "nucleic acid construct" as used herein, refer to heterologous nucleic acid comprising one or more cis-regulatory elements operably linked to a coding nucleic acid or nucleic acids. For example, a nucleic acid construct can be a heterologous nucleic acid stably integrated into the DNA of a target cell. A nucleic acid construct can, for example, also be an extracliromosomal sequence, including but not limited to a plasmid, expression vector, and so forth. Nucleic acid constructs can, for example, contain one or more selectable marker sequences and/or origins of replication. [0049] The term "operably linked," as used herein in the context of regulatory elements, as in, for example, a "cis-regulatory element operably linked to a reporter-coding nucleic acid," indicates that the regulatory element is present as part of the nucleic acid comprising the reporter-coding nucleic acid at a position appropriate for the regulatory element to exert its effect on the nucleic acid to which it is operably linked. For example, such an effect can refer to an initiation, increase, or repression of transcription of a reporter-coding nucleic acid, e.g., upon binding of a transcription factor to the regulatory element, or, as another example, an increase or decrease in the stability of a RNA transcript transcribed from a reporter-coding nucleic acid.

[0050] "Percent identical," "percent identity," or similar terms, used in respect of the comparison of a reference sequence and another sequence means that in an optimal alignment between the two sequences, the candidate sequence is identical to the reference sequence in a number of subunit positions equivalent to the indicated percentage, the subunits being nucleotides for polynucleotide comparisons or amino acids for polypeptide comparisons. As used herein, an "optimal alignment" of sequences being compared is one that maximizes matches between subunits and minimizes the number of gaps employed in constructing an alignment. Percent identities may be determined with commercially available implementations of algorith ms described by Needleman and Wunsch, 1970, J. MoI. Biol. 48:443-453 ("GAP" program of Wisconsin Sequence Analysis Package, Genetics Computer Group, Madison, WI). Other software packages in the art for constructing alignments and calculating percentage identity or other measures of similarity include the "BestFit" program, based on the algorithm of Smith and Waterman, 1981, Advances in Applied Mathematics 2:482-489 (Wisconsin Sequence Analysis Package, Genetics Computer Group, Madison, WI). In other words, for example, to obtain a DNA having a nucleic acid sequence at least 95 percent identical to a reference nucleic acid sequence, up to five percent of the nucleobases in the reference sequence many be deleted or substituted with another nucleobase, or a number of nucleobases up to five percent of the total nucleobases in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence many occur at the 3 ' or 5' positions of the reference nucleic acid sequence or anywhere between those terminal positions, interspersed either individually among bases in the reference sequence or in one or more contiguous groups within the references sequence.

[0051] A "polypeptide," as used herein, refers to a polymer of any number of two or more, typically ten or more, amino acid residues joined by peptide bonds, whether produced naturally or synthetically. As used herein, a "protein" is a macromolecule comprising one or more polypeptide chains.

[0052] As used herein, the term "release" of an encapsidated particle from a target cell is meant to refer to the process by which the encapsidated particle enters the extracellular milieu and achieves physical separation from a target cell to allow the recovery of the encapsidated particle without having to resort to techniques intended to lyse, permeate, break open or otherwise alter the integrity of the target cell plasma membrane (or cell wall, as the case may be). As used herein, the term "release" is not meant to indicate any particular mechanism by which an encapsidated particle, or a reporter RNA in particular, ends up in an extracellular location. Without intending to be bound by any theory or mechanism, however, release of an encapsidated particle is believed to occur through a "budding off process involving the secretory pathway.

[0053] A "reporter-coding nucleic acid," as used herein, can refer to any nucleic acid sequence, generally DNA, that can, under appropriate circumstances in a target cell, express a reporter RNA.

[0054] A "reporter RNA," as used herein, is an RNA whose transcription in a target cell is of interest. The reporter RNA is transcribed from a reporter-coding nucleic acid that can be native or can be heterologous to target cell.

[0055] The terms "substantially the same" or "substantially identical," as used herein in reference to a given polypeptide, refers to polypeptides having amino acid sequence variations in comparison to the given polypeptide but which variation do not materially affect the nature of the given polypeptide (i.e., the structure, stability characteristics, substrate specificity, and/or biological activity such as, e.g., the propensity to enable RNA packaging into an encapsidated particle, of the polypeptide). For example, amino acid sequence variations can be conservative substitutions and/or variations in regions of the given polypeptide not involved in determination of structure or function. As another example, amino acid variations can be the addition of peptide or polypeptide segments to the ends of a given polypeptide.

[0056] As used herein, a "target cell" is any cell that comprises a reporter-coding nucleic acid. 7. DETAILED DESCRIPTION

[0057] The present invention provides methods and compositions useful, for example, for non-invasively detecting transcription factor activities or RNA transcription in a target cell. Without intending to be bound by any particular mechanism or theory, the target cell is supplied with a packaging polypeptide that enables the encapsidation of an RNA of interest ("reporter" RNA) and formation of a subcellular particle, which is released as an encapsidated particle from the target cell into the extracellular milieu. In the extracellular milieu, the encapsidated reporter RNA is protected from degradation by RNA- degrading enzymes and can be detected without destruction of the target cell.

7.1. Methods

[0058] In one aspect, the present invention provides methods of detecting expression of a reporter RNA in a target cell. In particular, in certain embodiments, the methods provided comprise detecting an extracellular reporter RNA, wherein the reporter RNA is released extracellularly in an encapsidated particle comprising a packaging polypeptide from a target cell comprising the packaging polypeptide and a reporter-coding nucleic acid that expresses the reporter RNA when transcribed.

[0059] As used herein, a "target cell" is any cell that comprises a reporter-coding nucleic acid. In some embodiments, the target cell is a prokaryotic cell or eukaryotic cell, hi certain embodiments, the target cell can be a fungal cell, e.g., yeast cell, plant cell or animal cell. Animal cells can be, for example, an insect cell or mammalian cell, including a rodent cell, such as mouse or rat cell, or a primate cell, for instance, a monkey, ape or human cell, m certain embodiments, the target cell is a cell in culture, for example is a cultured cell line or tissue explant.

[0060] In some embodiments, the target cell is present within a human, hi certain embodiments, the target cell is present within a tissue or organ transplanted into a human. [0061] In other embodiments, the target cell is present within a non-human organism, e.g., a mouse, rat, sheep, goat, pig, dog or monkey, hi other embodiments, the target cell is a recombinant cell, that is, comprises one or more heterologous nucleic acids, hi still other embodiments, the target cell is a naturally occurring cell. [0062] A "reporter RNA," as used herein, is an RNA whose transcription, occurring in a target cell, is of interest. The reporter RNA is transcribed from a reporter-coding nucleic acid that can be native or can be heterologous to the target cell. That is, the present invention can non-invasively detect expression of either native, endogenous genes or heterologous coding sequences in a target cell. [0063] In certain embodiments, the reporter RNA is a RNA native to, or naturally occurring, in the target cell.

[0064] hi some embodiments, the reporter RNA is a heterologous RNA. hi some embodiments, the reporter RNA is expressed by reporter-coding nucleic acid in a reporter construct. Reporter constructs are discussed below.

[0065] In some embodiments, the reporter RNA is a nonviral RNA.

[0066] hi certain embodiments, the reporter RNA is a eukaryotic RNA.

[0067] hi general, a reporter RNA is not a protein coding RNA that is commonly expressed in most, if not all, eukaryotic cells. Such RNA molecules are encoded by

"housekeeping genes" and code for proteins are often teπned "housekeeping proteins" in the art. Hence, a reporter RNA usually is not a RNA encoding a protein such as, for example, actin, tubulin, ubiquitin, glyceraldehyde-3-phopsphate dehydrogenase (GAPDH), and the like. However, if such a reporter RNA is to be detected it is usually detected where the target cell contains a heterologous reporter construct, e.g., where the reporter RNA is operably linked to a heterologous cis-regulatory element. Further, such a reporter RNA is generally detected in combination with detection of other non-identical reporter RNAs, usually a plurality of other reporter RNAs that do not code for such housekeeping proteins.

For example, in embodiments of the methods provided where the detection of an amount of reporter RNA is compared between samples, one procedure by which to account for variations between samples can be to normalize a particular reporter RNA. Thus, for example, the concentration of a reporter RNA detected can be normalized to the concentration of RNA produced by such a housekeeping gene or genes (e.g., beta-actin,

GAPDH, etc.).

[0068] A "reporter-coding nucleic acid," can be any nucleic acid sequence, generally DNA, that can, under appropriate circumstances in a target cell, e.g., upon binding of a transcription factor to a cis-regulatory element, express a reporter RNA. Thus, in some embodiments, a reporter-coding nucleic acid can be native to the target cell, hi certain embodiments, the reporter-coding nucleic acid, or a segment or segments thereof, can be a heterologous nucleic acid.

[0069] hi embodiments where a target cell is in an animal, each cell of the animal can comprise a reporter-coding nucleic acid. In some embodiments, only certain cells of the animal will comprise the reporter-coding nucleic acid.

[0070] Transcription of a reporter RNA from a reporter-coding nucleic acid can be regulated by a cis-regulatory element or elements operably linked to the reporter-coding sequence. A cis-regulatory element can be, for example, a gene regulatory element, a promoter, an enhancer, a transcription factor response element, an RNA stability determinant, and so forth.

[0071] The cis-regulatory element can be placed upstream, downstream, or within the reporter-coding nucleic acid, provided that the cis-regulatory element regulates the amount of the reporter RNA transcripts.

[0072] In certain embodiments, the cis-regulatory element comprises a transcription factor binding domain, whereby binding of the transcription factor to the cis-regulatory element modulates expression of the reporter-coding nucleic acid to which it is operably linked. For example, a cis-regulatory element can comprise a NF-κB response element, peroxisome proliferator-activated receptor response element (PPRE), TGFce-inducible response element (TGFα), glucocorticoid receptor response element (GRE), interferon inducible response element (ISRE), cAMP response element (CRE), aryl hydrocarbon receptor response element (AhRE), estrogen receptor response element (ERE), liver X receptor response element (LXRE), p53 response element (p53), BMP-inducible response element (BRE), hypoxia-inducible factor \a (HIF- Ice) or SV40 immediately early promoter from simian virus (SV40). The sequences of these and many other cis-regulatory elements are well known to those of skill in the art. SEQ ID NOS: 1 and 9-20 are provided as non-limiting exemplifications of sequences for the response elements listed above. [0073] hi certain embodiments of the methods provided herein, a trans-acting polypeptide binds to the cis-regulatory element to modulate reporter RNA transcription. A trans-acting polypeptide can be, for example, a transcription factor or a KNA-binding polypeptide.

[0074] In some embodiments, a transcription factor binds to the cis-regulatory element to modulate reporter RNA transcription. In certain embodiments, the transcription factor bound to the cis-regulatory element induces transcription of the reporter RNA. hi certain embodiments, the transcription factor bound to the cis-regulatory element represses transcription.

[0075] In certain embodiments, a transcription factor can be a native transcription factor. In some embodiments, a transcription factor can be heterologous transcription factor, for example, a chimeric transcription factor representing a fusion of two or more proteins, or an artificial transcription factor.

[0076] A "reporter construct" is a nucleic acid construct comprising a reporter- coding nucleic acid that expresses a reporter RNA. A number of exemplary reporter constructs are described in the examples below. [0077] In general, a reporter construct can be any nucleic acid other than a native nucleic acid that is present at its naturally-occurring genomic position and that is associated with the nucleic acid molecule or molecules, e.g., regulatory elements, with which it is normally associated in nature. For example, a reporter construct can be an expression vector. As another example, a reporter construct can be a sequence stably integrated into a target cell DNA, such as a regulatory-sequence inserted next to an endogenous coding sequence, a coding sequence inserted into a endogenous regulatory sequence, and so forth. [0078] In some embodiments of the methods provided, a reporter construct comprises a reporter-coding nucleic acid, a cis-regulatory element operably linked to the reporter-coding nucleic acid, and, optionally, a packaging signal. Exemplary packaging signals are presented below.

[0079] In certain embodiments of the methods provided herein, a reporter construct is introduced into a target cell. In some embodiments, a plurality of non-identical reporter constructs are introduced into a target cell.

[0080] A reporter construct can be introduced into a target cell by any method known to those of skill in the art. For example, in some embodiments, a reporter construct can be transiently or stably transfected into cells by, e.g., electroporation, lipofection, conjugation with cell-permeable peptides, or by any other method that introduces the reporter construct into the target cell. The delivery of reporter constructs can be facilitated by various viral systems. For example, in some embodiments, the reporter constructs can be inserted into various viral delivery systems, such as retroviral, adenoviral, adeno-associated recombinant viruses, and the like as known in the art.

[0081] A "packaging polypeptide," as used herein, can be any polypeptide, naturally occuring or artificial, that enables the release of a reporter RNA, in an encapsidated particle, from a target cell to the extracellular milieu.

[0082] The term "encapsidated," as used herein, refers to a structure comprising a packaging polypeptide and a reporter RNA, whereby when released from a target cell, the reporter RNA in the encapsidated particle is more resistant to RNA degrading enzymes than it would be in the absence of the encapsidated particle. The encapsidated particle can further comprise a lipid, such as a lipid from the plasma membrane from the target cell. The terms "encapsidated" or "encapsidation" is not meant to suggest any particular manner or mechanism by which the reporter RNA is released from the target cell to the extracellular milieu. Without wishing to be bound by any particular theory or mechanism, it is believed that encapsidation involves a process by which reporter RNA of the invention is incorporated into a subcellular particle comprising a packaging polypeptide that is extracellularly released from a target cell.

[0083] In the context of the present invention, an encapsidated particle may or may not contain a capsid.

[0084] Typically, the packaging polypeptide is a viral or retroviral packaging polypeptide or a polypeptide substantially identical to a viral or retroviral packaging polypeptide. For example, in some embodiments of the methods provided herein, the packaging polypeptide can be a Rous sarcoma virus (RSV) packaging polypeptide, murine leukemia virus (MLV) packaging polypeptide, human immunodeficiency virus (HIV) packaging polypeptide, equine immunodeficiency virus (EIV) packaging polypeptide, influenza virus packaging polypeptide, Sindbis virus packaging polypeptide, vesicular stomatitis packaging polypeptide, Moloney murine leukemia virus (MoMLV) packaging polypeptide, Moloney murine sarcoma virus (MoMSV) packaging polypeptide, or a polypeptide substantially the same to any of the foregoing viral packaging polypeptides, the sequences of which are well known in the art.

[0085] In certain embodiments, the packaging polypeptide is a Gag polypeptide.

For example, in certain embodiments, the Gag polypeptide can be from MLV, HIV, EIV, other retrovirus Gag polypeptide that enables the release of a reporter RNA in an encapsidated particle, or a polypeptide substantially the same to any of the foregoing Gag polypeptides, hi certain embodiments, the packaging polypeptide is a variant, e.g., a truncated or mutated version, of a Gag polypeptide that nonetheless enables the release of a reporter RNA in an encapsidated particle from a target cell. Sequences of Gag polypeptides, and variants thereof, are well known in the art (see, e.g., Adam and Miller, 1988, J Virol. 62:3802-3806; Delchambre et al, 1989, EMBOJ. 8:2653-2660; Mann et al, 1985, J Virol. 54:401-407; Portela and Digard, 2002, J Gen. Virol. 83:723-734. Schlesinger et al, 1994, Virology 5: 39-49; Shields et al., 1978, Cell 14:601-609; Walker et al, 1988, Methods Achiev Exp Pathol. 13:18-54; Wills et al, 1991, 5:639-654). [0086] The packaging polypeptide can be a fusion polypeptide. Generally a fusion polypeptide will not contain amino acid sequences that interfere with the encapsidation and release of reporter RNA. A fusion polypeptide can be naturally occurring, for example, Gag-pol, which is a fusion of Gag polypeptide with the reverse transcriptase Pol polypeptide, hi other embodiments, a fusion packaging polypeptide is artificially designed and not naturally occurring, hi some embodiments the packaging polypeptide comprises an epitope suitable for affinity purification of encapsidated particles. [0087] A "packaging polypeptide-coding nucleic acid" can be any nucleic acid sequence, generally DNA, that can, under appropriate circumstances in a target cell, express a packaging polypeptide. In general, a nucleic acid construct comprising a packaging polypeptide-coding nucleic acid sequence can be introduced into a target cell that will express the package polypeptide intracellularly in the target cell. [0088] It will be understood that one or more packaging polypeptides, or nucleic acids encoding packaging polypeptides, can be introduced into a target cell by any method known to those of skill in the art. For example, in some embodiments, a target cell is transiently or stably transfected with an nucleic acid construct, such as an expression vector, comprising a packaging polypeptide-coding nucleic acid sequence that expresses a packaging polypeptide in the target cell. In certain embodiments, a packaging polypeptide can be introduced by microinjection of the polypeptide into the target cell. In some embodiments, packing polypeptide is introduced into the target cell by electroporation, by lipofection, or by any other means that provide intracellular polypeptide delivery. In certain embodiments, the packaging polypeptide can be produced as a fusion with a peptide transduction domain (PTD) that enables intracellular delivery of the recombinant fusion polypeptide into a target cell.

[0089] In certain embodiments where a target cell is located in an animal, the packaging polypeptide can be expressed throughout the body of the animal, which can be achieved using techniques known in the art. For example, a transgenic animal that constitutively expresses the packaging polypeptide in its cells can be generated. As another example, the packaging polypeptide can be delivered to most tissues by using systemic injection of recombinant polypeptide conjugated with peptides that enable intracellular polypeptide delivery, e.g., PTD peptides (Ho et ah, 2001, Cancer Res. 61:474-7). As yet another example, systemic gene transfer of package polypeptide-coding nucleic acid can be delivered to many cell types and tissues with delivery vehicles that do not discriminate between cell types.

[0090] In some embodiments of the methods provided wherein the target cell is located in an animal, each cell of an animal will contain and/or express a packaging polypeptide, hi other embodiments, only certain cells will contain and/or express a packaging polypeptide.

[0091] As demonstrated in the working example presented in Example 2 below, a packaging signal associated with a given reporter RNA can facilitate the extracellular release of increased amounts of that reporter RNA relative to the amount of reporter RNA released when the reporter RNA does not comprise a packaging signal. Typically, a packaging signal is a segment of nucleic acid in a reporter construct that is transcribed in association with a reporter RNA. Without intending to bound by any theory or mechanism, it is believed that packaging polypeptides recognize and preferentially form complexes with RNA transcripts containing an appropriate packaging signal as compared to KNA transcripts lacking a packaging signal.

[0092] The packaging signal can be introduced into, or within, any region of the reporter-coding nucleic acid of a reporter construct, provided that the packaging signal increases the efficacy of the extracellular release of increased amounts of the expressed reporter RNA relative to the reporter RNA expressed in the absence of the packaging signal. [0093] Certain packaging polypeptides selectively associate with a particular packaging signal. Thus, in preferred embodiments of the methods provided where a packaging signal is present in a reporter construct, the packaging signal is specific to the packaging polypeptide present in the target cell.

[0094] In some embodiments of the methods provided, a target cell comprises a Gag packaging polypeptide and a reporter construct wherein the reporter construct comprises a packaging signal (ψ) that is specifically recognized by the Gag packaging polypeptide. [0095] Encapsidated particles are much smaller than cells and can be easily separated from target cells, for example, by using a size exclusion method, e.g., filtration, sedimentation, centrifugation through a density gradient, and the like. [0096] In certain embodiments of the methods provided herein, the encapsidated particle comprises an epitope suitable for affinity purification of the encapsidated particle. For example, in certain embodiments, such an epitope can be within a packaging polypeptide.

[0097] In some embodiments, a target cell comprises a polypeptide comprising an epitope suitable for affinity purification of a encapsidated particle extracellularly released by the target cell.

[0098] In embodiments wherein a reporter particle comprises an epitope, the reporter particle can be purified by antibody capture, e.g., by immobilized antibodies, by antibody-coated beads, affinity columns, and the like. Any polypeptide that incorporates into the extracellularly released encapsidated particle can be used. Many polypeptides are available for this purpose. For example, in certain embodiments, a polypeptide comprising an epitope for use in the methods provided is a retrovirus Env polypeptide, a fusion of Env polypeptide with a heterologous polypeptide, or a polypeptide substantially the same as a retrovirus Env polypeptide. [0099] The epitope can be naturally occurring in the cell. In certain embodiments, the encapsidated particle is affinity purified by antibodies that recognize that naturally occurring epitope that incorporates into the encapsidated particle during the assembly [00100] As discussed above, reporter RNA is extracellularly released by a target cell in an encapsidated particle. Typically, reporter RNA can be isolated from the encapsidated particle and its presence is qualitatively or quantitatively determined using any protocol available to those skilled in the art. General procedures for detecting RNA are described, for example, in Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3^rd Ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 2001) and Current Protocols in Molecular Biology (Ausubel et ah, eds., John Willey& Sons, 1994-1998, Current Protocols, 1987-1994, as supplemented through July 2005 (Supplement 71)). For example, extracellular reporter RNA can be detected by Northern hybridization, by reverse- transcriptase-polymerase chain reaction (RT-PCR) amplification, by primer extension, or other procedure available to those skilled in the art.

[00101] In certain embodiments where a plurality of non-identical reporter RNAs are to be detected, an appropriate multi-transcript detection approach, such as array hybridization, multiplexed RT-PCR, and so forth, can be utilized. [00102] In embodiments where a target cell is localized in a biological organism, such as an animal for example, and the extracellularly released encapsidated particles are obtained in a fluid such as, for example, blood, plasma, urine, and so forth, appropriate handling or preparatory procedures well known to those of skill in the art can be employed to maintain the integrity of the reporter RNA to be detected. [00103] The methods provided can be applicable to detection of transcription activities of one or more transcription factors. For example, in some embodiments, the present invention provides a method of determining a transcription activity by a transcription factor, comprising: detecting an extracellular reporter RNA, wherein the reporter RNA is released extracellularly in an encapsidated particle from a target cell, wherein the encapsidated particle comprises a packaging polypeptide, and wherein the target cell comprises the packaging polypeptide and a cis-regulatory element operably linked to a reporter-coding nucleic acid that expresses the reporter RNA; wherein the transcriptional activity of the transcription factor is determined if the presence of the extracellular reporter RNA is detected.

[00104] In some embodiments, the present invention provides a method of determining transcription factor binding to a cis-regulatory element in a target cell, comprising: detecting an extracellular reporter RNA, wherein the reporter RNA is released extracellularly in an encapsidated particle from a target cell, wherein the encapsidated particle comprises a packaging polypeptide, and wherein the target cell comprises the packaging polypeptide and a cis-regulatory element operably linked to a reporter-coding nucleic acid that expresses the reporter RNA; wherein transcription binding to the cis- regulatory element is determined if the presence of the extracellular reporter RNA is detected.

[00105] In certain embodiments, a plurality of extracellular reporter RNAs are detected in the methods provided where the plurality of reporter RNAs are non-identical.. For example, the plurality of extracellular reporter RNAs can be transcribed in a target cell comprising a packaging polypeptide, wherein the target cell extracellularly releases an encapsidated particle comprising the packaging polypeptide and one or more of the plurality of non-identical reporter RNAs such that all of the plurality of reporter RNAs are extracellularly released in one or more encapsidated particles.

[00106] The use of distinguishable, i.e., non-identical, reporter RNAs, can be utilized to differentiate the activities of different transcription factors, for example, where a first reporter construct (wherein a first cis-regulatory element regulated by a first transcription factor is operably linked to a first reporter-coding nucleic acid) which is non-identical to a second reporter construct (wherein a second cis-regulatory element regulated by a second transcription factor is operably linked to a second reporter-coding nucleic acid all of which are non-identical to their counterparts in the first reporter construct) both of which are non-identical to a third reporter construct, and a fourth, and so on. [00107] Differences between non-identical reporter RNAs likely exist in terms of trancriptional efficiencies, RNA stability, packaging into encapsidated particles, and the like. Hence, it is helpful to minimize differences between each reporter in the plurality without eliminating the ability to distinguish between the non-identical reporter RNAs when detected. Typically, each reporter RNA can further comprise a "processing tag," that can be used to distinguish a given reporter RNA from another reporter RNA in a plurality of reporter RNAs when detected. A processing tag can be any sort of composition available in the art for distinguishing between RNAs. See, for example, U.S. provisional patent application No. 60/626,663, which is incorporated herein by reference in its entirety. [00108] In certain embodiments, a processing tag is a short segment, e.g. , a restriction site, located in different positions in a plurality of reporter RNAs, which otherwise can have identical sequences, wherein the presence of the processing tag serves to distinguish between reporter RNAs as detected. The working examples below provide an exemplary embodiment. [00109] In some embodiments, the plurality of reporter RNAs, or segments thereof, are 80%, 85%, 90%, 95%, 98% or 99% identical to each other. [00110] As demonstrated by the working examples below, the activation of the expression of reporter RNA to increase the intracellular concentration of the reporter RNA can be accurately reflected in an increased amount of extracelhilarly detected reporter RNA. Thus, it will be apparent that the methods of the invention provided are useful for non-invasively monitoring intracellular transcriptional activity of cis- and trans-regulatory elements, and/or reporter RNA expression.

[00111] In some embodiments, the present invention provides methods of monitoring transcription of a reporter RNA in a target cell, comprising: providing a target cell comprising a packaging polypeptide and a reporter-coding nucleic acid that expresses a reporter RNA, wherein the target cell extracellularly releases an encapsidated particle comprising the packaging polypeptide and reporter RNA; detecting the reporter RNA extracellularly at a first time point; and detecting the reporter RNA extracellularly at a second time point.

[00112] In certain embodiments, the induction of transcriptional activity of a cis- regulatory element by a transcription factor is determined. In some embodiments, the repression of transcriptional activity by a transcription factor is determined. [00113] The methods of the invention also provide methods for detecting modulation of reporter RNA transcription in a target cell by a test stimulus. For example, in some embodiments, the method provided comprises contacting a target cell with a test stimulus, wherein the target cell comprises a packaging polypeptide and a reporter-coding nucleic acid that expresses a reporter RNA; and detecting the reporter RNA extracellularly, wherein the reporter RNA is released extracellularly by the target cell in an encapsidated particle comprising the packaging polypeptide; wherein modulation of the reporter RNA transcription in the target cell by a test stimulus is determined if a change in amount of extracellularly detected reporter RNA occurs relative to the amount of extracellularly detected reporter RNA released extracellularly in an encapsidated particle from target cells in the absence of the test stimulus.

[00114] Methods of detecting modulation of reporter RNA transcription in a target cell by a test stimulus as provided herein are useful, for example, for the non-invasive assessment of various classes of compounds and treatments, including drugs and drug candidates, different diets, environmental pollutants and toxicants, bacteria, viruses, and toxins, peptides, and any other biologically active molecules, radiation, UV light, stress, and the like. [00115] The methods of the invention can be utilized for the detection of apoptosis.

This is useful, for example, where a target cell, or more typically, a target cell population, is in an animal. In particular, due to the extracellular release of encapsidated particles, reporter RNA can be detected in a sample from the animal and where the animal contains a transplanted or grafted organ or tissues or cells, and apoptosis can detected by comparing the amounts of detected reporter RNA in samples from the animal with the transplant or graft to amounts of detected reporter RNA in samples from appropriate control animals. [00116] In certain embodiments, a method of detecting apoptosis of a target cell comprises detecting the first reporter RNA in a subcellular and/or extracellular fraction; and detecting the second reporter RNA in the subcellular and/or extracellular fraction; wherein the target cell comprises 1) a first reporter-coding nucleic acid that expresses the first reporter RNA, 2) a second reporter-coding nucleic acid that express the second reporter RNA, and 3) a packaging polypeptide, wherein the first reporter RNA lacks a packaging signal and the second reporter RNA comprises a packaging signal, and wherein apoptosis in the target cell is detected when an increase in the ratio of the detected amount of first reporter RNA to the detected amount of second reporter RNA expressed in the target is present when compared to the ratio of the detected amount of first reporter RNA to the detected amount of second reporter RNA expressed in a non-apoptotic control cell. [00117] hi some embodiments, other than the packaging signal, the first packaging signal, the first reporter RNA is 80 % identical, 85 % identical, 90 % identical, 95 % identical, 91 % identical, 99 % identical or 100 % identical to the portion of the second reporter RNA.

[00118] hi some embodiments, the present invention provides a method of detecting reporter RNA transcription in a target cell in an animal, comprising: detecting the reporter RNA in a sample from an animal comprising a target cell wherein the target cell comprises a packaging polypeptide and a reporter-coding nucleic acid that expresses the reporter RNA, wherein the reporter RNA is extracellularly released by the target cell in an encapsidated particle comprising the packaging polypeptide, and wherein the reporter is a nonviral RNA. [00119] hi some embodiments, a target cell population can be assessed for transcriptional activities of cis- and/or trans-acting regulatory elements, e.g., promoters, enhancers, transcription factors, and the like, or RNA expression. A cell population can be homogenous, for example, where cells are of the same origin, same type, same cell line, or containing identical reporter constructs. In other embodiments, cells of a cell population can be heterogeneous, e.g., being of different origins, different types, different cell lines, or containing non-identical reporter constructs. IUU120] In certain embodiments, a method is provided to detect expression of one or more non-identical reporter RNAs in a target cell population. For example, the method can comprise providing a target cell population wherein each target cell of the population comprises a packaging polypeptide and one or more non-identical reporter RNAs, wherein the one or more non-identical reporter RNAs are intracellularly transcribed and are extracellularly released in an encapsidated particle by each target cell in the population wherein the encapsidated particle comprises the packaging polypeptide; and detecting the one or more non-identical reporter RNAs extracellularly.

[00121] In some embodiments, the one or more non-identical reporter RNAs comprises one reporter RNA, at least two non-identical reporter RNAs, at least five non- identical reporter RNAs, at least ten non-identical reporter RNAs, at least fifty non-identical reporter RNAs, or at least 100 non-identical reporter RNAs.

[00122] Target cell populations can be in vitro, in situ or in a plant or an animal.

[00123] In certain embodiments, the cell population comprises an organ or tissue in an animal.

7.2. Host Cells

[00124] In another aspect, the present invention provides a host cell. In some embodiments, a host cell comprises a packaging nucleic acid sequence encoding a packaging polypeptide, wherein the host cell extracellularly releases an encapsidated particle comprising the packaging polypeptide and a reporter RNA, wherein the reporter RNA is transcribed in the host cell.

[00125] In some embodiments, the reporter RNA is nonviral RNA.

[00126] In certain embodiments, the reporter RNA is a heterologous RNA.

[00127] hi certain embodiments, the host cell further comprises a reporter construct comprising a cis-regulatory element operably linked to a reporter-coding nucleic that expresses the reporter RNA when transcribed.

[00128] The host cell can be a prokaryotic or a eukaryotic cell, more typically, a fungal, e.g., yeast cell, a plant cell or an animal cell. [00129] In some embodiments, a host cell is a stem cell.

[00130] In certain embodiments, a host cell is a HEK 293 cell, HepG2 cell, HeLa cell, HCTl 16 cell, SW480 cell, MDA-MB-125 cell, MCF-7 cell, ZR75 cell, S102 cell, S149 cell, SH5 cell, NTH3T3 cell, or hTERT-immortilized normal human mammary epithelial cell.

[00131] The components of the host cell, e.g., reporter RNA, packaging polypeptide, and the like, are as defined in Section 6.1 [00132] In certain embodiments, the host cell comprises a plurality of non-identical

RNAs each of which is transcribed in the host cell and can be detected extracellularly as discussed above.

[00133] Host cells can be in vitro, in situ or in a plant or an animal.

[00134] Due to the extracellular release of the reporter RNA, host cells are useful, for example, for placing into an animal, e.g., as a tracer, where the reporter RNA can be detected in a sample from the animal.

[00135] Host cells in an animal can provide, for example, a useful means to non-invasively detect changes in the animal state in response to diet, age, disease, stress, and so forth.

[00136] In certain embodiments, the host cell comprises an organ or tissue in an animal.

[00137] In some embodiments, the organ is liver, spleen, skin, muscle, bone marrow, or brain.

[00138] In embodiments where the host cell is in an animal, the reporter RNA, or plurality of RNAs, if present, can be detected in a sample from the animal.

[00139] In certain embodiments, the sample is a fluid, e.g., blood, sera, plasma, urine, spit, tears, sweat, milk, synovial fluid, cerebrospinal fluid, amniotic fluid, and so forth.

7.3. Animals

[00140] In another aspect, the present invention provides an animal comprising a host cell as provided herein. Animals according to the present invention are useful, for example, for providing the ability to non-invasively analyze biological activities of molecules on the host cells where the host cells are in a physiologically relevant setting. [00141] In some embodiments, the animal is a non-human animal.

[00142] In certain embodiments, the animal is a mouse, rat, sheep, goat, cow, horse, rabbit, pig, dog, cat, guinea pig or monkey.

[00143] In some embodiments the present invention provides an animal wherein a reporter RNA is detectable in a sample from the animal. The sample can be a fluid, for example, blood, sera, plasma, urine, spit, tears, sweat, milk, synovial fluid, cerebrospinal fluid, amniotic fluid, and the like.

8. EXAMPLES

[00144] The following examples demonstrate successful use of methods for non- invasively detecting reporter RNA expression by detecting extracellular reporter RNA. The working examples also demonstrate, for example, detection of extracellular RNA can accurately reflect amounts of intracellularly transcribed reporter RNA, inter alia.

8.1. Example 1

[00145] Materials and general procedures used in the examples that follow are described in subsections below.

8.1.1. Cells

[00146] HEK 293 cells were maintained on DMEM media (Invitrogen, Carlsbad, CA,

USA) supplemented with 10% FBS (HyClone, Logan, UT, USA) supplemented with antibiotics. Human recombinant TNFα and IL-I β were purchased from Roche (Roche Diagnostics, Mannheim, Germany). Forskolin was purchased from Sigma (Sigma-Aldrich, St. Louis, MO, USA).

8.1.2. Nucleic Acids

[00147] All manipulations with nucleic acids were performed using standard molecular biology techniques known in the art as described, for example, in Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3^ld Ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001) and Current Protocols in Molecular Biology (Ausubel et al, eds., John Wiley & Sons, 1994-1998, Current Protocols, 1987-1994, as supplemented through July 2005 (Supplement 71)).

[00148] Packaging polypeptide expression vector, pCI-GPZ: The pCI-GPZ Gag-pol expression vector was prepared as previously described (Johnson et al., 1998, J. Virol. 72:8861-8872). This vector encodes the naturally occurring Gag-pol packaging polypeptide of the Moloney Murine Leukemia Virus (MoMLV). The Moloney Murine Sarcoma Virus (MoMSV) and MoMLV Gag polypeptides are highly homologous and both can efficiently package RNAs that contain the MoMSV or MoMLV packaging signals into secreted particles (Hibbert et al., 2004, J. Virol. 78:10927-10938). The MoMLV Gag-pol polypeptide was expressed by transfecting cells with the pCI-GPZ expression vector in which the expression of Gag-pol cDNA is driven by a constitutively active viral promoter from CMV.

[00149] Reporter constructs, NF-KB-SEAP and NF-K.B- Ψ-SEAP: As illustrated in

Figure 1, reporter constructs, NF-/cB-SEAP and NF-κB-Ψ-SEAP, were constructed having identical promoters inducible by the transcription factor NF-/cB and reporter nucleic acid sequence derived from the gene of secreted alkaline phosphatase (SEAP). NF-κB-Ψ-SEAP further contained the packaging signal from MoMSV (Ψ) that was inserted into the transcribed region of the reporter sequence, while NF-κB-SEAP lacked such a signal. More particularly, the inducible promoters contained four tandem NF-/cB binding sites and a minimal TATA-box-like sequence (Figure 6, SEQ ID NO: 1), placed upstream of the SEAP reporter sequence (Figure 7, SEQ ID NO: 2). For introduction of the packaging signal into NF-KB-Ψ-SEAP, a 560 bp DNA fragment. containing MoMSV packaging signal (Figure 8, SEQ ID NO: 3) was amplified from retroviral vector pQCXIH (Clontech, Palo Alto, CA, USA) by PCR using the following pair of primers: forward MoMSV primer 1, SEQ ID NO: 4; and reverse MoMSV primer 2, SEQ ID NO: 5. The PCR product was digested with Hind III and Nsi I restriction enzymes and inserted into the transcribed region of the reporter sequence of the NF-KB-SEAP construct between the HindIII and Pstl restriction sites to produce the NF-κB-Ψ-SEAP construct (Figure 9, SEQ ID NO: 6).

8.1.3. Transfections

[00150] For transfections, HEK 293 cells were plated at a subconfluent density

(5xlO⁵/well) in wells of a 12 well plate. Eighteen hours later, cells were transfected with FuGene 6 reagent (Roche Diagnostics, Mannheim, Germany) that was mixed with plasmid DNA at a ratio of 1.5 μl /0.5 μg of total plasmid DNA for each transfection, according to the manufacturer's protocol. Next day after transfection, the medium was replaced with 1 ml of fresh growth medium.

8.1.4. Isolation of Cellular RNA

[00151] Total cellular RNA was isolated by using TriZol reagent (Invitrogen,

Carlsbad, CA, USA) according to the manufacturer's protocol and re-dissolved in water. Routinely, .5 ml of the TriZol reagent was used to extract RNA from the confluent monolayer of HEK 293 cells in a well of a 12-well plate.

8.1.5. RNA Extraction from Reporter RNA Particles

[00152] Supernatants containing secreted reporter RNA particles were filtered through a low polypeptide binding 0.22 μm filters. The RNA was extracted from the filtered samples by using TriZol reagent. Routinely, 1 ml of Trizol reagent was used per 0.1 ml of the filtered medium.

8.1.6. Polymerase Chain Reaction (PCR) and Labeling; of PCR Products [00153] RT-PCR: Samples of RNA were treated with DNAse I (Ambion, Austin, TX USA) according to manufacturer's instructions. Residual DNAse was heat inactivated at 70° C for 15 min. The DNAse-treated RNA was reversely transcribed by using oligo-dT polynucleotides and Mo-MLV reverse transcriptase (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. One tenth of the reversely transcribed RNA was amplified in a PCR reaction, by using Taq DNA polymerase (Invitrogen, Carlsbad, CA, USA ) and the following reporter sequence-specific primers: (forward primer: 1: 5'-AAATACGAGATCCACCGAGACTCC-S' (SEQ ID NO: 7) and reverse primer 2: 5^t-GCAGGAACAGCGCCGATACAAT-3¹ (SEQ ID NO: 8)). PUK reactions were performed on a ABI 9700 GENEAMP thermo-cycler.

[00154] Quantitative real-time PCR: Samples of reversely transcribed RNA were mixed at a 1/10 ratio with the DYNAMO SYBR Q-PCR reagent (FinnZymes, Espoo, Finland) supplied with the pair of reporter sequence-specific primers (as above). Real time Q-PCR was performed on ABI PRISM 877 integrated thennocycler. For the quantification of PCR products, we used calibrating amplification curves obtained using serial dilutions of the NF-zcB-SEAP plasmid.

[00155] Labeling of PCR products: One tenth of each completed PCR reaction was diluted with a fresh PCR reaction mixture containing 6-carboxyfluorescein (6-FAM) 5'-labeled reporter polynucleotide-specific primer (primer 2:

5^t-GCAGGAACAGCGCCGATACAAT-3^l) and then incubated at 95⁰C for 2 min, at 68⁰C for 20 sec and at 72⁰C for 10 min.

8.1.7. Hpal Restriction

[00156] Hpal restriction endonuclease (New England Bio labs, Ipswich, MA, USA) was directly added to labeled PCR products at concentration of 5 U/reaction. The samples were digested for 2 hrs and purified using Qiaquick PCR purification columns (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

8.1.8. Capillary Electrophoresis

[00157] Serial dilutions of each Hpal digested sample were analyzed by capillary electrophoresis using ABI PRIZM 3100 genetic analyzer (Applied Biosystems, Foster City, CA, USA). A set of X-rhodamine-labeled MAPMARKERIOOO molecular weight standards (BioVentures, Murfreesboro, TN USA) was run in parallel to the analyzed samples as a molecular weight reference.

8.2. Example 2

[00158] This example demonstrates the detection of transcription factor activity and non-invasive detection of reporter RNA.

[00159] Reporter constructs, NF-zcB-SEAP and NF-κB-Ψ-SEAP, and Gag-pol packaging polypeptide expression vector, pCI-GPZ, were prepared as described in Section 8.1.2 above. HEK 293 cells (ca. 5x10⁵ cells) were transiently co-transfected with NF- KB-SEAP or with NF-/cB-Ψ-SEAP reporter constructs in a combination with the pCI-GPZ as described in Section 8.1.3 above. Two days later, after centrifugation, cell supernatants (extracellular media) and transfected cells were separately collected. Contaminating cells in the supernatant fractions were removed by passing the supernatants through a .22 μM filter. Total RNA samples were isolated in parallel from the cellular and the supernatant fractions as described in Section 8.1.3 above. The reporter RNA transcripts were reversely transcribed and amplified by using quantitative PCR (Q-PCR) with a pair of reporter sequence-specific primers as described in Section 8.1.6 above. The amounts of intracellular reporter RNA detected and of extracellular reporter RNA detected are provided in Figure 2. [00160] The results indicate that the insertion of the packaging signal in the reporter sequence somewhat affected the intracellular levels of the reporter RNA (ca. 2-fold increase), while the co-transfection of Gag-pol expression vector had little or no effect (Figure 2A). In contrast, cells that expressed Gag-pol packaging polypeptide in a combination with the reporter NF-κB-Ψ-SEAP, secreted a substantial amount of reporter RNA (2.5xlO⁵ copies of RNA transcripts per well) versus less than 10³ copies of RNA transcripts per well in supernatants of cells transfected with the reporter NF-κB-Ψ-SEAP alone (Figure 2B). The level of reporter RNA secreted by cells co-transfected with the Gag-pol packaging polypeptide in a combination with the reporter NF-KB-SEAP was below the level of detection (<10³ copies of reporter RNA). Thus, the expression of Gag-pol packaging polypeptide increased the secretion of reporter RNA messages containing a MoMSV packaging signal.

8.3. Example 3

[00161] The following example demonstrates that amounts of extracellularly detected reporter RNA accurately reflect amounts of reporter RNA expressed intracellularly. [00162] HEK 293 cells (ca. 5xlO⁵ cells) were co-transfected with the

NF-κB-ψ-SEAP reporter construct and the Gag-pol expression vector (pCI-GPZ) described above. Two days after transfection, cells were stimulated for 4 hrs. with a prototypical inducer of NF- /cB, tumor necrosis factor alpha (TNFα) at the concentration of 10 ng/ml. Following the stimulation, total RNA was isolated from cell lysates and from cell supernatants (extracellular media) filtered through a .22 filter. The total RNA was reversely transcribed and amplified by Q-PCR with a pair of reporter sequence-specific primers. Results demonstrate that the stimulation with TNFα increased intracellular amounts of the reporter RNA (by approximately 9-fold) (Figure 3A), and the induction was apparent in the extracellularly released RNA particles (an approximately 6-fold increase) (Figure 3B). Thus, the induction of the reporter RNA transcripts in the secreted reporter RNA particles mirrors the activation of the intracellular reporter.

8.4. Example 4

[00163] The following demonstrates that the methods of the invention are suitable for non-invasively monitoring expression of multiple reporter RNAs in a cell. [00164] A library of non-identical reporter constructs was prepared wherein each reporter construct contained a cis-regulatory element responsive to a particular transcription factor (TF) and which was associated with a distinguishable SEAP reporter nucleic acid sequence. In particular, the SEAP reporter sequences were distinguishable on the basis of a processing tag, a Hpal site in this exemplification, that was located at different positions in SEAP reporter nucleic acid sequence and that expressed reporter RNAs distinguishable due to the different positions of the processing tag within each RNA sequence. Figure 4 illustrates the principle of distinguishing between reporter sequences, where the processing tag "X" is located in different position between any two constructs having cis-regulatory elements ("REs") regulated by different TFs.

[00165] With this approach, transcripts of individual reporters can be distinguished by processing (i.e., digesting) the PCR products at the position of the processing tag (the ^• Hpal digest site) followed by separation of the processed PCR products by electrophoresis. The reporter library included the individual reporter constructs with the following cis- regulatory sequences: peroxisome proliferator-activated receptor response element (PPRE, SEQ ID NO: 9), TGFβ-inducible response element (TGFβ, SEQ ID NO: 10), glucocorticoid receptor response element (GRE, SEQ ID NO: 15), interferon inducible response element (ISRE, SEQ ID NO: 18), NF-κB response element (NF-/.B, SEQ ID NO: 1), cAMP response element (CRE, SEQ ID NO: 17), aryl hydrocarbon receptor response element (AhRE, SEQ ID NO: 11), estrogen receptor response element (ERE, SEQ ID NO: 16), liver X receptor response element (LXRE, SEQ ID NO: 12), p53 response element (p53, SEQ ID NO: 19), BMP -inducible response element (BRE, SEQ ID NO: 20), hypoxia-inducible factor 1 alpha response element (HIF- lα, SEQ ID NO: 13), and an immediately early promoter from simian virus (SV40, SEQ ID NO: 14). The complete sequences of the reporter constructs used can be found in U.S. provisional patent application No. 60/626,663, which is incorporated herein by reference in its entirety. [00166] An equimolar mix of the individual reporter constructs was co-transfected into HEK293 cells (ca. 5xlO⁵ cells) along with an equal amount of the Gag-pol expression vector (pCI-GPZ). Two days after transfection, the cells were stimulated for 4 hrs. with an inducer of NF-κB, interleukin-1 beta (IL- lβ) (at 100 U/ml), or with an inducer of CRE, forskolin (at 1 μM). Total RNA was extracted from the supernatants (extracellular media) of stimulated and unstimulated cells at the end of stimulation. The supernatants were filtered through an a .22 filter, total reporter RNA was isolated from the reporter RNA particles, and the profiles were assessed. Briefly, the total reporter RNA was reversely transcribed and amplified with a common pair of reporter sequence-specific primers, fluorescently labeled, processed ( by digestion with the Hpal restriction endonuclease), and resolved by using capillary electrophoresis as described in Sections 8.1.6-8.1.8 above. The relative activities of individual RNA reporters were calculated as the values of corresponding individual peaks on the elctrophoregram and normalized on the mean value of all reporter peaks. [00167] Figure 5 provides the profiles of induction of individual reporter RNAs in reporter particles released by the HEK 293 cells where the extracellularly detected amounts of RNA from stimulated cells were normalized to the amounts of RNAs in unstimulated cells. The profiles of the induction correspond to the specificity of the inducer (i.e., IL-I β stimulation resulted in a strong induction of RNAs of the NF-/cB reporter construct, while forskolin stimulation resulted in a strong induction of RNAs of the CRE reporter construct). These results demonstrate that the detection of reporter RNAs released extracellularly in reporter particles enables non-invasive determination of expression of multiple reporter RNAs within cells.

8.5. Example 5

[00168] This example demonstrates the use of the methods and compositions of the invention in an analysis of apoptosis.

[00169] Two reporter constructs, each comprising an identical cytomegalo virus- derived promoter (CMV) operably linked to the SEAP reporter nucleic acid sequence were made. The CMV promoter is well known to those of skill in the art. One reporter construct, termed CMV-Ψ-SEAP, contained the packaging signal from MoMSV inserted into the transcribed region of the SEAP reporter sequence, as described above for the NF-κB-Ψ- SEAP construct, while the second reporter construct, termed CMV-SEAP, did not have a packaging signal. To distinguish between the reporter RNAs transcribed from the two constructs, a Hpal cleavage site was introduced into different locations in the SEAP reporter sequences using the approach described in Example 4. Diagrams of the reporter constructs are shown in Figure 13. Sequences for the CMV-SEAP and CMV-Ψ-SEAP constructs are provided in Figures 15 and 16.

[00170] HEK 293 were co-transfected with an equimolar mix of the two reporter constructs, CMV-SEAP and CMV-Ψ-SEAP, along with an equal amount of the Gag-pol packaging polypeptide expression vector, pCI-GPZ, as described above. Two days after transfection, the cells were treated for 16 hours with genotoxic agent etoposide (100 μM, sigma-Aldrich, St. Louis, MO) in the presence of 0.5 μg/ml of human recombinant TNF- related apoptosis-induced ligand (TRAIL) (BIOMOL RL, Plymouth Meeting, PA) that synergistically provoke apoptosis in HEK 293 cells (Gibson et ah, 2000, MoI. Cell. Biol. 20:205-212). Following the treatment, supernatants (extracellular media) were collected from treated and untreated (control) cells. Extracellular RNAs were obtained and their relative amounts were determined by capillary electrophoreses as described above in Section 8.1.2. Ratios of the CMV-SEAP-expressed reporter RNA to CMV-Ψ-SEAP-expressed reporter RNA were calculated for both control and treated cells, as provided in Figure 14 A.

[00171] The results show that the ratio of reporter RNAs in the extracellular media of treated cells was three times that in control cell media (Figure 14A). These results are expected since during apoptosis (cell death) both reporter RNAs are equally likely to be detected "extracellularly" in subcellular fragments as compared to the situation in healthy cells where the reporter RNA with a packaging signal is much more likely to be detected extracellularly than the reporter RNA lacking a signal.

[00172] The methods of determining extracellular reporter RNAs provided herein were also found to agree with a commonly accepted apoptosis assay in which induction of apoptosis is measured by assessing changes in combined caspase 3/7 activity. To perform caspase activity measurements, control HEK 293 and HEK 293 cells were treated with etoposide and TRAIL as described above, then trypsinized and counted. Aliquots containing 20,000 of either treated cells or control cells were added to wells in a white walled 96 well plate in a total volume of 100 μl. Caspase activity was measured by using the CASPASE-GLO 3/7 assay (Promega, Madison, WI), according to the manufacturer's protocol. Briefly, the CASPASE-GLO 3/7 reagent containing pro-luminescence caspase substrate was added to each sample (100 μl). The plate was incubated for 30 min and luminescence in each sample was measured in a VERITAS microp late-reading luminometer (Turner BioSystems, Sunnyvale, CA). The combined caspase 3/7 activity was induced by 6-fold in etoposide and TRAIL treated cells as compared to control cells (Figure 14B). [00173] In short, the present invention provides methods for useful for analyzing apoptosis that agree with a commonly accepted apoptosis assay. However, the methods to detect apoptosis provided in the present invention can be used, for example, to non-invasivley detect apoptosis in animals.

[00174] All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

Claims

WHAT IS CLAIMED:

1. A method of detecting expression of a reporter RNA in a target cell, comprising: detecting an extracellular reporter RNA, wherein the reporter RNA is released extracellularly in an encapsidated particle from a target cell, wherein the encapsidated particle comprises a packaging polypeptide, and wherein the target cell comprises the packaging polypeptide and a reporter-coding nucleic acid that expresses the reporter RNA.

2. A method of determining activity of a cis-regulatory element in a target cell, comprising: detecting an extracellular reporter RNA, wherein the reporter RNA is released extracellularly in an encapsidated particle from a target cell, wherein the encapsidated particle comprises a packaging polypeptide, and wherein the target cell comprises the packaging polypeptide and a cis-regulatory element operably linked to a reporter-coding nucleic acid that expresses the reporter RNA; wherein activity of the cis-regulatory element is determined by the detection of the extracellular reporter RNA.

3. A method of determining activity of a trans-acting factor, comprising: detecting an extracellular reporter RNA, wherein the reporter RNA is released extracellularly in an encapsidated particle from a target cell, wherein the encapsidated particle comprises a packaging polypeptide, and wherein the target cell comprises the packaging polypeptide and a trans-acting factor operably linked to a reporter-coding nucleic acid that expresses the reporter RNA; wherein activity of the trans-acting factor is determined by the detection of the extracellular reporter RNA.

4. A method of detecting expression of a reporter RNA in a target cell comprising providing a target cell comprising a packaging polypeptide and a reporter-coding nucleic acid that expresses a reporter RNA, wherein the target cell extracellularly releases an encapsidated particle comprising the packaging polypeptide and reporter RNA; and detecting extracellular reporter RNA.

5. The method of claim 1, 2, 3, or 4 wherein the encapsidated particle further comprises a lipid.

6. The method of claim 1 , 2, 3 or 4 wherein the packaging polypeptide is Rous sarcoma virus (RSV) packaging polypeptide, murine leukemia virus (MLV) packaging polypeptide, human immunodeficiency virus (HIV) packaging polypeptide, equine immunodeficiency vims (EIV) packaging polypeptide, influenza virus packaging polypeptide, Sindbis virus packaging polypeptide, vesicular stomatitis packaging polypeptide, Moloney murine leukemia virus (MoMLV) packaging polypeptide, Moloney murine sarcoma virus (MoMSV) packaging polypeptide, or substantially identical packaging polypeptide thereof.

7. The method of claim 1 , 2, 3 or 4 wherein the reporter RNA comprises a packaging signal.

8. The method of claim 7, wherein the packaging signal is specific for Rous sarcoma virus (RSV) packaging polypeptide, murine leukemia virus (MLV) packaging polypeptide, human immunodeficiency virus (HIV) packaging polypeptide, equine immunodeficiency virus (EIV) packaging polypeptide, influenza virus packaging polypeptide, Sindbis virus packaging polypeptide, vesicular stomatitis packaging polypeptide, Moloney murine leukemia virus (MoMLV) packaging polypeptide, or Moloney murine sarcoma virus (MoMSV) packaging polypeptide.

9. The method of claim 1, 2 or 3, wherein the reporter RNA is a nonviral RNA.

10. The method of claim 1, 2 or 3, wherein the reporter RNA is a eukaryotic RNA.

11. The method of claim 1 , 2 or 3 , wherein the reporter RNA is heterologous to the target cell.

12. The method of claim 1 , 2 or 3, wherein the reporter RNA is native to the target cell.

13. The method of claim 1 or 4, wherein the target cell further comprises a cis-regulatory element operably linked to the reporter-coding nucleic acid.

14. The method of claim 13, wherein the cis-regulatory element comprises a gene regulatory sequence, a promoter, an enhancer or an RNA stability determinant.

15. The method claim 13, wherein a trans-acting polypeptide regulates transcription of the reporter-coding nucleic acid.

16. The method of claim 15, wherein the trans-acting polypeptide is a transcription factor.

17. The method of claim 16, wherein the transcription factor is a native transcription factor or a heterologous transcription factor.

18. The method of claim 13 , wherein the cis-regulatory element comprises a NF-KB response element, peroxisome proliferator-activated receptor response element (PPRE), TGFα-inducible response element (TGFo;), glucocorticoid receptor response element (GRE), interferon inducible response element (ISRE), cAMP response element (CRE), aryl hydrocarbon receptor response element (AhRE), estrogen receptor response element (ERE), liver X receptor response element (LXRE), p53 response element (p53), BMP-inducible response element (BRE), hypoxia-inducible factor Ia (HIF- lα) or SV40 immediately early promoter from simian virus (SV40).

19. The method of claim 13, wherein the target cell further comprises a reporter construct comprising the cis-regulatory element operably linked to the reporter-coding nucleic acid.

20. The method of claim 19, wherein the reporter construct is stably integrated into the target cell DNA.

21. The method of claim 19, wherein the reporter construct is extrachromosomally located in the target cell.

22. The method of claim 1, 2 or 3, wherein the target cell is an animal cell.

23. The method of claim 1, 2 or 3, wherein the target cell further comprises a packaging polypeptide-coding nucleic acid that expresses the packaging polypeptide.

24. The method of claim 3, wherein the transcriptional activity of the cis-regulatory element is regulated by a trans-acting polypeptide.

25. The method of claim 1 or 4, further comprising detecting extracellularly a plurality of non-identical reporter RNAs released extracellularly from the target cell in encapsidated particles comprising the packaging polypeptide, wherein the target cell comprises a plurality of non-identical reporter-coding nucleic acids that express the plurality of non-identical reporter RNAs.

26. The method of claim 25, wherein each reporter RNA of the plurality of non-identical reporter RNAs comprises a processing tag, wherein variation in the location of the processing tag in any one reporter RNA to another reporter RNA in the plurality of reporter RNAs establishes the non-identity between the two reporter RNAs.

27. The method of claim 26, wherein the target cell further comprises a plurality of non-identical cis-regulatory elements operably linked to the plurality of non-identical reporter-coding nucleic acids that express the plurality of non-identical reporter RNAs such that non-identity between any two cis-regulatory elements in the plurality of non-identical cis-regulatory elements exists only where the two cis-regulatory elements regulate expression of non-identical reporter RNAs.

28. A method of monitoring transcription of a reporter RNA in a target cell, comprising: providing a target cell comprising a packaging polypeptide and a reporter-coding nucleic acid that expresses a reporter RNA, wherein the target cell extracellularly releases an encapsidated particle comprising the packaging polypeptide and reporter RNA; detecting the reporter RNA extracellularly at a first time point; and detecting the reporter RNA extracellularly at a second time point.

29. A method of detecting modulation of reporter RNA transcription in a target cell by a test stimulus, comprising: a. contacting a target cell with a test stimulus, wherein the target cell comprises a packaging polypeptide and a reporter-coding nucleic acid that expresses a reporter RNA; and b. detecting the reporter RNA extracellularly, wherein the reporter RNA is released extracellularly by the target cell in an encapsidated particle comprising the packaging polypeptide; wherein modulation of the reporter RNA transcription in the target cell by a test stimulus is determined if a change in amount of extracellularly detected reporter RNA occurs relative to the amount of extracellularly detected reporter RNA released extracellularly in an encapsidated particle from target cells in the absence of the test stimulus.

30. The method of claim 29, wherein the reporter RNA comprises a packaging signal.

31. The method of claim 29, wherein the reporter RNA is a nonviral RNA.

32. The method of claim 29, wherein the reporter RNA is a heterologous RNA.

33. The method of claim 29, wherein an increase in the amount of extracellular reporter RNA is detected in response to the test stimulus determines the inducement of transcription of the reporter RNA.

34. The method of claim 29, wherein an reduction in the amount of extracellular reporter RNA is detected in response to the test stimulus determines the repression of transcription of the reporter RNA.

35. The method of claim 1, 2, 3, 28 or 29, wherein the target cell is in an animal and the reporter RNA is detected in a sample from the animal.

36. The method of claim 32, wherein the sample is a fluid.

37. The method of claim 33, wherein the fluid is blood, sera, plasma, urine, spit, tears, sweat, milk, synovial fluid, cerebrospinal fluid, or amniotic fluid.

38. A method of detecting apoptosis of a target cell, comprising: a. detecting a first reporter RNA in a subcellular and/or extracellular fraction; and b. detecting a second reporter RNA in the subcellular and/or extracellular fraction; wherein the target cell comprises 1) a first reporter-coding nucleic acid that expresses the first reporter RNA, 2) a second reporter-coding nucleic acid that express the second reporter RNA, and 3) a packaging polypeptide, wherein the first reporter RNA lacks a packaging signal and the second reporter RNA comprises a packaging signal, and wherein apoptosis in the target cell is detected when an increase in the ratio of the detected amount of first reporter RNA to the detected amount of second reporter RNA is present when compared to the ratio of the detected amount of first reporter RNA to the detected amount of second reporter RNA present in the subcellular and/or extracellular fraction of a non-apoptotic cell.

39. The method of claim 38, wherein, other than the packaging signal, the first reporter RNA is 85 % identical to the portion of the second reporter RNA.

40. The method of claim 38, wherein, other than the packaging signal, the first reporter RNA is 95 % identical to the portion of the second reporter RNA.

41. The method of claim 38, wherein, other than the packaging signal, the first reporter RNA is 98 % identical to the portion of the second reporter RNA.

42. The method of claim 38, wherein the target cell is in a cell culture.

43. The method of claim 38, wherein the target cell is in an animal and the subcellular and/or extracellular fraction is detected in a sample from the animal.

44. A method of detecting reporter RNA transcription in a target cell in an animal, comprising: detecting the reporter RNA in a sample from an animal comprising a target cell wherein the target cell comprises a packaging polypeptide and a reporter-coding nucleic acid that expresses the reporter RNA, wherein the reporter RNA is extracellularly released by the target cell in an encapsidated particle comprising the packaging polypeptide, and wherein the reporter is a nonviral RNA.

45. The method of claim 44, wherein the animal is a transgenic animal.

46. The method of claim 44, wherein the animal is a gene-knockout animal.

47. The method of claim 45 or 46, further comprising detecting the reporter RNA in a sample from a wildtype animal.

48. The method of claim 44, wherein the reporter RNA comprises a packaging signal.

49. The method of claim 44, wherein the reporter RNA is heterologous to the target cell.

50. The method of claim 44, wherein the target cell further comprises a reporter construct comprising a cis-regulatory element operably linked to the reporter-coding nucleic acid.

51. The method of claim 44, further comprising detecting a second reporter RNA in the sample from the animal, wherein the second reporter KNA is extracellularly released in an encapsidated particle comprising the packaging polypeptide from the target cell, and wherein the target cell further comprises a second reporter-coding nucleic acid that expresses the second reporter RNA.

52. A method of detecting expression of one or more non-identical reporter RNAs in a target cell population, comprising: providing a target cell population wherein each target cell of the population comprises a packaging polypeptide and one or more non-identical reporter RNAs, wherein the one or more non-identical reporter RNAs are intracellularly transcribed and are extracellularly released in an encapsidated particle by each target cell in the population wherein the encapsidated particle comprises the packaging polypeptide; and detecting the one or more non-identical reporter RNAs extracellularly.

53. The method of claim 51, wherein the one or more non-identical reporter RNAs comprises one reporter RNA.

54. The method of claim 51 , wherein the one or more non-identical reporter RNAs comprises two non-identical reporter RNAs.

55. The method of claim 51 , wherein the one or more non-identical reporter RNAs comprises five non-identical reporter RNAs.

56. The method of claim 51, wherein the one or more non-identical reporter RNAs comprises ten non-identical reporter RNAs.

57. The method of claim 51 , wherein the one or more non-identical reporter RNAs comprises fifty non-identical reporter RNAs.

58. The method of claim 51 , wherein the one or more non-identical reporter RNAs comprises 100 non-identical reporter RNAs.

59. The method of claim 51, wherein the cell population comprises an in vitro cell culture.

60. The method of claim 51 , wherein the cell population comprises an animal.

61. The method of claim 51, wherein the cell population comprises an organ or tissue in an animal.

62. The method of claim 60 or 61 , wherein the one or more non-identical reporter RNAs are detected in a sample from the animal.

63. The method of claim 51, wherein the detection of the one or more non-identical reporter RNAs extracellularly detects modulation of one or more transcription factors regulating transcription of the one or more non-identical reporter RNAs.

64. The method of claim 51 , wherein the detection of the one or more non-identical reporter RNAs extracellularly detects the regulation of transcription of the one or more non- identical reporter RNAs by one or more cis-regulatory elements wherein each one or more one or more cis-regulatory element is operably linked to one or more reporter-coding nucleic acids that express the one or more reporter RNAs when transcribed.

65. The method of claim 52 further comprising detecting the one or more non-identical reporter RNAs extracellularly a plurality of times, wherein changes in amounts of transcribed reporter RNA between detections at different times can be determined.

66. The method of claim 52 further comprising detecting expression of one or more non- identical reporter RNAs in a second target cell population.

67. The method of claim 66 further comprising comparing the detected expression of the one or more non-identical reporter RNAs in the target cell population to the detected expression of the one or more non-identical reporter RNAs in the second target cell population

68. The method of claim 66 further comprising detecting the one or more non-identical reporter RNAs extracellularly a plurality of times in the second target cell population, wherein changes in amounts of transcribed reporter RNA in the second target cell population between detections at different times can be determined.

69. A host cell comprising a packaging nucleic acid sequence encoding a packaging polypeptide, wherein the host cell extracellularly releases an encapsidated particle comprising the packaging polypeptide and a first reporter RNA, wherein the first reporter RNA is transcribed in the host cell, and wherein the first RNA is a nonviral RNA.

70. The host cell of claim 69, wherein the host cell is a eukaryotic cell.

71. The host cell of claim 70 further comprising a first reporter construct comprising a first cis-regulatory element operably linked to a first reporter-coding nucleic acid that expresses the transcribed first reporter RNA.

72. The host cell of claim 70, wherein the first reporter RNA comprises a packaging signal.

73. The host cell of claim 70 further comprising a second reporter construct, a third reporter construct, and, optionally, additional reporter constructs, wherein the second reporter construct, third reporter construct, and optional additional reporter constructs, each comprise a cis-regulatory element and a reporter-coding nucleic acid that expresses a reporter RNA wherein the cis-regulatory elements of the first reporter construct, second reporter construct, third reporter construct, and optional additional reporter constructs are non-identical and the reporter RNA expressed by the first reporter construct, second reporter construct, third reporter construct, and optional additional reporter constructs are non- identical.

74. A method of detecting expression of a reporter RNA, comprising: detecting extracellular first reportor RNA transcribed in the host cell according to claim 70

75. A non-human animal comprising one or more host cells according to claim 69, wherein the reporter RNA is detectable in a sample from the animal.

76. The non-human animal of claim 75wherein the sample is a fluid.

77. The non-human animal of claim 76, wherein the fluid is blood, sera, plasma, urine, spit, tears, sweat, milk, synovial fluid, cerebrospinal fluid, or amniotic fluid.

78. The non-human animal of claim 75, wherein the one or more host cells are in an organ.

79. The non-human animal of claim 78, wherein the organ is liver, spleen, skin, muscle, bone marrow, or brain.

80. The non-human animal of claim 75, wherein the one or more host cells are stem cells.

81. The non-human animal of claim 75, wherein the one or more host cells are derived from a species different than the animal.

82. The non-human animal of claim 81, wherein the animal comprises one or more host cells of human origin.