WO2022159664A1

WO2022159664A1 - Engineered multi-segmented rna viruses for large-scale combinatorial genetic screening

Info

Publication number: WO2022159664A1
Application number: PCT/US2022/013253
Authority: WO
Inventors: Joseph L. DERISI; Hanna RETALLACK
Original assignee: Chan Zuckerberg Biohub, Inc.; The Regents Of The University Of California
Priority date: 2021-01-22
Filing date: 2022-01-21
Publication date: 2022-07-28

Abstract

Engineered multi-segmented RNA viruses are provided. These viruses can be used to generate large-scale combinatorial libraries, for example sgRNAs libraries.

Description

ENGINEERED MULTI-SEGMENTED RNA VIRUSES FOR LARGE-

SCALE COMBINATORIAL GENETIC SCREENING

CROSS REFERENCE TO RELATED PATENT APPLICATIONS

[0001] The present patent application claims benefit of priority to U.S. Provisional Patent Application No. 63/140,470, filed January 22, 2021, which is incorporated by reference for all purposes

BACKGROUND OF THE INVENTION

[0002] Library screening for biological effects of molecules on cells or other biological entities can be useful to dissect biological pathways. One example of screens are genetic screens, for example where one or more molecule is introduced into a cell, or an endogenous gene is modified, and the effect of this perturbation is measured, for example by an output such as cell proliferation, cell death, expression of a gene, which can be a natural gene or a reporter gene that responds to activation or inhibition of a certain gene product or pathway. More recently, genetic targeting screens, e.g., CRISPR-based screens, have been developed. Depending on the library and mode of action, the screens can knock out genes, or transcriptionally-activate or -inhibit genes. In some cases, multiple genes are targeted at the same time. This can be especially helpful in dissecting genetic pathways where a phenotype or output is only readily observable where two or more genes have been targeted. It can however be difficult to generate libraries that comprise a comprehensive combination of targeting molecules (e.g., sgRNAs in the context of CRISPR) whose identity can be readily determined following the screen, i.e., to identify the combination of targeting molecules that result in “hits” in a screen. This limitation in generating combinations of targeted genes is a major obstacle in understanding biological pathways that may have redundancy or complex interactions of molecules such that the pathway output only varies when multiple molecules are targeted. BRIEF SUMMARY OF THE INVENTION

[0003] In some embodiments, a population of engineered Arenavirus virions is provided.

In some embodiments, the virions comprises: an RNA genome encoding each of NP, L, GP and Z proteins, wherein the RNA genome is made up of three or more different RNA molecules, wherein the RNA genome comprises: a first RNA encoding a first sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z; a second RNA encoding at least one Arenavirus protein selected from one of NP, L, GP or Z; and a third RNA encoding at least one Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and wherein: i. in at least some virions, the second RNA further encodes a second sgRNA; or ii. at least some virions further comprise an RNA encoding a different sgRNA than the first sgRNA and the same Arenavirus protein as the first RNA; or iii. both i and ii.

[0004] In some embodiments, the third RNA encodes two Arenavirus proteins selected from one of NP, L, GP or Z. In some embodiments, the first RNA encodes GP and the second RNA encodes NP and the third RNA encodes L and Z. In some embodiments, the first RNA encodes NP and the second RNA encodes GP and the third RNA encodes L and Z.

[0005] In some embodiments, the third RNA further encodes a third sgRNA, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and different gRNAs.

[0006] In some embodiments, the virions comprise a fourth RNA encoding a fourth sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA and fourth RNA encode different Arenavirus proteins and different gRNAs.

[0007] In some embodiments, at least some different virions in the population have different first sgRNA sequences or different second sgRNA sequences or both.

[0008] In some embodiments, RNAs comprising an sgRNA coding sequence and a coding sequence for an Arenavirus protein comprise a RNA self-cleaving sequence between the sgRNA coding sequence and the coding sequence for an Arenavirus protein. In some embodiments, the RNA self-cleaving sequence is a ribozyme.

[0009] In some embodiments, the first RNA encodes GP and the second RNA encodes NP and either: i the third RNA encodes L and Z; or ii. the third RNA encodes L and the virion comprises a fourth RNA that encodes Z.

[0010] In some embodiments, at least one RNA encodes two sgRNA sequences.

[0011] In some embodiments, the RNAs comprise 5’-3’: a 5’ untranslated region (UTR); a

5’ portion of a protein coding sequence, wherein the coding sequence encodes the Arenavirus protein selected from one of NP, L, GP or Z; first RNA self-cleaving sequence ; a coding sequence the sgRNA; a second RNA self-cleaving sequence; and a 3’ portion of said protein coding sequence.

[0012] In some embodiments, the Arenavirus is a Lymphocytic Choriomeningitis Virus (LCMV).

[0013] In some embodiments, the first or second RNA self-cleaving sequence or both are ribozymes

[0014] Also provided are methods of generating a mixture of cells expressing different combinations of sgRNAs. In some embodiments, the methods comprise infecting a plurality of cells with the population of virions as described above or elsewhere herein, wherein at least some different virions in the population encode different sgRNAs, under conditions that allow for viral replication and expression of the sgRNAs in the cells.

[0015] In some embodiments, the population of virions comprise at least 5, 10, 25, 50, or 100 different virions, each comprising an RNA encoding a different sgRNA. In some embodiments, the method further comprises identifying sgRNAs that affect cell function.

[0016] Also provided are methods of making a library of virions comprising a diverse plurality of sgRNAs. In some embodiments, the method comprises introducing into a plurality of cells polynucleotides (e.g., as plasmids, or contained in virions) encoding: a first RNA encoding a first sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z; a second RNA encoding a second sgRNA and at least one Arenavirus protein selected from one of NP, L, GP or Z; and at least a third RNA encoding at least one Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and the polynucleotides in total encode RNAs encoding NP, L, GP or Z, wherein the polynucleotides include different sequence options for the first sgRNA and the second sgRNA; incubating the cells under conditions to allow for reassortment of RNAs in virions resulting from cells infected by multiple initial virions that carry different sgRNAs into at least some cells; harvesting virions generated from the cells, wherein different virions comprise different combinations of first sgRNA and second sgRNA sequence options.

[0017] In some embodiments, the third RNA encodes two Arenavirus proteins selected from one of NP, L, GP or Z. In some embodiments, the first RNA encodes GP and the second RNA encodes NP and the third RNA encodes L and Z. In some embodiments, the first RNA encodes NP and the second RNA encodes GP and the third RNA encodes L and Z.

[0018] In some embodiments, the third RNA further encodes a third sgRNA, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and different gRNAs.

[0019] In some embodiments, the virions comprise a fourth RNA encoding a fourth sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA and fourth RNA encode different Arenavirus proteins and different gRNAs.

[0020] Also provided is a polynucleotide encoding an engineered Arenavirus RNA comprising 5 ’-3’: a 5’ untranslated region (UTR); a 5’ portion of a protein coding sequence, wherein the coding sequence encodes an Arenavirus protein selected from one of NP, L, GP or Z; a first RNA self-cleaving sequence; a coding sequence for a heterologous protein or heterologous RNA; a second RNA self-cleaving sequence; and a 3’ portion of said protein coding sequence.

[0021] In some embodiments, the polynucleotide is an RNA. In some embodiments, said coding sequence encodes a single guide RNA (sgRNA). [0022] In some embodiments, the polynucleotide is DNA.

[0023] Also provided is an Arenavirus virion comprising the RNA as described above. In some embodiments, the Arenavirus is a Lymphocytic Choriomeningitis Virus (LCMV).

[0024] Also provided is a method of expressing a heterologous protein or RNA in a cell, the method comprising expressing the polynucleotide as described above in a cell, wherein expression of the polynucleotide results in expression of the heterologous protein or heterologous RNA.

DEFINITIONS

[0025] As used herein, the following terms have the meanings ascribed to them unless specified otherwise.

[0026] The terms “a,” “an,” or “the” as used herein not only include aspects with one member, but also include aspects with more than one member. For instance, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a cell” includes a plurality of such cells and reference to “the agent” includes reference to one or more agents known to those skilled in the art, and so forth.

[0027] Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this technology belongs. Although exemplary methods, devices and materials are described herein, any methods and materials similar or equivalent to those expressly described herein can be used in the practice or testing of the present technology. For example, the reagents described herein are merely exemplary and that equivalents of such are known in the art. The practice of the present technology can employ, unless otherwise indicated, conventional techniques of tissue culture, immunology, molecular biology, microbiology, cell biology, and recombinant DNA, which are within the skill of the art. See, e.g., Sambrook and Russell eds. (2001) Molecular Cloning: A Laboratory Manual, 3rd edition; the series Ausubel et al. eds. (2007) Current Protocols in Molecular Biology; the series Methods in Enzymology (Academic Press, Inc., N.Y.); MacPherson et al. (1991) PCR I: A Practical Approach (IRL Press at Oxford University Press); MacPherson et al. (1995) PCR 2: A Practical Approach; Harlow and Lane eds. (1999) Antibodies, A Laboratory Manual; Freshney (2005) Culture of Animal Cells: A Manual of Basic Technique, 5th edition; Miller and Calos eds. (1987) Gene Transfer Vectors for Mammalian Cells (Cold Spring Harbor Laboratory); and Makrides ed.

(2003) Gene Transfer and Expression in Mammalian Cells (Cold Spring Harbor Laboratory).

[0028] An "expression cassette" refers to a nucleic acid construct that, when introduced into a host cell, results in transcription and/or translation of an RNA or polypeptide, respectively.

[0029] A variety of Arenavirus proteins are referenced in this application and are referenced by the standard terms used for them in the art. See, e.g., Salvato, et al., Virology 1989; 173 : 1-10. The genome of naturally-occurring lymphocytic choriomeningitis virus (LCMV), an Arenavirus, consists of two negative-sense single-stranded RNA segments, designated L and S. Both segments contain two viral genes in an ambisense coding strategy, with the genes being separated by an intergenic region (IGR). See, e.g., Jeong et al., J Virol. 2000 Apr; 74(8): 3470-3477. The S RNA directs synthesis of the three major structural proteins: the nucleoprotein, NP (ca. 63 kDa, e.g., UniProtKB - P09992 (NCAP LYCVA)); and two mature virion glycoproteins, GP-1 (40 to 46 kDa) and GP-2 (35 kDa), that are derived by posttranslational cleavage of a precursor polypeptide, GP-C (75 kDa; e.g., UniProtKB - P09991 (GLYC LYCVA)) (Romanowski V, et al., Virus Res. 1985;2:35-51; Southern P J, et al., Virology 1987;157: 145-155; Xing Z, Whitton J L. J ViroL

1992;66: 1361-1369). The NP, the most abundant viral protein in virally infected cells, is associated with the viral RNA (vRNA) to form the nucleocapsid (NC) which is the template for the viral RNA polymerase (Fuller-Pace F V, Southern P J. Virology. 1988;162:260-263). The L RNA segment encodes a high-molecular-mass protein (L; ca. 200 kDa; e.g., UniProtKB - P14240 (L LYCVA)) which has the characteristic motifs conserved in all the viral RNA-dependent RNA polymerases and a small polypeptide Z (ca. 11 kDa, e.g., UniProtKB - P18541 (Z LYCVA)) which contains a RING finger motif and whose function is unknown. The L protein is thought to be the main viral component of the arenavirus polymerase (Fuller-Pace F V, Southern P J. J Virol. 1989;63: 1938-1944).

[0030] The term “heterologous” when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a “heterologous polypeptide” refers to a protein that is not found naturally in the cell or mixture in question.

[0031] The term “viral replication protein” refers to a protein that must be expressed in a cell (e.g., by expression from a viral genome) in order for the virus to successfully replicate and form new infectious viral particles. As explained herein all viral replication proteins need not be encoded by the same viral particle so long as multiple virions infect a cell and the sum of proteins expressed from the virion genomes result in all replication proteins needed by the virus to replicate.

[0032] The “CRISPR/Cas” system refers to a widespread class of bacterial systems for defense against foreign nucleic acid. CRISPR/Cas systems are found in a wide range of eubacterial and archaeal organisms. CRISPR/Cas systems include various types and subtypes based on shared characteristics and evolutionary similarity. These are grouped into two large classes based on the structure of the effector complex that cleaves genomic DNA. The Type II CRISPR/Cas system was the first used for genome engineering, with Type V following. Wild-type type II CRISPR/Cas systems utilize an RNA-mediated nuclease Cas protein or homolog complex with guide RNA to recognize and cleave foreign nucleic acid. The term “Cas nuclease” or “Cas” refers to CRISPR associated protein, an RNA-guided nuclease that introduces a double stranded break in nucleic acid. The Cas nuclease can be CRISPR associated protein 9 (“Cas9 nuclease” or “Cas9”) or any other targeted In someembodiments, the programmable nuclease comprises Casl, CaslB, Cas2, Cas3,Cas4, Cas5, Cas6, Cas7, Cas8, Csyl, Csy2, Csy3, Csel, Cse2,Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4,Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3,Csxl, Csxl5, Csfl, Csf2, Csfi, Csf4, Cpfl, C2cl, C2c3, Casl2a, Casl2b,Casl2c, Casl2d, Casl2e, Casl3a, Casl3b, or Casl3. Cas9 and some other targeted nuclease proteins also use an activating RNA (also referred to as a transactivating or tracr RNA). Guide RNAs can have activity of either a guide RNA or both a guide RNA and an activating RNA, depending on the type of CRIS PR-associated endonuclease used. Dual activity guide RNAs are referred to as a single guide RNA (sgRNA). In this disclosure, the term “sgRNA” is used to refer to an RNA molecule that complexes with a CRISPR- associated endonuclease and localizes the ribonucleoprotein complex to a target DNA sequence. Typically, an sgRNA comprises a “scaffold” sequence for binding the nuclease and a “targeting” sequence that defines the target nucleic acid site (for example, a genomic DNA site). “Activity” in the context of CRISPR/Cas activity, CRISPR-associated endonuclease activity, sgRNA activity, sgRNA:CRISPR-associated endonuclease nuclease activity and the like refers to the ability to bind to a target genetic element. Typically, activity also refers to the ability of the sgRNA: CRISPR-associated endonuclease nuclease complex to make double-strand breaks at a target genomic region. A catalytically inactive variant of Cas endonuclease, such as a catalytically inactive variant of Cas9, which is referred to as “dead Cas9” or “dCas9” in the present disclosure, lacks endonuclease activity. For example, dCas9 is a mutant form of Cas9 whose endonuclease activity is eleminated through point mutations in its endonuclease domains. When coexpressed with a guide RNA, such as an sgRNA, the guide RNA and dCas9 generate a DNA recongnition complex that can specifically interfere with transcription of a nucleotide sequence, to which the guide RNA is targeted. CRISPR interference (CRISPRi) methods and systems use dCas9 paired with sgRNA to hinder transcription of a target gene. Similarly CRISPR activation (CRISPRa) can be used to activate transcriptopm of target genes.

BRIEF DESCRIPTION OF THE DRAWINGS

[0033] FIG. 1 : Overview of some embodiments. Tripartite virus with at least one guide RNA encoding segment is provided. Also shown is an optional mCherry reporter. As shown, the virus may package multiple segments allowing reassortment of guide RNAs at a high multiplicity of infection (MOI). The virus may feature multiple guide RNAs attached to different viral genes, forcing higher levels of reassortment. In the Arenavirus depicted, at most, a virus with 4 guide RNAs can be made such that all 4 are required for viral growth. Cells containing a sgRNA-guided enzyme, for example Cas9, dCas9, or aCas9, can be infected by the viruses. For example, the cells can include a reporter or phenotype to be interrogated (options include but are not limited to, differentiation, pathways, or drug response, for example). Passage of the viruses and/or sorting of cells allows reassortment and selection to achieve optimal combinations of guide RNAs, for example that cause the reporter activity or phenotype. Resulting virus sequences can be sequenced to identify those combinations that emerge in the desired reporter activity or phenotype cells. In some embodiments, nucleic acids from single cells are sequenced, capturing in some embodiments both sgRNAs and transcriptome to read cellular state (e.g., differentiation).

[0034] FIG. 2A-2E: Recombinant LCMV designs. Genome diagrams showing each RNA segment in a virus particle of (A) wildtype LCMV, (B) tripartite recombinant LCMV with transgenes X and Y (Emonet 2009 PNAS), and (C) tripartite recombinant LCMV expressing a guide RNA and the fluorophore mCherry. Diagram of RNA expressed from the NP locus of (D) wildtype LCMV and (E) tripartite gRNA-expressing LCMV. Arrowheads (triangles) indicate ribozyme cleavage sites. The design in (C) and (E) produces a functional gRNA that targets DNA complementary to the spacer sequence when complexed with cas9 protein. GP: glycoprotein, NP: nucleoprotein, Z: matrix protein, L: polymerase, UTR: untranslated region, IGR: intergenomic region, term: terminus, RE: restriction enzyme, gRNA: guide RNA.

[0035] FIG. 3 : Growth curves of gRNA-expressing recombinant LCMV. Cultured human cells were inoculated with LCMV wildtype or tripartite recombinant strains expressing an AAVS1 -targeting gRNA at an MOI of 0.1. Supernatants were collected at timepoints from 2 to 72 hours post-inoculation, and titered by focus forming assay to quantify production of infectious virions. Tripartite recombinant LCMV strains expressing gRNAs appear similar in fitness to the wildtype virus.

[0036] FIG. 4: Genome editing by gRNA-expressing recombinant LCMV. Cultured human cells constitutively expressing nuclease cas9 protein were inoculated with LCMV wildtype or tripartite recombinant strains. Recombinant LCMV strains expressed gRNAs that were either non-targeting, or targeted the genomic locus AAVS1 (shading indicates increasing MOI). Cells were collected at time points from 24 hours to 6 days post-inoculation, and assayed for genome editing using the Inference of CRISPR Edits method, which reports the percentage of genome sites containing an insertion or deletion (indel %). Strains targeting AAVS1 resulted in >50% genome editing as early as 48hpi, and achieved as high as 94% genomes edited indicating high efficiency.

[0037] FIG.: 5 Co-infection is common. Cultured human cells were inoculated with a recombinant LCMV strain carrying a red or green reporter, or with both strains simultaneously. At 24 and 48 hours post infection (hpi) cells were assayed for expression of the reporter. At 48 hpi, >60% of cells inoculated with both strains expressed both reporters, indicating that a majority of cells can be rapidly co-infected by multiple LCMV strains.

DETAILED DESCRIPTION OF THE INVENTION

[0038] The inventors have discovered engineered virus systems that can be used to generate large populations of diverse virions that express different heterologous sequences. The design of the virions allows for convenient and thorough mixing of different heterologous sequences in virions to generate a virion population representing a mixture of a large number of different heterologous sequences. The resulting diverse population of virions can be used for many aspects, including screening libraries for biological activities, including activities of combinations of two or three or more different heterologous systems that are introduced into cells by the virions. Ultimately, the methods allow for selection of virions that are present in cells having a desired phenotype. Sequence virions form such cells reveals the identity of the sgRNA combinations therein, indicating gene combinations involved in the phenotype.

[0039] The examples below describe a proof of concept system based on engineering of the RNA virus LCMV (Lymphocytic Choriomeningitis Virus), though the system can be applied to other viruses that support multipartite genomes (genomes represented by multiple independent genetic components in the same virion). For example, the genome of LCMV is bipartite, but the virion will package multiple (more than two) RNAs.

[0040] Several methods, which can be used alone or in combination, can be used to generate diverse virion populations. The systems described herein involve virions that comprise multiple RNAs as part of a multi-RNA genome. The virions comprise one or more RNA segment in the viral genome that encodes (i) at least one viral protein required for viral replication and (ii) at least one heterologous sequence. Each viable virion will also include additional RNA molecules encoding any remaining proteins necessary for virus replication. By linking a sequence encoding a protein required for viral replication to the sequence encoding the heterologous sequence, selection for virions containing the RNA comprising the heterologous sequence is achieved, reducing the chance the sequence will be lost during viral replication.

[0041] In one aspect, the virion population can have RNAs comprising different heterologous sequences linked to the same viral protein coding sequence, allowing for a population where different single heterologous sequences are present in virions in the population.

[0042] In another aspect, the virion genome includes: a first RNA encoding (i) at least a first viral protein required for viral replication and (ii) at least a first heterologous sequence; and a second RNA encoding (i) at least a second viral protein required for viral replication and (ii) at least a second heterologous sequence. As in the aspect above, different first and second heterologous sequences can be inserted in the first RNA and the second RNA, respectively. As discussed further below, in this aspect, multiple options for the first and second heterologous sequences allows for a generation of a population of virions that comprise a wide variety of combinations of the first and second heterologous sequences.

[0043] As an example, in a virus genome where viral proteins X and Y are required for viral replication, a first RNA segment can encode X and also include heterologous sequence A, A’, or A” and a second RNA segment can encode Y and heterologous sequence B, B’, and B”. Expressing such RNAs in cells will result in virions such as:

Virion 1 : first RNA encoding X and heterologous sequence A and second RNA encoding Y and heterologous sequence B;

Virion 2: first RNA encoding X and heterologous sequence A’ and second RNA encoding Y and heterologous sequence B;

Virion 3 : first RNA encoding X and heterologous sequence A’ ’ and second RNA encoding Y and heterologous sequence B; and

Virion 4: first RNA encoding X and heterologous sequence A’ and second RNA encoding Y and heterologous sequence B”.

[0044] The above example shows only some possible combinations of A, A”, A”, B, B’ and B”.

[0045] In further aspects the virions can include three or four RNA molecules, each encoding a different protein required for viral replication and also linked to a different heterologous sequence. In this way, a greater variety of different virions can be established where different versions of each heterologous sequence is available for recombination in a virion population following expression in cells.

[0046] By combining selection on a virus-packaged set of RNA segments as described herein with the dynamics of viral infection and reassortment, a large number of combinations of heterologous sequences can be made. As described further herein the heterologous sequence can be a non-coding RNA, e.g., an sgRNA, or a coding RNA, i.e., encoding a protein. One particular advantage of the systems described herein is that a library of virions comprising a mixture of single guide RNAs can be generated and later be used in various screening methods to identify single and/or combined guide RNAs (e.g., a first and a second sgRNA) that result in a desired or altered phenotype as explained more below.

[0047] Any type of virus that has a multi-partite genome can be used. In some embodiments, the viruses are RNA viruses, i.e., viruses having an RNA genome. Exemplary multi-partite RNA viruses are arenaviruses, which can be used in the methods described herein. Arenaviruses have a bipartite genome, wherein each of the two naturally-occurring RNA segments express two proteins required for replication. A first natural arenavirus RNA encodes the GP and NP proteins and the second natural arenavirus encodes the L and Z proteins. See, e.g., Salvato, et al., Virology 1989;173: 1-10. Arenaviruses, e.g., LCMV, will tolerate split of the two RNA segments into three or four RNA segments, each encoding separate viral proteins, and thus RNA encoding each can be linked to different heterologous sequences.

[0048] RNA segments encoding a protein (e.g., a viral replication protein) and a heterologous sequence can be generated as single RNAs that contain a self-cleaving sequence between the portion of the RNA encoding the protein and the heterologous sequence such that once the RNA segment is transcribed in the cell, the self-cleaving sequence cleaves between the two portions, releasing an RNA encoding the viral protein from the remaining portion of the RNA, which comprises the heterologous sequence. In some embodiments, the RNA segment can comprise three or more separate RNA sequences, in which case each can be separated from the adjacent sequence by a self-cleaving sequence. Exemplary selfcleaving sequences include but are not limited to hammerhead ribozyme sequences (positioned such that cleavage occurs 5' to the released RNA), and Hepatitis D virus ribozyme (positioned such that cleavage occurs immediately adjacent to the desired 3' end of the released RNA).

[0049] In some embodiments, RNA segments encoding a protein (e.g., a first viral replication protein) and a heterologous sequence can be generated by inserting the heterologous sequence within the coding sequence of a second viral replication protein encoded on the RNA, with RNA self-cleaving sequences on both ends of the heterologous sequence, but retaining at least some of the coding sequence of the second viral replication protein at either end of the inserted heterologous sequence, which can enhance replication and transcription of that RNA. For example, in some embodiments, an RNA segment comprises in the following order 5’-3’: a 5’ portion of a viral protein coding sequence linked to a first self-cleaving sequence linked to the heterologous sequence linked to a second selfcleaving sequence linked to the remaining (3’) portion of the viral replication protein coding sequence. This configuration can provide further selection of the heterologous sequence.

[0050] Populations of virions can be generated using any method commonly used to cause viral expression in cells. Any cells that support viral replication can be used. For example, in some embodiments, various rodent cells or human cells can be used to replicate the virus. For example, RNA constructs encoding all required proteins for viral replication can be expressed in a cell that supports viral replication, allowing for their expression and resulting virion assembly. Emonent et al. (Proc. Natl. Acad. Sci. USA March 3, 2009 106 (9) 3473- 3478) for example describes a viral tripartite system, where the normally bi-segmented LCMV genome is split into three RNA pieces, and introducing genes of interest. In some embodiments, one or more DNA constructs comprising a promoter controlling expression of the RNA are introduced into the cell and RNA are expressed from the DNA. For example one or more plasmid encoding the RNA segments can be introduced into cells and the cells can be cultured under conditions to allow for expression from the plasmids. See, e.g., Flatz, et al., Proc. Natl. Acad. Sci. USA March 21, 2006 103 (12) 4663-466. Following formation of virions in the cells, the virions can be harvested. In some embodiments, the virions can be passaged in cells to allow for further recombination of the RNA segments to generate a population of virions with different RNA segments, so long as they include all RNA segments sufficient to provide a copy of each protein required for viral replication.

Exemplary conditions for storage and propagation of LCMV can be found, for example, in Welsh and Seedhom, Curr Protoc Microbiol. 2008 Feb; CHAPTER: Unit-15 A.1.

[0051] Virion populations generated in cells result in random packaging of the available RNA segments as produced in a cell. Virions comprising sufficient coding sequences for packaging and replicating are automatically selected by their ability to replicate. By providing multiple options for heterologous sequences, or combinations of heterologous sequences (see for instance, the example above of options A, A’, and A” and B, B’ and B”) linked to the required viral gene products, the resulting virions will have combinations of heterologous sequences.

[0052] One use of the described viral populations, which comprise random combinations of heterologous sequences, is for screening libraries. One particular use involves the heterologous sequences being different sgRNAs useful for screening in a CRISPR-based assay. A variety of such assays can be used, including for example, CRISPR (mutation or deletion of target sequences), CRISPR-a (transcriptional activation of target sequences) or CRISPR-i (transcriptionally inhibiting the target sequences). See, e.g., Gilbert et al., Cell Vol. 154(2), P442-451, JULY 18, 2013 for a description of such assays. One previous difficulty has been in generating diversity of sgRNAs, and more specifically, combinations of sgRNAs that can be used in such assays. The virion populations address this issue when the heterologous sequences are sgRNAs.

[0053] sgRNAs can be selected for a preferred CRISPR system. sgRNA architectures and sequences will differ for example depending on whether the active or inactive RNA-guided nuclease is for example, Cas9, Casl2a, Casl3, Casl4, etc. For example, the protospacer adjacent motif (PAM) sequence will be selected for use for a particular CRIPSR/Cas system, e.g., Cas9, Casl2a, Casl3, Casl4. Moreover, the targeting sequences of the sgRNAs can be selected to be random or they can be selected to target genes as desired.

[0054] In some embodiments, cells can be inoculated with the population of virions comprising sgRNAs as heterologous sequences as generated herein. The Cas enzyme or other RNA-guided nuclease that partners with and is targeted by the sgRNA can be either expressed in cells (e.g., a cell line) or be encoded by the virus. The cells may also be engineered with a readout of pathways or other functions in the cell (e.g., GFP production dependent on a certain pathway being activated; or quantifiable luciferase production dependent on pathway targeted by a drug). One or more selection pressure or other molecule being interrogated (e.g. drug treatment, or a molecule to activate a certain cellular response or pathway, or even none if assaying for host factors that affect LCMV itself) can be added. The read-out for effect of gene disruption or modification of expression targeted by the sgRNA heterologous sequences expressed by the virion RNAs will vary depending on the system used. In some embodiments, for example, cells can be sorted (e.g., via FACS) based on a fluorescent or other reporter. In other exemplary embodiments in which survival depends on factors altered by the sgRNA-targeted Cas protein, cells can be incubated for a sufficient time such that target cells are enriched (e.g., due to death of other cells, proliferation of selected cell, or both). Optionally, additional rounds of infection can be allowed to occur to further the selection and opportunities for recombination in the virus carrying sgRNAs that are being selected for the particular screen used. The output can be compared to a control cell population, for example cells treated the same way but not put under a certain condition or stimulus.

[0055] In some embodiments, output of the screening assay can be tracked back to what particular combinations of heterologous sequences (in virions) that cause the selected output in the screening assay. For example, where cell survival is an output, the surviving cells can be collected and virions residing therein can be harvested and the particular sgRNAs (or other heterologous sequence(s)) therein determined (e.g., by nucleotide sequencing). Alternatively, expression of a fluorescent protein can be the cellular output and cells expressing the output can be enriched, e.g., using FACS, and the virions in the cells can be obtained. The identity of sgRNAs in these harvested virions and the combinations of heterologous sequences therein can be assayed to determine their identity. For example, in some embodiments, harvested virions are individually encapsulated in partitions (e.g., droplets, e.g. nanodroplets, in an oil emulsion), nucleic acids are from the virions in the droplets are barcoded (e.g., with a unique oligonucleotide sequence for the partition, thereby barcoding different segments of the same virion with the same barcode), and then nucleotide sequenced. Virion sequences having the same barcode are assumed to be from the same partition (and same virion), thereby identifying combinations of heterologous sequences combinations in virions that are enriched in the assay. This method thereby allows for identification of genes (targeted by the identified sgRNAs) playing a role in control of the cellular output of the assay.

EXAMPLE

[0056] We have designed, generated, and tested tripartite recombinant LCMV virions that carry a functional sgRNA targeting the cellular genomic locus AAVS1, for comparison with virions carrying non-targeting sgRNAs. For the design, a tripartite recombinant LCMV system is used, with each viable virion carrying at least 3 RNAs (Fig 2): one that is the viral L segment containing the Z and L proteins, one that is a partial S segment containing the viral GP gene and a gRNA cassette, and one that is a partial S segment containing the viral NP gene and a fluorescent marker. The gRNA cassette corresponds to an sgRNA sequence flanked by a 5' hammerhead ribozyme and 3' HDV ribozyme, inserted to replace the majority of the viral NP sequence. We showed that virions of this design containing gRNAs targeting the AAVS1 locus are infectious similar to wildtype virions (Fig 3). We further showed that when these virions infect cells which express Cas9, the sgRNA released by the viral genome is functional for the Cas9 to cleave at the targeted AAVS1 site (Fig 4). Moreover, coinfection is a frequent event, allowing for cells that contain viral segments from multiple initial virions, allowing for reassortment and generation of diverse libraries of virions containing combinations of sgRNAs (Fig 5).

[0057] The above examples are provided to illustrate the invention but not to limit its scope. Other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, databases, internet sources, patents, patent applications, and accession numbers cited herein are hereby incorporated by reference in their entireties for all purposes.

Claims

WHAT IS CLAIMED IS:

1. A population of engineered Arenavirus virions, the virions comprising: an RNA genome encoding each of NP, L, GP and Z proteins, wherein the RNA genome is made up of three or more different RNA molecules, wherein the RNA genome comprises a first RNA encoding a first sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z; a second RNA encoding at least one Arenavirus protein selected from one of NP, L, GP or Z; and a third RNA encoding at least one Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and wherein: i. in at least some virions, the second RNA further encodes a second sgRNA; or ii. at least some virions further comprise an RNA encoding a different sgRNA than the first sgRNA and the same Arenavirus protein as the first RNA; or iii. both i and ii.

2. The population of claim 1, wherein the third RNA encodes two Arenavirus proteins selected from one of NP, L, GP or Z.

3. The population of claim 2, wherein the first RNA encodes GP and the second RNA encodes NP and the third RNA encodes L and Z.

4. The population of claim 2, wherein the first RNA encodes NP and the second RNA encodes GP and the third RNA encodes L and Z.

5. The population of claim 1, wherein the third RNA further encodes a third sgRNA, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and different gRNAs.

6. The population of claim 2, wherein the virions comprise a fourth RNA encoding a fourth sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA and fourth RNA encode different Arenavirus proteins and different gRNAs.

7. The population of claim 1, wherein at least some different virions in the population have different first sgRNA sequences or different second sgRNA sequences or both.

8. The population of any one of claims 1-7, wherein RNAs comprising an sgRNA coding sequence and a coding sequence for an Arenavirus protein comprise a RNA self-cleaving sequence between the sgRNA coding sequence and the coding sequence for an Arenavirus protein .

9. The population of claim 8, wherein the RNA self-cleaving sequence is a ribozyme.

10. The population of any one of claims 1-4, wherein the first RNA encodes GP and the second RNA encodes NP and either: i the third RNA encodes L and Z; or

11. the third RNA encodes L and the virion comprises a fourth RNA that encodes Z.

11. The population of any one of claims 1-4, wherein at least one RNA encodes two sgRNA sequences.

12. The population of any one of claims 1-4, wherein the RNAs comprise 5’-3’: a 5’ untranslated region (UTR); a 5’ portion of a protein coding sequence, wherein the coding sequence encodes the Arenavirus protein selected from one of NP, L, GP or Z ; a first RNA self-cleaving sequence ; a coding sequence the sgRNA; a second RNA self-cleaving sequence; and a 3’ portion of said protein coding sequence.

13. The population of any one of claims 1-4, wherein the Arenavirus is a

Lymphocytic Choriomeningitis Virus (LCMV).

14. The population of any one of claims 1-13, wherein the first or second RNA self-cleaving sequence or both are ribozymes.

15. A method of generating a mixture of cells expressing different combinations of sgRNAs, the method comprising, infecting a plurality of cells with the population of virions of any one of claims 1-6, wherein at least some different virions in the population encode different sgRNAs, under conditions that allow for viral replication and expression of the sgRNAs in the cells.

16. The method of claim 16, wherein the population of virions comprise at least 100 different virions, each comprising an RNA encoding a different sgRNA.

17. The method of claim 16, further comprising identifying sgRNAs that affect cell function.

18. A method of making a library of virions comprising a diverse plurality of sgRNAs, the method comprising, introducing into a plurality of cells polynucleotides (e.g., as plasmids, or contained in virions) encoding: a first RNA encoding a first sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z; a second RNA encoding a second sgRNA and at least one Arenavirus protein selected from one of NP, L, GP or Z; and at least a third RNA encoding at least one Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and the polynucleotides in total encode RNAs encoding NP, L, GP or Z, wherein the polynucleotides include different sequence options for the first sgRNA and the second sgRNA; incubating the cells under conditions to allow for reassortment of RNAs in virions resulting from cells infected by multiple initial virions that carry different sgRNAs into at least some cells;

19 harvesting virions generated from the cells, wherein different virions comprise different combinations of first sgRNA and second sgRNA sequence options.

19. The method of claim 18, wherein the third RNA encodes two Arenavirus proteins selected from one of NP, L, GP or Z.

20. The method of claim 19, wherein the first RNA encodes GP and the second RNA encodes NP and the third RNA encodes L and Z.

21. The method of claim 19, wherein the first RNA encodes NP and the second RNA encodes GP and the third RNA encodes L and Z.

22. The method of claim 18, wherein the third RNA further encodes a third sgRNA, wherein the first RNA and second RNA and third RNA encode different Arenavirus proteins and different gRNAs.

23. The method of claim 19, wherein the virions comprise a fourth RNA encoding a fourth sgRNA and an Arenavirus protein selected from one of NP, L, GP or Z, wherein the first RNA and second RNA and third RNA and fourth RNA encode different Arenavirus proteins and different gRNAs.

24. A polynucleotide encoding an engineered Arenavirus RNA comprising 5’-3’: a 5’ untranslated region (UTR); a 5’ portion of a protein coding sequence, wherein the coding sequence encodes an Arenavirus protein selected from one of NP, L, GP or Z; a first RNA self-cleaving sequence; a coding sequence for a heterologous protein or heterologous RNA; a second RNA self-cleaving sequence; and a 3’ portion of said protein coding sequence.

25. The polynucleotide of claim 24, wherein the polynucleotide is an RNA.

26. The polynucleotide of claim 25, wherein said coding sequence encodes a single guide RNA (sgRNA).

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27. The polynucleotide of claim 24, wherein the polynucleotide is DNA.

28. An Arenavirus virion comprising the RNA of claim 25.

29. The Arenavirus of claim 28, wherein the Arenavirus is a Lymphocytic Choriomeningitis Virus (LCMV).

30. A method of expressing a heterologous protein or RNA in a cell, the method comprising expressing the polynucleotide of any one of claims 24-29 in a cell, wherein expression of the polynucleotide results in expression of the heterologous protein or heterologous RNA.

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