PROMOTER SEQUENCES

RELATED APPLICATIONS

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

62/801,524, filed on February 5, 2019, and U.S. Provisional Application No. 62/950,848, filed on December 19, 2019. The entire teachings of the above applications are incorporated herein by reference.

BACKGROUND

[0002] Viruses infect their hosts and introduce their genetic material into cells of the host as part of their replication cycle. This genetic material contains basic“instructions” for producing more copies of these viruses by hijacking the body’s normal production machinery to serve the needs of the virus. The host cell will carry out these instructions and produce additional copies of the virus, leading to more and more cells of the host becoming infected. As such, viruses can be used as vehicles to carry genes that may provide therapeutic benefits into a cell.

SUMMARY

[0003] In one aspect, the present invention provides a recombinant vector for expression of a target gene in a host cell, comprising: a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4; a cloning site for insertion of a nucleic acid encoding the target gene; and at least one non-promoter regulatory element required for the expression of the target gene in the host cell.

[0004] In another aspect, the present invention provides a recombinant vector for expression of a target gene in a host cell, comprising: a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8; a cloning site for insertion of a nucleic acid encoding the target gene; and at least one non-promoter regulatory element required for the expression of the target gene in the host cell.

[0005] In another aspect, the present invention provides a recombinant vector for expression of a target gene in a host cell, comprising: a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9; a cloning site for insertion of a nucleic acid encoding the target gene; and at least one non-promoter regulatory element required for the expression of the target gene in the host cell.

[0006] In some embodiments, the at least one non-promoter regulatory element comprises an enhancer element. In some embodiments, the at least one non-promoter regulatory element comprises an inducer element.

[0007] In some embodiments, the recombinant vector further comprises a selectable marker element.

[0008] In some embodiments, the vector is a viral vector. In certain embodiments, the viral vector is an adeno-associated virus (AAV) vector.

[0009] In some embodiments, the vector is a non-viral vector.

[0010] In some embodiments, the host cell is a mammalian cell. In some embodiments, the host cell is a neuronal cell. In some embodiments, the host cell is a non-neuronal cell (e.g., a liver cells, a kidney cell, a retinal cell).

[0011] In another aspect, the present invention provides a host cell comprising a recombinant vector as described herein.

[0012] In one aspect, the present invention provides recombinant polynucleotide molecules comprising a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4. In another aspect, the present invention provides recombinant

polynucleotide molecules comprising a nucleic acid encoding a target gene, wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4.

[0013] In another aspect, the present invention provides recombinant polynucleotide molecules comprising a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8. In another aspect, the present invention provides recombinant

polynucleotide molecules comprising a nucleic acid encoding a target gene, wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8. [0014] In another aspect, the present invention provides recombinant polynucleotide molecules comprising a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9. In another aspect, the present invention provides recombinant polynucleotide molecules comprising a nucleic acid encoding a target gene, wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9.

[0015] In another aspect, the present invention provides a recombinant polynucleotide molecule comprising a cloning site for insertion of a nucleic acid encoding a target gene, wherein the cloning site is operably linked to a promoter comprising a nucleic acid having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4.

[0016] In another aspect, the present invention provides a recombinant polynucleotide molecule comprising a cloning site for insertion of a nucleic acid encoding a target gene, wherein the cloning site is operably linked to a promoter comprising a nucleic acid having at least 70% sequence identity to a sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.

[0017] In another aspect, the present invention provides a recombinant polynucleotide molecule comprising a cloning site for insertion of a nucleic acid encoding a target gene, wherein the cloning site is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9.

[0018] In another aspect, the present invention provides methods of expressing a target gene in a host cell, comprising: contacting the host cell with a recombinant polynucleotide molecule such that the recombinant polynucleotide molecule is introduced into the host cell, wherein the recombinant polynucleotide molecule comprises a nucleic acid encoding the target gene and wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4, whereby expression of the target gene occurs in the host cell.

[0019] In another aspect, the present invention provides methods of expressing a target gene in a host cell, comprising: contacting the host cell with a recombinant polynucleotide molecule such that the recombinant polynucleotide molecule is introduced into the host cell, wherein the recombinant polynucleotide molecule comprises a nucleic acid encoding the target gene and wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8, whereby expression of the target gene occurs in the host cell.

[0020] In another aspect, the present invention provides methods of expressing a target gene in a host cell, comprising: contacting the host cell with a recombinant polynucleotide molecule such that the recombinant polynucleotide molecule is introduced into the host cell, wherein the recombinant polynucleotide molecule comprises a nucleic acid encoding the target gene and wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9, whereby expression of the target gene occurs in the host cell.

[0021] In some embodiments, the recombinant polynucleotide molecule is introduced into the host cell by transduction upon contacting the host cell with the recombinant polynucleotide. In another embodiment, the recombinant polynucleotide molecule is introduced into the host cell by transfection upon contacting the host cell with the

recombinant polynucleotide.

[0022] Features of the LAP sequences disclosed herein include: i) Smaller size when compared to similar promoters, such as EFla, CAG, TH, CaMKIIa, among others. This is an advantage in the context of AAV vectors that have a limited genetic payload ii) Long-term expression that is less prone to repression of transcription. The LAP sequences disclosed herein achieve long-term, chronic transcription of transgenes. This is particularly useful for gene therapy where the therapeutic transgene may need to be expressed for the lifespan of the patient/host.

BRIEF DESCRIPTION OF THE DRAWINGS

[0023] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

[0024] The foregoing will be apparent from the following more particular description of example embodiments, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating embodiments.

[0025] FIGs. 1A-1D depict the characterization of PRV latency-associated transcript promoters (LAPs). FIG. 1A depicts the complete nucleotide sequence of PRV LAP of 902 base pair (bp), and the sub-regions LAP1 of 498 bp (bold and underlined), LAP2 of 404 bp (underlined), and LAP1 2 of 880 bp. LAP1 2 includes most of the LAP1 and LAP2 sequences, but lacks the first 22 nucleotides of LAP 1. The black boxes depict consensus sequences for transcription factors (TFs) including, the GC box: specificity protein 1 and 3 (Spl and Sp3); the CCAAT box: nuclear factor Y (NF-Y); and the TATA box: TATA- binding protein (TBP). Colored boxes indicate the coordinates for the binding motif sites of the TFs: 1, green: SRY-Box 10 (SOX10); 2, red: cAMP response element-binding protein (CREB); 3, blue: CCCTC-binding factor (CTCF); 4, brown: oligodendrocyte transcription factor 2 (01ig2); 5, pink: signal transducer and activator of transcription (STAT1). FIG. IB depicts the plasmid maps of the four AAVs designed to transcribe mCherry fluorescent reporter from LAPl, LAP2, LAP 1 2 and the EFla promoter. WPRE of 609 bp is a woodchuck hepatitis virus posttranscriptional enhancer element. All AAVs contain a 479 bp human growth hormone (hGH poly A) poly adenylation sequence, and flanking AAV2 inverted terminal repeats (ITRs) of 141 bp each. The vectors were packaged into the AAV- PhP.eB serotype capsid. The total size of the enhancer-promoter elements and promoter sequence are: AAV-LAPl : 1.87 Kb; AAV-LAP2: 1.77 Kb; AAV-LAP1_2: 2.25 Kb; and AAV-EFla: 2.63 Kb. FIG. 1C depicts the four AAVs used to transduce primary cultures of rat SCG neurons to quantify mCherry expression over a 90-day time-lapse. The relative fluorescence intensity of mCherry expression was measured at 3, 5, 7, 9, 11, 14, 17, 21, 24, 28, 31, 34, 38, 41, 45, 49, 52, 59, 67, 73, 82, and 90 days post infection (dpi) with 3 x 10 ¹¹ AAV genomes. Scale bar = 100 pm. Data are represented as mean ± SEM; n = 3 SCG culture dishes per group. FIG. ID shows that AAV-driven mCherry expression in SCG cell bodies at 28 days post AAV transduction with LAPl-mCherry, LAP2-mCherry, LAP 1_2 -mCherry, or EFla-mCherry.

[0026] FIGs. 2A-2P show stable and long-term LAP-mediated transgene expression. FIG. 2A is a schematic diagram of the systemic route of AAV administration and CNS tissue processing. Intravenous administrations of AAV vectors were performed by unilateral injections into mouse retro-orbital sinuses (4 x 10 ¹¹ vg/mouse). Brains and spinal cords were collected at 30 dpi and 190 dpi. The right hemispheres of the brains were processed for iDISCO+ tissue clearing and light-sheet microscopy analysis. The left hemispheres of the brains were sagittally sectioned at 50 pm for immunofluorescence and confocal microscopy analysis. Spinal cords were transversally sliced at 20 pm for immunofluorescence and confocal microscopy analysis. FIGs. 2B-2P quantify the densities of mCherry positive cells per mm ³ across different brain regions in iDISCO+-cleared tissue samples at 30 dpi and 190 dpi. Data are represented as mean ± SEM; n = 2 animals per group, and between five and ten 500 um sections per animal. Data were normalized to those of a vehicle-injected control animal. Significance was determined with Student’s t-test (if only two groups were compared), or analysis of variance one-way (ANOVA) followed by Bonferroni post hoc test (if more than two groups were compared). A p value of < 0.05 was statistically significant (*p < 0.033; **p < 0.002; ***p < 0.001).

[0027] FIGs. 3A-3J4 show that all three AAV-LAP sequences drive widespread and long-term transgene expression throughput the brain after retro-orbital injection.

Representative immunofluorescence images of sagittal sections show whole-brain

distributions of anti-mCherry staining (green) for AAV-LAP1 (FIG. 3A), AAV-LAP2 (FIG. 3B), AAV-LAP 1 2 (FIG. 3C), and AAV-EFla (FIG. 3D) at 190 dpi. Cx, cortex; Hip, hippocampus; MRN, midbrain reticular nucleus; Cb, cerebellum; Thai, thalamus; Pn, pons; Hypo, hypothalamus; Str, striatum; OB, olfactory bulb. Scale bar = 1mm. Representative confocal images show anti-mCherry signals (green) in the cortex (FIG. 3E), the dentate gyrus (FIG. 3F), the striatum (FIG. 3G) and the cerebellum (FIG. 3H) at 30 dpi and 190 dpi. All images are stack confocal sections. Scale bar = 100 pm. FIGs. 311-314 quantify the indirect fluorescence intensities of the anti-mCherry signals driven by the AAV-LAP sequences and AAV-EFla at 30 dpi and 190 dpi in the cortex, the dentate gyrus, the striatum and the cerebellum. FIGs. 3J1-3J4 quantify the number of cells expressing mCherry signal per pixels ² by immunohistochemistry (IHC) at 190 dpi in the cortex, the dentate gyrus, the striatum and the cerebellum. Data are represented as mean ± SEM; n = 2 animals and six tissue sections per animal. Data were normalized to those of a vehicle-injected control animal. Significance was determined with Student’s t-test (if only two groups were compared), or analysis of variance one-way (ANOVA) followed by Bonferroni post hoc test (if more than two groups were compared). A p value of < 0.05 was statistically significant (*p < 0.033; **p < 0.002; ***p < 0.001).

[0028] FIGs. 4A-4E4 show that LAP2 drives stable and long-term transgene expression in the brain. Representative confocal images show native mCherry fluorescence (red) for AAV-LAP 1, AAV-LAP2, AAV-LAP1_2, and AAV-EFla in the cortex (FIG. 4A), the dentate gyrus (FIG. 4B), the striatum (FIG. 4C) and the cerebellum (FIG. 4D) at 30 dpi and 190 dpi. All images are stack confocal sections. Scale bar = 100 pm. FIGs. 4E1-4E4 quantify the direct fluorescence intensities of native mCherry signal driven by AAV-LAP sequences and AAV-EFla at 30 dpi and 190 dpi is shown in the cortex, the dentate gyrus, the striatum and the cerebellum. Data are represented as mean ± SEM; n = 2 animals and six tissue sections per animal. Data were normalized to those of a vehicle-injected control animal. Significance was determined with Student’s t-test (if only two groups were compared) or analysis of variance one-way (ANOVA) followed by Bonferroni post hoc test (if more than two groups were compared). A p value of < 0.05 was statistically significant (*p < 0.033; **p

< 0.002; ***p < 0.001).

[0029] FIGs. 5A-5E show that AAV-LAP2 drives long-term transgene transcription in the CNS. The presence of mCherry mRNA was verified by FISH in brain tissues at 190 dpi using a riboprobe specific to mCherry (green). Nuclei were counterstained with DAPI (blue). FIGs. 5A-5E show 20-pm sagittal brain slices for AAV-LAP2 or AAV-EFla in the cortex, the dentate gyrus, the striatum, the cerebellum and the olfactory bulb, respectively. Panels 2 and 4 depict higher magnification images of the indicated regions (square) in Panels 1 and 3, respectively. Images are stack confocal sections. Scale bars = 100 pm.

[0030] FIGs. 6A-6F show that AAV-LAP transgene expression is predominantly in neurons and not oligodendrocytes. Representative confocal images of AAV-mediated mCherry expression (red) in neurons (FIGs. 6A and 6B: green label for the pan-neuronal marker NeuN) or oligodendrocytes (FIGs. 6C and 6D: green label for the oligodendrocyte marker 01ig2) in the cortex or the dentate gyrus at 30 dpi. Cells were counterstained with DAPI (blue). NeuN signal can localize with the neuronal cell nucleus as well as the cytoplasm, while the staining for 01ig2 signal is mostly nuclear. Arrows depict co-labelling between the cell marker and mCherry. Scale bar = 100 pm. FIGs. 6E and 6F quantify the percentage of mCherry labelled cells corresponding to neurons (NeuN-positive) or oligodendrocytes (01ig2-positive) in the cortex (Cx) or the dentate gyrus (DG) for each promoter. Images are stack confocal sections. Data are represented as mean ± SEM; n = 2 animals and six tissue sections per animal.

[0031] FIGs. 7A-7D show that AAV-LAP transgene expression is not detected in microglia and astrocytes. Representative confocal immunofluorescence images of anti- mCherry signal (red), microglia (FIGs. 7A and 7B: green, labeled as Ibal -positive), astrocytes (FIGs. 7C and 7D: green, labeled as SI 00-positive) in the cortex and dentate gyrus at 30 dpi. The absences of co-labelling between mCherry in astrocytes and microglia are indicated with stars (*). Cells were counterstained with DAPI (blue). Images are stack confocal sections. Scale bar = 100 pm. [0032] FIGs. 8A-8F show that LAP sequences drive widespread and long-term transgene expression in the spinal cord. Spinal cords (lumbar region) were sectioned in a transversal fashion at 20 pm. Representative confocal images at 190 dpi of native AAV-mediated mCherry expression (red, panels 1 and 4), pan-neuronal marker NeuroTrace (green, panels 2 and 5), and merge signal (yellow, panels 3 and 6) for AAV-LAPl, AAV-LAP2, AAV- LAP1 2 and AAV-EFla. Images are stack confocal sections. DH: dorsal horn; VH ventral horn. Higher magnification images are shown in Panels 4-6. Scale bar = 100 pm.

[0033] FIGs. 9A-9C show that LAP sequences drive efficient transgene expression in porcine kidney cells. Representative images of PK15 cells at 48 hours post transfection of a reporter plasmid comprising mCherry driven by LAP1 (FIG. 9A), LAP2 (FIG. 9B) or LAP1 2 (FIGs. 9C). Panel 1 : bright field; Panel 2: fluorescence; Panel 3: merge. Scale bar = 50 pm.

[0034] FIGs. 10A and 10B show that LAP2 drives efficient transgene expression in human kidney cells. Representative images of HEK-293 cells at 48 hours post transfection of a reporter plasmid comprising mCherry driven by LAP2 (FIGs. 10A) or the EF la-promoter (FIGs. 10B). Panel 1 : bright field; Panel 2: fluorescence; Panel 3: merge. Scale bar = 50 pm.

[0035] FIGs. 11A and 11B show that LAP2 drives efficient transgene expression in human liver cells. Representative images of HepG2 cells at 48 hours post transfection of a reporter plasmid comprising mCherry driven by LAP2 (FIGs. 11 A) or the EF la-promoter (FIGs. 11B). Panel 1 : bright field; Panel 2: fluorescence; Panel 3: merge. Scale bar = 50 pm.

[0036] FIGs. 12A1-12B4 show that LAP2 drives long-term transgene expression throughout the liver. Intravenous administrations of AAV-LAP2 (FIGs. 12A1-12A4) or AAV-EFla- vector (FIGs. 12B1-12B4) were performed by unilateral injection into the mouse retro-orbital sinuses (4 x 10 ¹¹ vg/mouse). The liver was collected at 190 dpi and

longitudinally sectioned at 20 pm for IHC and confocal microscopy analysis. Representative confocal images of native mCherry fluorescence (FIGs. 12A1 and 12B1: red), anti-mCherry immunostaining (FIGs. 12A2 and 12B2: green), DAPI nuclear counterstain (FIGs. 12A3 and 12B3: blue), and merged immuno-fluorescence and DAPI images (FIGs. 12A4 and 12B4). CV: central vein. Scale bar = 75 pm.

[0037] FIGs. 13A1-13B4 show that LAP2 drives long-term transgene expression in the mouse kidney. Intravenous administrations of AAV-LAP2 (FIGs. 13A1-13A4) or AAV- EF la-vector (FIGs. 13B1-13B4) were performed by unilateral injection into the mouse retro- orbital sinuses (4 x 10 ¹¹ vg/mouse). The kidneys were collected at 190 dpi and longitudinally sectioned at 20 mih for IHC and confocal-microscopy analysis. Representative confocal images show native mCherry fluorescence (FIGs. 13A1 and 13B1: red), anti-mCherry immunostaining (FIGs. 13A2 and 13B2: green), DAPI nuclear counterstain (FIGs. 13A3 and 13B3: blue), and merged immune-fluorescence and DAPI images (FIGs. 13A4 and 13B4). AV: arcuate vessel. Scale bar = 75 pm.

[0038] FIGs. 14A1-14B4 show that LAP2 drives long-term transgene expression in the mouse retina. Intravenous administrations of AAV-LAP2 (FIGs. 14A1-14A4) or AAV- EF la-vector (FIGs. 14B1-14B4) were performed by unilateral injection into the mouse retro- orbital sinuses (4 x 10 ¹¹ vg/mouse). The retinae were collected at 190 dpi and transversely cryosectioned at 20 pm for IHC and confocal-microscopy analysis. Representative confocal images show native mCherry fluorescence (FIGs. 14A1 and 14B1: red), anti-mCherry immunostaining (FIGs. 14A2 and 14B2: green), DAPI nuclear counterstain (FIGs. 14A3 and 14B3: blue), and merged immunofluorescence and DAPI images (FIGs. 14A4 and 14B4). GCL: ganglion-cell layer; INL: inner nuclear layer; ONL: outer nuclear layer. Scale bar = 75 pm.

DETAILED DESCRIPTION

[0039] A description of example embodiments follows.

[0040] Several aspects of the invention are described below, with reference to examples for illustrative purposes only. It should be understood that numerous specific details, relationships, and methods are set forth to provide a full understanding of the invention. One having ordinary skill in the relevant art, however, will readily recognize that the invention can be practiced without one or more of the specific details or practiced with other methods, protocols, reagents, cell lines and animals. The present invention is not limited by the illustrated ordering of acts or events, as some acts may occur in different orders and/or concurrently with other acts or events. Furthermore, not all illustrated acts, steps or events are required to implement a methodology in accordance with the present invention. Many of the techniques and procedures described, or referenced herein, are well understood and commonly employed using conventional methodology by those skilled in the art.

[0041] Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. It will be further understood that terms, such as those defined in commonly-used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and/or as otherwise defined herein.

[0042] The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. As used herein, the indefinite articles “a,”“an” and“the” should be understood to include plural reference unless the context clearly indicates otherwise.

[0043] As used herein, a“cloning site” refers to a short segment of nucleotides in the vector that contain one or more unique restriction sites that allow for insertion of a nucleotide “target gene” or“gene of interest” into the vector.

[0044] As used herein, a“promoter” refers to a region of DNA to which an RNA polymerase binds and initiates transcription (e.g., of a gene).

[0045] As used herein, a“non-promoter regulatory element” refers to non-promoter sequence(s) of a nucleic acid molecule that are capable of increasing or decreasing the expression of specific genes within the recombinant vector. Such non-promoter regulatory elements include, but are not limited to, e.g., enhancer elements, inducer elements, silencer elements, 5’ untranslated regions (UTRs), 3’UTRs, terminator elements, CAAT boxes, CCAAT boxes, Pribnow boxes, SECIS elements, polyadenylation signals, A-boxes, Z-boxes, C-boxes, E-boxes, G-boxes, and Cis-regulatory elements (CREs).

[0046] As used herein, the phrase“operably linked” means that the nucleic acid is positioned in the recombinant polynucleotide, e.g., vector, in such a way that enables expression of the nucleic acid under control of the element (e.g., promoter) to which it is linked.

[0047] As used herein, a“selectable marker element” is an element that confers a trait suitable for artificial selection. Examples of selectable marker elements useful in the present invention include, but are not limited to, beta-lactamase, neomycin resistance genes, mutant Fabl genes conferring triclosan resistance, URA3 elements, fluorescent gene products, affinity tags such as GST, His, CBP, MBP, and epitope tags such as Myc HA, FLAG.

Selectable marker elements can be negative or positive selection markers.

[0048] The present invention provides, in various embodiments, vectors, such as viral vectors (e.g., adeno-associated viral vectors (AAV)), containing promoter sequences that are small in size yet able to provide long-lasting transcription of a gene of interest. The promoter sequences have a size that is less than that of many commonly used promoters, and can drive transcription of a transgene in most tissue and cell types (e.g., in mammals). The promoter sequences disclosed herein are less prone to repression or inactivation, making them particularly useful for gene therapies requiring chronic expression of a therapeutic transgene.

[0049] In one aspect, the present invention provides gene delivery vectors expressing a gene of interest. In some embodiments, the gene delivery vector comprises a promoter derived from a genomic region of an alphaherpesvirus genome, e.g., from the pseudorabies virus. In some embodiments, the promoter comprises a latency-associated promoter (LAP) region from an alphaherpesvirus genome.

[0050] In particular embodiments, the LAP region utilized in the vectors of the present invention is selected from SEQ ID NO: 1 (also referred to herein as LAP1), SEQ ID NO: 2 (also referred to herein as LAP2), SEQ ID NO: 3 (also referred to herein as LAP1 2), and SEQ ID NO: 4 (Table 1). LAP1 2 (880 bp) includes a 476-bp sequence of LAP1 (498 bp) and the complete LAP2 sequence (404 bp), i.e., LAP1 and LAP2 in tandem but missing the first 22 bp of the LAP1 sequence. SEQ ID NO: 4 (902 bp) comprises the complete sequences of SEQ ID NO: 1 and SEQ ID NO: 2, and is 22 bp longer than SEQ ID NO: 3.

[0051] In some embodiments, the promoter comprises a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4. In some

embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4.

[0052] Without wishing to be bound by theory, it is believed that certain active portions or fragments of a LAP region from an alphaherpesvirus genome can drive expression of a transgene in a variety of cell and tissue types. In some embodiments, the promoter used in the present invention comprises a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9 (Table 1). SEQ ID NO: 9 consists of a 232-bp“core” sequence of LAP2 and includes a TATA box sequence. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to SEQ ID NO: 9. In some embodiments, the promoter comprises SEQ ID NO: 9. [0053] Without wishing to be bound by theory, LAP sequences further comprising SEQ ID NO: 10, SEQ ID NO: 11, and/or SEQ ID NO: 12 (Table 1) may have improved transcriptional performance. Accordingly, in some embodiments, the promoter further comprises SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, or a combination thereof, e.g., at the 5’ or the 3’ of SEQ ID NO: 9. SEQ ID NO: 10 (the“CTCF” motif) has been shown to be involved in the epigenetic regulation of herpes virus gene expression, chromatin remodeling and recruitment of transcription factors and proteins (Lang et al., 2017, Lee et al., 2018). SEQ ID NO: 11 (the“alternative CTCF with upstream stabilizer” motif) has been shown to stabilize an alternative CTCF motif and facilitate binding of four more zinc finger domains (Zimmerman et al., 2018). SEQ ID NO: 12 (the“Nuclear transcription factor Y (NF- Y)” motif) is recognized by a transcription factor that binds to the CAAT box located in the promoter regions of several eukaryotes (Chikhirzhina et al., 2008; Fleming et al., 2013).

Table 1. Latency-Associated Promoter (LAP) Nucleic Acid Sequences

The 232-bp“core” sequence (SEQ ID NO: 9) is underlined.

The TATA box DNA sequence (ATATA) is underlined and in bold text.

The“CTCF” motif (SEQ ID NO: 10), the“alternative CTCF with upstream stabilizer” motif (SEQ ID NO: 11), and the“NF-Y” motif are italicized.

[0054] In some embodiments, the promoter comprises a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity a nucleic acid sequences selected from SEQ ID NOs: 13-58 (Table 1). In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NOs: 13-58.

[0055] The vectors comprising the LAP sequences disclosed herein can be used for gene delivery (e.g., in mammals, such as a human) and basic and translational research. The host cell may be a cultured cell (i.e., in vitro ) or reside in a subject (e.g., in an animal model (i.e., in vivo)).

[0056] In some embodiments, the vector is a lentivirus gene delivery vector, a retrovirus gene delivery vector, or an adenovirus gene delivery vector. One advantage of the LAP sequences described herein is that they have a considerably smaller size than other commonly used promoters in viral vectors, yet can sustain prolonged transcription in different cell types.

[0057] A relatively small LAP region may be advantageous, given that the DNA payload capacity is highly limited in vectors. For example, the packaging capacity or payload of the AAV vectors is limited to a maximum size of an approximate 5,000 bp. In some embodiments, the LAP region utilized in the vectors of the present invention is between about 200 bp and about 410 bp in length, e.g., about 220-410 bp, about 220-400 bp, about 240-400 bp, about 240-380 bp, about 260-380 bp, about 260-360 bp, about 280-360 bp, about 280-340 bp, about 300-340 bp, or about 320-340 bp in length.

[0058] In particular embodiments, the promoter sequences of the present invention can be used when strong, long-term expression of transgenes is required in cells in culture, in animals or in humans. The promoters are useful in situations where there are genome space constraints but long-lasting promoter transcriptional activity is needed. AAVs are particularly useful for human gene therapy; as such, the LAP sequences of the present invention provide gene therapy applications when utilized with AAVs.

[0059] In some embodiments, a gene of interest is expressed under control of the LAP sequences provided herein for at least about 30 days, about 60 days, about 90 days, about 120 days, about 150, about 180 days, or about 190 days in vitro. In some embodiments, a gene of interest is expressed under control of the LAP sequences provided herein for at least about 30 days, about 60 days, about 90 days, about 120 days, about 150, about 180 days, or about 190 days in vivo (e.g., in a tissue such as a brain). In some embodiments, a gene of interest is expressed under control of the LAP sequences provided herein for at least about 30 days, about 60 days, about 90 days, about 120 days, about 150, about 180 days, or about 190 days ex vivo (e.g., in cultured cells such as neurons).

[0060] In one aspect, the present invention provides a recombinant vector for expression of a target gene in a host cell, comprising a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4; a cloning site for insertion of a nucleic acid encoding the target gene; and at least one non-promoter regulatory element required for the expression of the target gene in the host cell.

[0061] In some embodiments, the promoter comprises a nucleic acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4.

[0062] The LAP sequences described herein can be used in a variety of gene expression vectors, such as a plasmid, a bacterial artificial chromosome (BAC), a cosmid or other non-viral or viral systems to express transgene(s).

[0063] In some embodiments, the vector is a viral vector. In some embodiments, the viral vector is an adeno-associated virus (AAV) vector. Non-limiting examples of viral vectors that can be utilized by the present invention include DNA or RNA viral vectors including but not limited to retroviral vectors, herpes virus vectors, adenovirus vectors, lentivirus vectors, rabies virus vectors, lentiviral vectors, VSV vectors, vaccinia virus vectors, reovirus vectors, semliki forest virus, yellow fever virus, and sindbis virus vectors.

[0064] In some embodiments, the vector is a non-viral vector. Non-viral vectors can be plasmid DNA, liposome-DNA complexes (lipoplexes), and polymer-DNA complexes

(polyplexes). Non-viral vectors can be plasmid RNA, liposome-RNA complexes (lipoplexes), and polymer-RNA complexes (polyplexes). Oligonucleotides and their analogues, either alone or in complexes, are also possible non-viral vector-mediated gene transfer constructs.

[0065] The vectors (e.g., viral vectors) provided herein can be used to express therapeutic transgenes in organs or tissues of animal models and humans, for example, in gene therapies to treat acquired or inherited diseases (e.g., of the nervous system).

[0066] The LAP sequences disclosed herein were derived from the genome of pseudorabies virus (PRV). PRV is an alphaherpesvirus capable of infecting various animals. Although the natural host is the adult pig, PRV can infect a broad range of vertebrates including cattle, sheep, dog, bird, cat, goat, raccoon, chicken, skunk, possum, guinea pig, horse, rabbit, rat, mouse and nonhuman primates (Pomeranz et ah, 2005). Cultured human cells are also susceptible to PRV infection and zoonotic PRV infections in humans was reported (Wong et al., 2019).

[0067] Besides PRV being able to infect several different animal species, it is also a pantropic virus. This means that most tissues and organs of an infected host can be susceptible and permissive to PRV infection (Blanchard et al., 2006; Boldogkoi et al., 2000; Fan et al., 2019; Gasparini et al., 2019; Pomeranz et al., 2005). Therefore, the LAP sequences can be potentially used for gene therapies in diverse cell and tissue types.

[0068] In another aspect, the present invention provides a host cell comprising a recombinant vector as described herein. In some embodiments, the host cell is a mammalian cell (e.g., a neuronal cell). In other embodiments, the host cell is selected from a bird cell, a fish cell, an amphibian cell, and a reptile cell. In some embodiments, the host cell comprises an in vitro neuronal cell, an ex vivo neuronal cell, or both. In some embodiments, the host cell a neuronal cell of a subject. In some embodiments, the neuronal cell resides in a primary motor area, a secondary motor area, a primary somatosensory area, a supplemental somatosensory area, a visual area, a hippocampal formation, striatum, pallidum, thalamus, hypothalamus, a midbrain area, hind brain, an olfactory area or a combination thereof, of the subject. In some

embodiments, the midbrain area comprises a motor-related area, a sensory-related area, or both. In some embodiments, the neuronal cell resides in cortex, dentate gyrus, striatum, cerebellum, olfactory bulb or a combination thereof, of the subject. In some embodiments, the neuronal cell comprises a neuron, a microglia cell, an astrocyte, or a combination thereof. In some

embodiments, the neuronal cell comprises a neuron. [0069] In some embodiments, the host cell is selected from the group consisting of a bladder cell, a blood cell, a bone cell, an endothelial cell, an epithelial cell, a fat cell, a heart cell, an intestinal cell, a stomach cell, a kidney cell, a liver cell, a lung cell, a muscle cell, a pancreatic cell, a retina cell, a sex cell, a skin cell, a spleen cell, a stem cell, and a combination thereof. In some embodiments, the host cell is a cancer cell.

[0070] In another aspect, the present invention provides recombinant polynucleotide molecules comprising a nucleic acid encoding a target gene, wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4. In some embodiments, the nucleic acid encoding the target gene comprises more than about 4 kb.

[0071] In a further aspect, the present invention provides a recombinant polynucleotide molecule comprising a cloning site for insertion of a nucleic acid encoding a target gene, wherein the cloning site is operably linked to a promoter comprising a nucleic acid having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4.

[0072] In another aspect, the present invention provides a recombinant vector for expression of a target gene in a host cell, comprising a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8; a cloning site for insertion of a nucleic acid encoding the target gene; and at least one non-promoter regulatory element required for the expression of the target gene in the host cell. SEQ ID NO: 5 comprises a LAP sequence of an equine herpes virus; SEQ ID NO: 6 comprises a LAP sequence of a bovine herpes virus; SEQ ID NO: 7 comprises a LAP sequence of a varicella zoster virus; and SEQ ID NO: 8 comprises a LAP sequence of a Macacine herpesvirus 1 (Table 1). In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO:

5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8.

[0073] In another aspect, the present invention provides recombinant polynucleotide molecules comprising a nucleic acid encoding a target gene, wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8. In some embodiments, the nucleic acid encoding the target gene comprises more than about 4 kb.

[0074] In a further aspect, the present invention provides a recombinant polynucleotide molecule comprising a cloning site for insertion of a nucleic acid encoding a target gene, wherein the cloning site is operably linked to a promoter comprising a nucleic acid having at least 70% sequence identity to a sequence selected from SEQ ID NO:5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8. [0075] In another aspect, the present invention provides a recombinant vector for expression of a target gene in a host cell, comprising a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9; a cloning site for insertion of a nucleic acid encoding the target gene; and at least one non-promoter regulatory element required for the expression of the target gene in the host cell. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to SEQ ID NO: 9. In some embodiments, the promoter comprises SEQ ID NO: 9. In some embodiments, the promoter further comprises the nucleic acid sequence of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:

12, or a combination thereof. In some embodiments, the promoter comprises a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 13-58. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NOs: 13-58.

[0076] In some embodiments, the at least one non-promoter regulatory element comprises an enhancer element. In some embodiments, the at least one non-promoter regulatory element comprises an inducer element. In some embodiments, the recombinant vector further comprises a selectable marker element.

[0077] In another aspect, the present invention provides recombinant polynucleotide molecules comprising a nucleic acid encoding a target gene, wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to SEQ ID NO: 9. In some embodiments, the promoter comprises SEQ ID NO: 9. In some embodiments, the promoter further comprises the nucleic acid sequence of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, or a combination thereof. In some embodiments, the promoter comprises a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 13-58. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NOs: 13-58. In some embodiments, the nucleic acid encoding the target gene comprises more than about 4 kb.

[0078] In a further aspect, the present invention provides a recombinant polynucleotide molecule comprising a cloning site for insertion of a nucleic acid encoding a target gene, wherein the cloning site is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to SEQ ID NO: 9. In some embodiments, the promoter comprises SEQ ID NO: 9. In some embodiments, the promoter further comprises the nucleic acid sequence of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:

12, or a combination thereof. In some embodiments, the promoter comprises a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 13-58. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NOs: 13-58.

[0079] In another aspect, the present invention provides methods of expressing a target gene in a host cell, comprising: contacting the host cell with a recombinant polynucleotide molecule such that the recombinant polynucleotide molecule is introduced into the host cell, wherein the recombinant polynucleotide molecule comprises a nucleic acid encoding the target gene and wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 1, SEQ ID NO:

2, SEQ ID NO: 3 and SEQ ID NO: 4, whereby expression of the target gene occurs in the host cell. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4.

[0080] In another aspect, the present invention provides methods of expressing a target gene in a host cell, comprising: contacting the host cell with a recombinant polynucleotide molecule such that the recombinant polynucleotide molecule is introduced into the host cell, wherein the recombinant polynucleotide molecule comprises a nucleic acid encoding the target gene and wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to a sequence selected from SEQ ID NO: 5, SEQ ID NO:

6, SEQ ID NO: 7 and SEQ ID NO: 8, whereby expression of the target gene occurs in the host cell. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8.

[0081] In another aspect, the present invention provides methods of expressing a target gene in a host cell, comprising: contacting the host cell with a recombinant polynucleotide molecule such that the recombinant polynucleotide molecule is introduced into the host cell, wherein the recombinant polynucleotide molecule comprises a nucleic acid encoding the target gene and wherein the nucleic acid is operably linked to a promoter comprising a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 9, whereby expression of the target gene occurs in the host cell. In some embodiments, the promoter comprises a nucleic acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to SEQ ID NO: 9. In some embodiments, the promoter comprises SEQ ID NO: 9. In some embodiments, the promoter further comprises the nucleic acid sequence of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, or a combination thereof. In some embodiments, the promoter comprises a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 13-58. In some embodiments, the promoter comprises a nucleic acid sequence selected from SEQ ID NOs: 13-58.

[0082] In some embodiments, the neuronal cell resides in the spinal cord of the subject. In some embodiments, the neuronal cell resides in the dorsal horn of the spinal cord. In some embodiments, the neuronal cell resides in the lumbar spinal cord, thoracic spinal cord, cervical spinal cord or a combination thereof.

[0083] In some embodiments, the recombinant polynucleotide molecule is introduced into the host cell by transduction (e.g., infection by a viral vector) upon contacting the host cell with the recombinant polynucleotide. In another embodiment, the recombinant polynucleotide molecule is introduced into the host cell by transfection upon contacting the host cell with the recombinant polynucleotide. In another embodiment, the recombinant polynucleotide molecule is introduced into the host cell by electroporation upon contacting the host cell with the recombinant polynucleotide.

[0084] Recombinant adeno-associated viral vectors (AAV) are essential neuroscience tools to define connectivity and function of the central nervous system (CNS). Additionally, AAVs are used as gene therapy vectors to treat inherited and acquired CNS diseases. Despite their safety and broad tropism, important issues need to be corrected such as the limited payload capacity and the lack of small gene promoters providing long-term, pan-neuronal transgene expression in the CNS. Commonly used gene promoters are relatively large and can be repressed a few months after viral CNS transduction, risking the long-term performance of single-dose gene therapy applications.

[0085] Recent improvements to recombinant AAVs, including capsid engineering and novel gene promoters to optimize transgene expression have substantially improved gene therapy applications (Mak, Rajapaksha et al. 2017; Hudry and Vandenberghe 2019; Ogden, Kelsic et al. 2019). AAV vectors are widely used in neuroscience and clinical applications given their safety, serotype-dependent broad tropism and transduction efficiency (Aschauer, Kreuz et al. 2013; Samulski and Muzyczka 2014; Mak, Rajapaksha et al. 2017). AAV-9 variant PHP.eB (Chan, Jang et al. 2017), with an enhanced ability to permeate the mouse blood-brain barrier (BBB) and broadly transduce neurons both in the brain and spinal cord after peripheral vascular

administration, is one example of recent capsid improvements (Dayton, Grames et al. 2018). A major limitation of recombinant AAVs is their small capsid with limited payload capacity of only ~ 4.9 kb (Russell and Hirata 1998). Accordingly, the discovery of short promoter sequences that sustain strong and long-lived transcription is paramount to expand the transgene payload and achieve chronic therapeutic effect with one viral dose. [0086] Several strong promoters such as neuron-specific enolase (NSE, 1800 bp) (Peel, Zolotukhin et al. 1997; Delzor, Dufour et al. 2012), calcium/calmodulin-dependent protein kinase II alpha (CaMKIIa, 1300 bp) (Sohal, Zhang et al. 2009) and human elongation factor 1 alpha (EFla, 1264 bp) (Sohal, Zhang et al. 2009; Qin, Zhang et al. 2010) have been used in systemic AAV delivery (Bedbrook, Deverman et al. 2018). However, the considerable size of these promoter sequences (Bedbrook, Deverman et al. 2018) limit the use of large therapeutic transgenes or multiple small transgenes. Moreover, short promoters such as the human cytomegalovirus immediate-early enhancer and promoter (CMV, 600 bp) (Gray, Foti et al. 2011) or truncated versions of the human synapsin promoter (hSyn, 468 bp) (Jackson, Dayton et al. 2016), have considerably weaker to drive gene transcription and expression, and in some cases, are completely repressed or inactivated only weeks after delivery (Brooks, Harkins et al. 2004; Nathanson, Jappelli et al. 2009; Qin, Zhang et al. 2010; Back, Dossat et al. 2019). Similarly, small ubiquitous promoters like beta glucuronidase (GUSB, 378 bp) (Husain, Passini et al. 2009) or ubiquitin C (UBC, 403 bp) (Qin, Zhang et al. 2010; Powell, Rivera-Soto et al. 2015) have shown weak transcription levels.

[0087] Three alphaherpesvirus latency-associated promoters (LAP), called LAP1 (498 bp), LAP2 (404 bp) and LAP1 2 (880 bp) obtained from the genome of the herpesvirus pseudorabies virus (PRV) are described and validated herein. The Alphaherpesvirinae subfamily of the family Herpesviridae , includes bovine herpes virus-1 (BHV-1), varicella-zoster virus (VZV), herpes simplex virus (HSV) and PRV. These viruses share genome organization and establish latent infections in sensory ganglia of different mammalian hosts (Koyuncu, Hogue et al. 2013).

[0088] The LAP region of PRV encompasses two independent promoters, LAPl and LAP2 (Cheung 1989; Cheung and Smith 1999; Jin and Scherba 1999; Jin, Schnitzlein et al. 2000)

(FIG. 1A). PRV LAPl contain two GC boxes and three CAAT boxes upstream of the first TATA box. PRV LAP2 containing two GC boxes before the second TATA box (Cheung 1989; Jin and Scherba 1999; Taharaguchi, Kobayashi et al. 2002). It has been proposed that the binding of different transcription factor (TFs) to consensus promoter elements present in LAP, may facilitate escape from nucleosome silencing during the latent infection during the latent infection (Deshmane and Fraser 1989; Leib, Bogard et al. 1989; Devi-Rao, Goodart et al. 1991; Jin, Schnitzlein et al. 2000; Ono, Tomioka et al. 2007). In transgenic mouse lines, PRV LAP promoted transcription is neuron-specific in the absence of PRV infection (Taharaguchi, Yoshino et al. 2003). However, in transient expression assays, PRV LAP1 and LAP2 promote

transcription both in cultured neuronal as well as non-neuronal cells (Cheung and Smith 1999; Taharaguchi, Kobayashi et al. 2002). Furthermore, the activity of tandem LAP1 and LAP2 sequences is significantly increased compared to LAP1 or LAP2 alone (Cheung and Smith 1999).

[0089] Here, a whole-CNS screening approach based on retroorbital systemic delivery of AAV-PHP.eB, iDisco+ tissue-clearing and light-sheet microscopy, was used to identify three small latency-associated promoters (LAP) from the herpesvirus pseudorabies virus (PRV). These promoters are LAPl (404bp), LAP2 (498bp) and LAP 1 2 (880bp). They drive chronic transcription of the virus encoded latency-associated transcript (LAT) during productive and latent phases of PRV infectious cycle. Stable, pan-neuronal transgene transcription and translation were observed from AAV-LAP in brain and spinal cord for six months post AAV transduction. The data suggest that the LAPs are suitable candidates for viral vector-based CNS gene therapies requiring chronic transgene expression after one-time viral-vector administration, PRV LAPl, LAP2 and tandem LAP 1 2 promoters are likely suitable for systemic, less invasive, pan-neuronal gene delivery applications that may require stable, chronic transgene expression after a single administration.

[0090] Example 1. Materials and Methods

[0091] Construction of PRV LAP sequences

[0092] The PRV latency-associated transcript promoter (LAP) was PCR amplified from coordinates 95106-96007 of PRV Becker strain genome (GenBank: JF797219.1). The LAPl region (498bp), was amplified using primer pairs LAP IF (5’- GCA CGC GTA TCT CCG GAA AGA GGA AAT TGA -3’) (SEQ ID NO: 59) and LAP1R (5’- GCG GAT CCT ATA TAC ACG ATG TGC ATC CAT AAT -3’) (SEQ ID NO: 60). The LAP2 region (404bp), was amplified using primer pairs LAP2F (5’- GCA CGC GTA TCC CCG GTC CGC GCT CCG CCC ACC CA -3’) (SEQ ID NO: 61) and LAP2R (5’- GCG GAT CCG AGC TCC CTC TTC CTC GCC GCG GAC TGG -3’) (SEQ ID NO: 62). LAP1 2 (902bp) spanning the entire LAP region was amplified using LAP IF and LAP2R (Cheung and Smith 1999). The 5’ and 3’ regions of these PCR sequences contained the Mlul and BamHI restriction sites respectively, used for directional cloning into vector pAAV-Efla-mCherry. pAAV-Efla-mCherry was a gift from Karl Deisseroth (Addgene plasmid # 114470). The three AAV-LAP plasmids were constructed by double digestion of vector pAAV-Efla-mCherry with Mlul and BamHI followed by subcloning of the appropriate LAP fragment upstream of the mCherry reporter gene, flanked by AAV2 inverted terminal repeats (ITRs) and terminated with the SV40 poly A signal.

[0093] Construction of AAV Vectors

[0094] All expression cassettes were packaged into AAV-PhP.eB capsids (gift from Daniela Gradinaru, Addgene plasmid #103005) at the Princeton Neuroscience Institute Viral Core Facility and purified by iodixanol step gradient and column ultrafiltration as previously described (Zolotukhin, Byrne et al. 1999; Chan, Jang et al. 2017). Capsid-protected viral genomes were measured by TaqMan qPCR and reported as genome copies per milliliter (GC/ml).

[0095] Animals

[0096] Animal studies were performed following guidelines and protocols approved by the Institutional Animal Care and Use Committee of Princeton University (protocol # 1943-16 and 1047). Timed-pregnant Sprague-Dawley rats were obtained from Hilltop Labs Inc. (Scottsdale, PA). El 7 rat embryos were harvested for isolation of sympathetic SCG neurons. Adult (4 to 6- week-old) wild type C57BL/6J male mice were obtained from Jackson Laboratory (The Jackson Laboratory, Bar Harbor, ME). Mice had at least 48hr of acclimation to the holding facility in the Princeton Neuroscience Institute vivarium before experimental procedures were performed.

[0097] Primary superior cervical ganglia cell culture

[0098] SCG neurons from rat embryos (El 7) were cultured in tri chambers as previously described (Curanovic, Ch'ng et al. 2009). Briefly, SCG were dissociated with trypsin (2.5 mg/ml, Sigma-Aldrich, The Woodlands, TX) and plated on poly-O-Ornithine and laminin-coated dishes with media containing neurobasal media supplemented with 2% B-27, 100 ng/ml nerve growth factor (NGF), and 1% penicillin-streptomycin-glutamine (Thermo Fisher Scientific, Rockford, IL). Approximately two-thirds of a single ganglia were placed for S (soma) compartment of the trichamber. Three days post seeding, culture medium was treated with 0.1 mM cytosine-D- arabinofuranoside, Ara C (Sigma-Aldrich, The Woodlands, TX) for at least 2 days to eliminate dividing, nonneuronal cells. Culture media was replaced every 5 days, and neurons were incubated at 37°C with 5% C0 _2. [0099] Retro-orbital sinus injection

[00100] Intravenous administration of AAV vectors was performed in mice by unilateral injection into the retro-orbital venous sinus (Yardeni, Eckhaus et al. 2011). Animals were anesthetized using ketamine (80 mg/kg)/xylazine (10 mg/kg) cocktail prior to the procedure.

Once unresponsive, animals were placed in lateral recumbence for injection into the medial canthus. Injection volume was 100 mΐ containing a total of 4 x 10 ¹¹ viral genomes administered with a 29G1/2 insulin syringe. Animals were placed on regulated heating pads and monitored until ambulant.

[00101] Tissue processing and histological procedures

[00102] Mice were anesthetized with an overdose of ketamine (400 mg/kg)/xylazine (i.p.) and perfused with 4% paraformaldehyde (PFA) at 30 and 190 days post infection (dpi). Brain and spinal cord were post-fixed overnight in 4% PFA at 4°C. After rinsing with phosphate buffered saline (PBS), brains were stored at 4°C in PBS with 0.1% sodium azide. Brains were divided into two parts with the left hemispheres sagittally sectioned at 50 pm using a Leica VT1200 vibratome and at 20 pm using a Leica CM3050 S cryostat. Right hemispheres were used for iDISCO+ tissue clearing protocol (below). Fixed brains and spinal cords were serially incubated in 10% sucrose, 20% sucrose and 30% sucrose at 4°C for cryoprotection. Tissues were embedded in OCT (tissue-Tek, Torrance, CA), frozen in dry ice and stored at -80 °C until sectioning. For cryosectioning, spinal cords were placed in an embedding mold (Sigma- Aldrich, The Woodlands, TX) and filled with ultrapure low melting point agarose (Thermo Fisher Scientific, Rockford, IL) at 37°C. The semi-solid agarose cube was removed and glued (Loctite, Rocky Hill, CT) in the horizontal orientation for transversal slicing at 20 pm using a cryostat.

[00103] Immunostaining

[00104] For immunohistochemistry, free-floating brain sections were washed with PBS and blocked for lh with 3% bovine serum albumin (BSA), 2% donkey serum and 0.5% Triton X-100 (Sigma-Aldrich, St. Louis, MO). Samples were incubated with primary overnight at 4°C and secondary antibodies for lh at RT (room temperature) diluted in PBS containing 1% BSA, 1% donkey serum and 0.5% Triton X-100. Cell nuclei were counterstained with 0.5 pg/ml DAPI for 5 minutes (Thermo Fisher Scientific, Rockford, IL). The following primary antibodies were used: rabbit anti-RFP Rockland (1 : 1000; Limerick, PA), chicken anti-mCherry Abeam (1 :500; Cambridge, MA), mouse anti-NeuN (1 :500; Millipore Bioscience Research Reagents, Temecula, CA), rabbit anti-01ig2 (1 :500, EMD Millipore, Temecula, CA), rabbit anti-Ibal (1 : 1000, Wako Chemical, Richmond, VA) and rabbit anti-SlOO (1 :5000, Dako, Glostrup, Denmark). The following secondary antibodies were used: Alexa Fluor 488 donkey anti-rabbit IgG, Alexa Fluor 488 donkey anti-mouse IgG, Alexa Fluor 647 donkey anti-rabbit IgG, Alexa Fluor 647 donkey anti-chicken IgG (1 :1000, Thermo Fisher Scientific, Rockford, IL). Spinal cord free-floating sections were stained with 1 :300 dilution ofNeuroTrace 500/525 green fluorescent Nissl stain (Molecular Probes, Eugene, OR) for lhr. The sections were permeabilized with 0.1% Triton X- 100 in PBS at 10 minutes and washed first with PBS followed by PBS with 0.1% Triton X-100 for 10 minutes. Samples were incubated with 0.5 pg/ml DAPI for 5 min and then washed with PBS for 2 hours at room temperature. Fluoromount-G mount medium (Southern Biotech, Birmingham, AL) was applied to brain and spinal cord sections before mounting.

[00105] Microscopy

[00106] Neuronal SCG cultures were imaged with a Nikon Ti-E inverted epifluorescence microscope (Nikon Instruments Inc, Tokyo, Japan), containing a Cool Snap ES2 camera

(Photometries, Tucson, AZ) and 4X objective. Tiled images of the entire S compartment were assembled with the Nikon NIS Elements software. To quantify AAV transduction efficacy in various brain regions, brain slices were imaged with a NanoZoomer S60 fluorescent microscope scanner (Hamamatsu, Hamamatsu, Japan). Brain slices were imaged with a Leica STP8000 confocal laser-scanning microscope (Leica Microsystems, Wetzlar, Germany) using 20X and 63X objectives, hybrid (HyD) detectors for sensitive detection, and over a 1024 x 1024 pixels area. The ImageJ software was used to calculate corrected total cell fluorescence as previously reported (Maturana, Aguirre et al. 2017). Cells were selected drawing a region of interest (ROI) and normalized to background intensity from non-fluorescent cells. The calculation of corrected total cell fluorescence was measured as relative fluorescence intensity (RFI) considering area integrated, density and mean gray value of each cell.

[00107] iDISCO+ tissue clearing

[00108] Permeabilization

[00109] Right brain hemispheres were used for iDISCO+ tissue clearing. Brain samples were fixed overnight in 4% PFA prior to tissue clearing as previously described (Renier, Wu et al. 2014). Fixed samples were washed/dehydrated in 20, 40, 60, 80, 100% methanol/water solutions for lhr each, followed by a 5% hydrogen peroxide/methanol overnight wash (Sigma- Aldrich, St. Louis, MO) and rehydration with a reverse gradient of methanol/water 100, 80, 60, 40, 20% for 1 hour each. Finally, brains were washed with 0.2% Triton X-100 /PBS, followed by 20% DMSO (Thermo Fisher Scientific, Rockford, IL)/0.3M glycine (Sigma-Aldrich, St. Louis, MO)/0.2% Triton X- 100/PBS at 37°C for 2 days.

[00110] Immunolabeling

[00111] Samples were incubated in a blocking solution of 10% DMSO/6% donkey serum (EMD Millipore, Temecula, CA)/0.2% Triton X-100/PBS at 37°C for 2-3 days, followed by two lhr/washes, in PBS/0.2% Tween-20 (Sigma-Aldrich, St. Louis, MO) with 10 pg/ml heparin (solution hereinafter referred to as PTwH, Sigma-Aldrich, St. Louis, MO). Brains were incubated with primary rabbit anti-RFP antibody (1 : 1000; Rockland, Limerick, PA) in 5% DMSO/3% donkey serum/PTwH at 37°C for 7 days. Next, brains were washed with PTwH 5 times (wash intervals: 10 minutes, 15 minutes, 30 minutes, 1 hour, 2 hours) and incubated at 37°C for 7 days with secondary Alexa Fluor 647 donkey anti-rabbit IgG (1 :450, Thermo Fisher Scientific, Rockford, IL) in 3% donkey serum/PTwH and then washed in PTwH for 5 times.

[00112] Tissue clearing

[00113] Brains were sequentially dehydrated in 20, 40, 60, 80, 100% methanol/water for 1 hour each step, followed by 2: 1 dichloromethane (DCM; Sigma-Aldrich, St. Louis,

MO)/methanol, and 100% DCM washes. Finally, samples were cleared with DBE (Sigma- Aldrich, St. Louis, MO) and stored in the dark at room temperature until imaged.

[00114] Light-sheet microscopy and analysis of cleared tissue

[00115] After immunolabeling and clearing, brain volumes were acquired using a light-sheet Ultramicroscope II (LaVision Biotec, Bielefeld, Germany). Brain halves were glued in the horizontal orientation on a custom-designed 3D-printed holder (Renier, Wu et al. 2014; Renier, Adams et al. 2016) and submerged in DBE. Brains were imaged in the autofluorescent channel for registration purposes with a 488-nm laser diode excitation and a 525-nm maximum emission filter (FF01-525/39-25, Semrock, Rochester, NY), and at 640-nm excitation with a 680-nm maximum emission filter (FF01-680/42-25, Semrock) for cellular imaging of AAV infected cells (anti-RFP). Separate left- and right-sided illumination autofluorescent images were acquired every 10 micrometers (z-steps size) using a 0.017 excitation- sheet NA and 1.3x magnification. Left and right sided images were sigmoidally blended at the midline. Autofluorescent volumes were registered to the volumetric Allen brain atlas (2015) using affine and b-spline

transformations, as described by Renier and colleagues (Renier, Wu et al. 2014; Renier, Adams et al. 2016). To account for movement during acquisition and different imaging parameters between channels, cell signal volumes were registered to autofluorescent volumes with an affine transform. Brain volumes were analyzed with our modified ClearMap software:

“ClearMap cluster” (github.com/PrincetonUniversity/clearmap_cluster), compatible with high performance computing clusters. For all analyzed samples, detected objects on brain edges and ventricles were eroded by 75 pm from the edge of the structure to minimize false positives.

[00116] RNAscope in situ hybridization

[00117] Brain cryosections were mounted on superfrost plus adhesion slides (Thermo Fisher, Waltham, MA) and stored at -80°C. RNA staining was performed using the RNAscope multiplex fluorescent reagent kit (Advanced Cell Diagnostics (ACD), Newark, CA) following the manufacturer’s protocol. The mCherry probe ACD# 431201-C2 was used. Slices were pretreated with protease IV for 30 minutes at 40 °C, followed by probe incubation for 2 hours at 40 °C. Then, different amplifier solutions were performed for 30 minutes, 30 minutes, and 15 minutes at 40 °C. Signal was detected with TSA plus fluorescein system (Perkin Elmer, Waltham, MA). Incubation steps were done in the ACD HybEZ hybridization system. Slides were counterstained with DAPI for 30 seconds at room temperature and then washed twice with PBS. Finally, slides were mounted with VECTASHIELD Vibrance antifade mounting medium (Vector Laboratories, Burlingame, CA).

[00118] Statistics

[00119] Statistical data analysis was performed using GraphPad Prism 7 software (GraphPad Software, Inc., La Jolla, CA). Two-tailed Student’s test was used to compare between two groups, and non-parametric one-way ANOVA test followed by a Bonferroni multiple

comparison post-test to compare among multiple groups. A p value < 0.05 was statistically significant. Data are represented as the mean with SEM.

[00120] Example 2 Small PRV LAP sequences can drive transgene expression in neurons independently of herpesvirus infection. [00121] The PRV LAP region includes at least two promoter regions defined here as LAP1 and LAP2 (FIG. 1A). In the PRV genome, LAP1 and LAP2 are present in tandem as PRV LAP1 2. These sequences, alone or combined, are capable of efficient expression of reporter transgenes in primary sympathetic neurons when used in AAV vectors without PRV infection (FIGs. 1C and ID). The LAP sequences were analyzed to identify putative regulatory elements using the Jasper (Sandelin, Alkema et al. 2004; Wasserman and Sandelin 2004), the RSAT (Nguyen, Contreras-Moreira et al. 2018) and the CTCFBSDB 2.0 (Ziebarth, Bhattacharya et al. 2013) software. Three cyclic AMP response element-binding protein (CREB) binding motifs were detected upstream of the LAP1 TATA box, and one was detected upstream of the LAP2 TATA box. Moreover, two CCCTC-binding factor (CTCF) binding motifs were detected upstream of the LAP1 TATA box and one was detected downstream of the LAP2 TATA box. Downstream promoter elements (DPE) were identified in LAP2, including three CG boxes and four signal transducer and activator of transcription 1 (STAT1) binding motifs. Additionally, there were lineage-determining TFs (Wang, Pol et al. 2014), such as SRY-Box 10 (SOX10) and oligodendrocyte transcription factor 2 (01ig2), upstream of the LAP1 TATA box and the LAP2 TATA box, respectively (FIG. 1A).

[00122] Four AAV recombinants were packaged into serotype PHP.eB capsids by standard methods. Three promoter constructs, LAP1 (498 bp, corresponding to SEQ ID NO: 1), LAP2 (404 bp, corresponding to SEQ ID NO: 2) and LAP1 2 (880 bp, corresponding to SEQ ID NO: 3), were prepared. The ubiquitous EF-la promoter (1264 bp) was used as a positive control for transgene expression. All four AAV recombinants expressed the fluorescent reporter mCherry (FIG IB). To verify the in vitro performance of each promoter, rat primary superior cervical ganglia (SCG) neuronal cultures were transduced with 3 x 10 ¹¹ genomes of each AAV, and the relative mCherry fluorescence intensity (RFI) was quantified over a 90-day period.

[00123] For neurons transduced with AAV-LAP1, mCherry expression increased abruptly at 11 dpi (64220 RFI) but to a lower level when compared with AAV-LAP2, AAV-LAP1 2 and AAV-EFla. AAV-EFla expression increased ~120-fold more at 17 dpi (8.70 x 10 ⁶ ; 2.39 x 10 ⁶ ; 8.01 x 10 ⁶ RFI respectively) (FIG. 1C). The highest level of expression by all four recombinants was at 28 dpi: LAP1 (291,242 RFI); LAP2 (1.36 x 10 ⁷ RFI); LAP 1 2 (4.36 x 10 ⁶ RFI) and EFla (1.40 x 10 ⁷ RFI) (FIGs. 1C and ID). LAP2 and EF1 a had the highest mCherry RFI (LAP2 = EFla > LAP1 2 > LAP1). Between 38 dpi and 90 dpi, all four AAV recombinants showed a subtle but sustained RFI decrease (FIG. 1C), most likely due to the senescence of primary SCG neurons after more than 100 days in culture. Importantly, all three AAV-LAP recombinants showed mCherry transcription in primary neurons for 90 days in the context of AAV transduction and in the absence of PRV infection.

[00124] Example 3 Whole-CNS screening reveals pan-neuronal AAV-LAP transgene expression after six months.

[00125] AAV serotype PHP.eB was used for a promoter screening assay given the enhanced capacity to cross the BBB and transduce C57/BL6 mice CNS after systemic, intravascular delivery (Chan, Jang et al. 2017). AAV-LAP 1 -mCherry, AAV-LAP2-mCherry, AAV-LAP 1 2- mCherry and AAV-EFla-mCherry were delivered by unilateral retro-orbital venous sinus injection of 4 x 10 ¹¹ viral genomes/mouse (vg/mouse). As illustrated in FIG. 2A, the brains and spinal cords were harvested 30 days and 190 days post- AAV transduction to quantify mCherry transcription and translation. LAP -mCherry expression in the whole intact brain was determined after the tissues were cleared, immunostained with iDISCO+ (immunolabeling-enabled three- dimensional imaging of solvent-cleared organs), and analyzed by light-sheet microscopy and volumetric registration (Renier, Wu et al. 2014; Renier, Adams et al. 2016).

[00126] As demonstrated in FIGs. 2B-2P, all four promoters showed stable mCherry expression at both 30 dpi and 190 dpi. The density (number of mCherry positive cells per mm ³ of brain tissue) of LAP2 was higher than those of LAP 1 and LAP 1 2, and was not significantly different from that of EFla in different areas of the brain: cortex: primary motor, secondary motor, primary somatosensory and supplemental somatosensory, FIGs 2B-2E); hippocampal formation (FIG. 2G), pallidum (FIG. 21), hypothalamus (FIG. 2K) and olfactory areas (FIG. 2P). In cerebellum, LAP2 showed higher mCherry density than LAPl, LAP1 2 and EFla (FIG. 20). Furthermore, in striatum (FIG. 2H); thalamus (FIG. 2J); midbrain, motor and sensory areas (FIGs. 2L and 2M), and hindbrain (FIG. 2N), LAP2 and LAP1_2 showed significantly higher density than EFla (p < 0.05). Note that the LAP2 nucleotide sequence is 68% shorter than that of EFla, yet outperforms EFla in several brain areas.

[00127] To further validate LAP transgene expression in the CNS, mCherry protein expression was assessed by immunohistochemistry (IHC) in sagittal brain sections at 30 dpi and 190 dpi (FIGs. 3A-3H). Confocal microscopy analysis showed abundant mCherry staining throughout the cortical somatosensory area (FIG. 3E), the dentate gyrus in the hippocampal formation (FIG. 3F), the caudoputamen in the striatum (FIG. 3G), and the cerebellar cortex (FIG. 3H) at 30 dpi. Importantly, mCherry expression was stable for all three LAP sequences at 190 dpi and was similar to that of the larger AAV-EFla-mCherry promoter (FIGs. 3E-3H, Panels 5-8). Next, mCherry expression was quantified at 30 dpi and 190 dpi. The mCherry RFI was similar for all AAV promoters with no significant differences (FIGs. 311-314). The number of mCherry positive cells per pixel ² after 190 days was subsequently quantified. In the cortex, the number of LAP2 mCherry expressing cells was higher than those observed for LAP1- mCherry and LAPl_2-mCherry [LAP2: 297 ± 19.82 vs. LAP1 : 149 ± 5.61 vs LAP1_2: 168 ± 9.22 (n = 6, p < 0.001) (FIG. 3J1). In the dentate gyrus, the striatum and the cerebellum, the number of mCherry positive cells was similar for all LAP variants and EFla (FIGs. 3J2-3J4). Thus, all AAV-LAP variants promote mCherry expression in the brain, further demonstrating that a single administration of AAV-LAP recombinants can be sufficient for driving long term, pan-neuronal transgene expression in the mouse CNS.

[00128] Example 4 The small LAP2 promoter variant drives strong and stable pan-neuronal transgene expression after systemic AAV administration.

[00129] The efficacies of mCherry expression under the control of different PRV LAP sequences were compared. Abundant signal in the cortex (FIGs. 4A and 4E1), dentate gyrus (FIGs. 4B and 4E2), striatum (FIGs. 4C and 4E3) and cerebellum (FIGs. 4D and 4E4) at 30 dpi and 190 dpi were observed. Moreover, the AAV-LAP2 RFI was stable and similar to AAV-EFla both at 30 dpi and 190 dpi (p < 0.05) (FIGs. 4E1-4E4; Table 2). Although AAV-LAP1 and AAV-LAP1 2 mCherry RFI levels were stable and not significantly different between them at 30 dpi and 190 dpi in cortex, dentate gyrus, striatum and cerebellum (FIGs. 4E1-4E4; Table 2), both promoters showed significantly less transgene expression compared to LAP2 and EFla.

Table 2. mCherry Expression in Mouse Brain with Different AAV-PHP.eB-Promoter

adpi: days post AAV injection

bRFI: relative fluorescence intensity

[00130] Since mRNA half-life is typically shorter than that of the translated protein (Chan, Mugler et al. 2018), mCherry transcripts in AAV-LAP transduced mouse brain slices were measured. AAV-LAP2-mCherry mRNA at 30 dpi (data not shown) and 190 dpi were measured using a mCherry-specific riboprobe. Fluorescent in situ hybridization (FISH) showed abundant AAV-LAP2 mCherry RNA in cortex, dentate gyrus, striatum, cerebellum and olfactory bulb (FIGs. 5A-5E), further confirming that PRV LAP2 can drive chronic and robust transgene transcription in the CNS.

[00131] Example 5 AAV-LAP transgene expression in the brain is predominant in neurons but not in glial cells. [00132] The tropism and specificity of AAV transduction and subsequent transgene expression depend on the AAV serotype (Aschauer, Kreuz et al. 2013, Bedbrook; Deverman et al. 2018) and the promoter (von Jonquieres, Frohlich et al. 2016; Hammond, Leek et al. 2017; Dayton, Grames et al. 2018). To characterize which cell-types showed AAV-LAP-mCherry expression after systemic AAV-PHP.eB delivery, co-immunostainings of mCherry protein with markers for neurons (NeuN), oligodencrocytes (01ig2), microglia (Ibal) and astrocytes (S100) were performed in the cortex and dentate gyrus. Co-staining with NeuN and mCherry revealed that over 90% of the neurons imaged expressed mCherry driven by the different AAV-LAP variants in both the cortex and dentate gyrus (FIGs. 6A, 6B and 6E). Conversely, less than 4% of mCherry-positive oligodendrocytes were detected for all LAP variants (FIGs. 6C, 6D and 6F). Moreover, no co-labelling of mCherry with microglia and astrocyte markers for any of the LAP recombinants was observed (FIGs. 7A-7D). Overall, these results demonstrate that in the context of systemic brain transduction with AAV-PHP.eB, LAP-mCherry expression is abundant in neurons but not in glial cells.

[00133] Example 6 AAV-LAP constructs exhibit broad stable and long-term transgene expression throughout the spinal cord.

[00134] In addition to the brain, AAV-LAP performance in spinal cord, where the serotype PHP.eB has shown widespread transduction of gray matter (Chan, Jang et al. 2017; Dayton, Grames et al. 2018), was evaluated.

[00135] Abundant native mCherry expression in both dorsal and ventral horns of the spinal cord at cervical, thoracic (data no shown) and lumbar levels at 190 dpi were observed (FIGs. 8A-8D). Quantification of native mCherry fluorescence (RFI) for all promoters was similar, with no statistically significant differences (FIG. 8E). However, the LAP2 and LAP 1 2 recombinants showed the highest density of mCherry-positive cells per pixel ² , followed by EFla and LAPl; LAP2 = LAP 1 2 > EFla > LAPl (FIG. 8F). Therefore, all three PRV LAP sequences effectively mediate pan-neuronal, long-term transgene expression in the spinal cord.

[00136] Gene therapy has been used to restore gene function in specific target cells in neurologic and neurodegenerative disorders (Deverman, Ravina et al. 2018). Gene transfer by systemic vector delivery via peripheral vascular transduction can be difficult for efficient expression in a neuron-specific or pan-neuronal fashion in the CNS (Ingusci, Verlengia et al. 2019). Recombinant AAV vectors are among the most efficient vehicles to achieve gene expression in the CNS (Hudry and Vandenberghe 2019, Wang, Tai et al. 2019). Moreover, engineered AAV capsids have shown improved CNS transduction and enhanced capacity to cross the BBB with higher efficiency than naturally-occurring serotypes (Chan, Jang et al. 2017; Bedbrook, Deverman et al. 2018; Hordeaux, Yuan et al. 2019; Qin Huang and Alejandro B. Balazs 2019). Despite these advances, AAV gene therapy is hindered by the small payload size limit of 4.9 Kb for the AAV capsid (Chamberlain, Riyad et al. 2016). For example, CNS therapies for Pompe disease (Colella, Sellier et al. 2019) and Parkinson’s disease (Wang, Muramatsu et al. 2002) are based on delivery of relatively large genes such as GAA (2.9 Kb) and GDNF (2.5 Kb). For these and other similar cases, the use of larger promoters or even smaller CMV and hSyn promoters has been shown to be quickly repressed after delivery (Gray, Foti et al. 2011, Jackson, Dayton et al. 2016).

[00137] As described herein, three small pan-neuronal promoters isolated from the genome of the alphaherpesvirus PRV were identified, showing efficient and long-term transgene expression in the mice CNS after systemic AAV PHP.eB delivery. The results presented herein demonstrate that these small PRV LAP sequences can drive long-term expression of a reporter transgene (> 6 months) in brain and spinal cord. PRV LAP uniformly transduced neurons in the cortex, striatum, dentate gyrus and cerebellum. The distribution of mCherry-positive cells was not significantly different between LAP sequences in the dentate gyrus, striatum and cerebellum. However, LAP2 transgene expression was significantly higher in cortex compared to LAPl and LAP 1 2. The whole-brain screening assay demonstrated that the LAP2 variant of only 402 bp can drive stronger mCherry expression than the larger LAPl and LAP1 2 sequences. Moreover, abundant mCherry mRNA transcribed from LAP2 was detected in every screened brain region at 190 dpi. These results demonstrate both efficient transcription and translation driven from the small PRV LAP2 in CNS after systemic AAV-LAP2 delivery in the absence of PRV infection.

[00138] Although the LAPl -mCherry cell density was significantly lower than that for LAP2, mCherry expression remained stable and long-lasting. Therefore, LAPl might be useful in cases where low amounts of the therapeutic protein are needed (e.g. enzyme deficiencies) or for cross correction to non-transduced cells. For example, for lysosomal enzyme deficiency (Husain, Passini et al. 2009) and mucopolysaccharidosis VII diseases (Cearley and Wolfe 2007), where the enzyme restored by AAV therapy can be secreted from the transduced cell and improve neighboring diseased cells.

[00139] AAV tropism is determined primarily by interactions between the capsid and specific receptors in susceptible and permissive cells (Aschauer, Kreuz et al. 2013; Bedbrook, Deverman et al. 2018). Different AAV serotypes have different tissue tropism. However, the promoter sequence and other sequences included in the vector such as the inverted terminal repeat sequence (ITR), can have a substantial impact on tropism (Haberman and McCown 2002). In addition, the promoter region transcribing the transgene is critically important to optimize AAV vector performance. Efficient transgene expression either in a broad or cell-type specific fashion, requires binding and action of cell-derived TFs to the promoter region (Dayton, Grames et al. 2018; Andersson and Sandelin 2019). Changes in the neuronal environment such as aging or differentiation, also can alter the recruitment of cell-specific regulatory proteins and therefore gene expression in the CNS (Herdegen and Leah 1998). The analysis of the PRV LAP sequence presented herein identified DPE in LAP2, which could control transgene expression onset, duration and cell-type specificity. Additionally, four STAT1 motifs, that in HSV-1 LAP seem to regulate viral reactivation from latency (Kriesel, Jones et al. 2004), were identified. Strikingly, one of these STAT1 motifs in PRV LAP2 was found to co-localize with the TATA box and an 01ig2 motif, a known multifaceted TFs promoting neuronal and oligodendrocyte fates (Emery and Lu 2015). The proximity effects associated with these motifs and the transcriptional start site could explain the different levels of CNS transgene expression between LAP2, LAPl and LAP1 2. Additionally, one CTCF motif was found downstream of the LAP2 TATA box, which could have a role in the resistance to epigenetic silencing during latency, as shown for HSV-1 (Lang, Li et al. 2017; Lee, Raja et al. 2018). Indeed, Zimmerman and colleagues (Zimmerman, Patel et al. 2018) found that insertion of a CTCF motif downstream of the EFla promoter increased transgene expression significantly compared to native EFla and CMV promoters. Interestingly, the insertion of a secondary CTCF motif downstream of the CMV TATA box, had no effect on luciferase reporter expression, presumably due to the redundant presence of a native CTCF motif (Zimmerman, Patel et al. 2018). Accordingly, gene expression is susceptible to changes depending of the genetic context and sequence-specific DNA binding proteins. The recruitment of specific TFs from different host cells can modulate transgene transcription by the same mechanisms regulating resistance to inactivation during latency. Insulator elements like the CTCF-binding factor are independently regulated (Washington, Musarrat et al. 2018) and can protect promoter regions from repression by heterochromatin, maintaining long-lasting transcription (Lang, Li et al. 2017).

[00140] Histological assessment of cell-specific transduction by colocalization of LAP - mCherry, glial and neuronal markers, revealed that LAP sequences express more efficiently in neurons than glia, in cortex and dentate gyrus. LAP-mCherry positive cells colocalized predominantly with neuron-specific markers, and to a lesser extent with oligodendrocytes but not microglia or astrocytes. These findings suggest that PRV LAP sequences have a pan-neuronal promoter profile in the CNS after PHP.eB systemic delivery. This activity has also been found for the HSV LAP sequences due to the presence of a CRE motif upstream of the TATA box (Leib, Nadeau et al. 1991; Kenny, Krebs et al. 1994; Bloom, Stevens et al. 1997). PRV LAP1 and LAP2 are neuron-specific promoters in the absence of other viral proteins and that transgene expression levels vary across different neuronal types (Taharaguchi, Yoshino et al. 2003).

Importantly, AAV-PHP.eB transduces neurons predominantly (Chan, Jang et al. 2017), and the combination of this capsid variant with PRV LAP sequences exhibits a strong, long-lasting, pan neuronal expression profile in the CNS. Thus, PRV LAP sequences may be used not only in the context of recombinant viral vectors (AAV, adenovirus, lentivirus, herpesvirus), but also with non-viral gene delivery platforms. The natural host of PRV is the adult swine, but the virus has an extremely broad tropism and can infect some birds, fish and many types of mammals including some primates (Baskerville and Lloyd 1977). Moreover, human cells in culture are susceptible to PRV infection and there have been some reports of zoonotic infections (Wong, Lu et al. 2019). Therefore, the PRV LAP sequence may be optimized for gene therapy-applications requiring efficient and long-term transgene expression in several different mammals including humans.

[00141] In summary, the data presented herein demonstrated that PRV LAP promoter activity is independent of PRV infection and that small AAV-PHP.eB -LAP sequences express transgenes in a stable and pan-neuronal fashion in brain and spinal cord (CNS). Long-term transgene transcription and translation is paramount for effective and long-lasting single-dose gene therapy applications. Thus, PRV LAP sequences may be useful for the treatment of genetic CNS diseases.

[00142] Example 7 LAP sequences efficiently drive transgene expression in non-neuronal cells and tissues.

[00143] In the following examples, LAP sequences were demonstrated to efficiently drive transgene expression of a fluorescent reporter protein (mCherry) in several cell and tissue types, including kidney, liver and retina. Furthermore, LAP was found to be compatible with viral vectors (such as AAV) as well as non-viral vectors (such as direct transfection of plasmid DNA).

[00144] As shown in FIGs. 9A-9C, the LAP sequences drive efficient transgene expression in porcine kidney cells. Representative images of PK15 cells (porcine kidney epithelial cells,

ATCC CCL-33) were obtained at 48 hours post transfection of a reporter plasmid comprising mCherry driven by LAPl (FIG. 9A), LAP2 (FIG. 9B), or LAP1_2 (FIG. 9C).

[00145] As shown in FIGs. 10A and 10B, LAP2 drives efficient transgene expression in human kidney cells. Representative images of HEK-293 cells (human embryonic kidney epithelial cells, ATCC CRL-1573) were obtained at 48 hours post transfection of a reporter plasmids comprising mCherry driven by LAP2 (FIG. 10A) or the EFla promoter (FIGs. 10B).

[00146] As shown in FIGs. 11A and 11B, LAP2 drives efficient transgene expression in human liver cells. Representative images of HepG2 cells (human liver epithelial cells, ATCC HB-8065) were obtained at 48 hours post transfection of a reporter plasmid comprising mCherry driven by LAP2 (FIG. 11 A) or the EFla promoter (FIG. 11B).

[00147] As shown in FIGs. 12A1-12B4, LAP2 drives long-term transgene expression throughout the liver. Intravenous administrations of the AAV-LAP2 (FIGs. 12A1-12A4) or the AAV-EF la- vector (FIGs. 12B1-12B4) were performed by unilateral injections into the mouse retro-orbital sinuses (4 x 10 ¹¹ vg/mouse). The liver was collected at 190 dpi and longitudinally sectioned at 20 pm for subsequent IHC and confocal microscopy analysis. Representative confocal images show native mCherry fluorescence (FIGs. 12A1 and 12B1: red), anti-mCherry immunostaining (FIGs. 12A2 and 12B2: green), DAPI nuclear counterstain (FIGs. 12A3 and 12B3: blue) and merged immunofluorescence and DAPI images (FIGs. 12A4 and 12B4).

[00148] As shown in FIGs. 13A1-13B4, LAP2 drives long-term transgene expression in the mouse kidney. Intravenous administrations of the AAV-LAP2 (FIGs. 13A1-13A4) or the AAV- EFla-vector (FIGs. 13B1-13B4) were performed by unilateral injections into the mouse retro- orbital sinuses (4 x 10 ¹¹ vg/mouse). The kidneys were collected at 190 dpi and longitudinally sectioned at 20 pm for subsequent IHC and confocal-microscopy analysis. Representative confocal images show native mCherry fluorescence (FIGs. 13A1 and 13B1: red), anti-mCherry immunostaining (FIGs. 13A2 and 13B2: green), DAPI nuclear counterstain (FIGs. 13A3 and 13B3: blue) and merged immunofluorescence and DAPI images (FIGs. 13A4 and 13B4).

[00149] As shown in FIGs. 14A1-14B4, LAP2 drives long-term transgene expression in the mouse retina. Intravenous administrations of the AAV-LAP2 (FIGs. 14A1-14A4) or the AAV- EF la-vector (FIGs. 14B1-14B4) were performed by unilateral injections into the mouse retro- orbital sinuses (4 x 10 ¹¹ vg/mouse). The retinae were collected at 190 dpi and transversely cryosectioned at 20 pm for subsequent IHC and confocal-microscopy analysis. Representative confocal images show native mCherry fluorescence (FIGs. 14A1 and 14B1: red), anti-mCherry immunostaining (FIGs. 14A2 and 14B2: green), DAPI nuclear counterstain (FIGs. 14A3 and 14B3: blue) and merged immunofluorescence and DAPI images (FIGs. 14A4 and 14B4).

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[00231] The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety.

[00232] While example embodiments have been particularly shown and described, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the embodiments encompassed by the appended claims.