GENE THERAPY TREATMENT

[0001] This disclosure concerns transcription cassettes comprising nucleic acid molecules comprising a nucleotide sequence encoding at least one subunit of the heterotetrametric adaptor protein complex 4 (AP-4); vectors comprising said transcription cassettes; pharmaceutical compositions comprising said vector; and vectors or compositions for use in the treatment of AP-4 hereditary spastic paraplegias.

[0002] Hereditary Spastic Paraplegias (HSPs) are a family of rare inherited, progressive, lower-limb spasticity disorders with an overall prevalence of 0.5-5.5 individuals per 100,000. Hereditary spastic paraplegia (HSP) in young patients is often characterised by weakness and spasticity (stiffness) of the legs and can later in life lead to further complications and may require the assistance of a cane, walker or wheelchair. There are a variety of genetic types of HSP such as autosomal dominant, autosomal recessive, X-linked, and maternally inherited (mitochondrial) forms with the autosomal dominant form most commonly found affecting between 75-80% of HSP patients. A variety of diagnostic methods for the identification of mutations in genes responsible for different forms of HSP, such as autosomal-recessive HSP (AR-HSP) caused by mutations in genes KIAA1840 (U.S. Pat. No. 10,519,503) or ZFYVE26 (US2017152562), or autosomal-dominant HSP caused by mutations in SPG3A, are disclosed in CN1958605.

[0003] AP-4-associated hereditary spastic paraplegia (AP-4-HSP), sometimes known as AP-4 deficiency syndrome or Adaptor protein complex 4 (AP-4) deficiency, is caused by loss-of-function mutations in any one of the four genes encoding the protein subunits of the AP-4 adaptor complex [10]. AP-4-HSP is autosomal recessive in nature. AP-4-HSP that is caused by mutations in the AP4B1 gene is sometimes called spastic paraplegia type 47 (SPG47) or hereditary spastic paraplegia 47 (HSP47) and it results in a significant decrease in AP4B1 protein levels [2]. AP-4-HSP may also be caused by mutations in the three other AP-4 subunits: AP4M1 mutations cause AP-4-HSP which is sometimes called SPG50 or HSP50, AP4E1 mutations cause AP-4-HSP which is sometimes called SPG51 or HSP51 and AP4S1 mutations cause AP-4-HSP which is sometimes called SPG52 or HSP51. AP-4-HSP characteristics are very similar regardless of the gene in which the causative mutations occur. The onset of AP-4-HSP usually occurs in early childhood and results in spasticity, intellectual disability from moderate to severe, impaired or absent speech, microencephaly, seizures, a shy character and in severe cases tetraplegia [11]. AP-4-HSP has so far been characterised in 199 children worldwide [1], however, incidents are most likely underreported. AP-4-HSP is progressive and there are no disease-modifying treatments. There is therefore a need to develop new therapies to improve patient outcomes for those suffering from AP-4-HSP.

[0004] AP4B1 is one component of the AP-4 heterotetramer (FIG. 1A). The complete AP-4 complex is composed of two large adaptins (epsilon-type subunit AP4E1 and the beta-type subunit AP4B1), a medium adaptin (mu-type subunit AP4M1) and a small adaptin (sigma-type AP4S1). The AP-4 complex forms a non clathrin-associated coat on vesicles departing the trans-Golgi network (TGN) and may be involved in the targeting of proteins from the trans-Golgi network to the endosomal-lysosomal system (FIG. 1B). It is also involved in protein sorting to the basolateral membrane in epithelial cells and the proper asymmetric localization of proteins in neurons. AP-4 positive TGN derived vesicles are essential for correct spatial formation of autophagosomes and loss of the AP-4 complex can therefore impair autophagosome formation in the distal axon. Thus, the AP-4 complex is key to normal functioning in the brain.

[0005] Adeno-associated virus (AAV) vectors are known in the art and offer, when compared to retroviral or lentiviral vectors, a variety of advantages such as their mild immune response, capability to infect a broad range of cells and that the desired DNA is not integrated into the genome resulting in potential disruption and knock out of other genes but is stored extrachromosomal in the cell. AAV comprises single-stranded DNA genome of approximately 4.8 kilobases (kb) comprising three genes with coding sequences flanked by inverted repeats which are required for genome replication and packaging. Uses of AAVs and modified AAV vectors are known in the art and disclosed in WO2019/032898, WO2020041498 or WO2019/028306. AAV vectors have completed a variety of phase I and II clinical trials for the delivery of genes in the treatment of cystic fibroses and congestive heart failure and approved therapies for the treatment of spinal muscular atrophy.

[0006] In our co-pending application WO2021/205028, the content of which is incorporated in its entirety, we disclose transcription cassettes comprising nucleic acid molecules encoding AP-4 polypeptides.

[0007] We herein disclose optimised expression vectors that include AP-4 nucleic acid molecules operably linked to expression control sequences adapted for expression in mammalian neurones, for example motor neurones, and the use of the modified expression vectors to deliver and functionally replace dysfunctional AP-4 proteins in the prevention or treatment of symptoms associated with HSPs. This disclosure relates to the development of modified vectors, for example AAV vectors, enhanced AAV vectors, including nucleic acid molecules encoding proteins of the AP-4 complex.

[0008] According to an aspect of the invention there is provided an isolated nucleic acid molecule comprising: a transcription cassette comprising in a 5′ to 3′ direction between first and second inverted repeat sequences:

• • [0009] i) a promoter adapted for expression in a mammalian neurone wherein said promoter is associated with an enhancer nucleotide motif;
  • [0010] ii) an intron nucleotide sequence; and
  • [0011] iii) a polyadenylation signal nucleotide sequence; wherein said cassette further comprises a nucleic acid molecule comprising a nucleotide sequence that encodes at least one protein of the AP-4 complex.

[0012] In a preferred embodiment of the invention said enhancer motif is a CMV enhancer.

[0013] In a preferred embodiment of the invention said CMV enhancer motif comprises or consists of the nucleotide sequence in SEQ ID NO: 1, or polymorphic nucleotide sequence variant thereof,

[0014] Preferably said hybrid intron comprises or consists of the nucleotide sequence in SEQ ID NO: 2, or polymorphic sequence variant thereof.

[0015] In a preferred embodiment of the invention said polyadenylation signal is a growth hormone (GH) polyadenylation signal.

[0016] Preferably, said GH polyadenylation signal comprises or consists of the nucleotide sequence in SEQ ID NO: 4, or polymorphic sequence variant thereof.

[0017] In a preferred embodiment of the invention said promoter is the chicken beta actin promoter.

[0018] Preferably, said chicken beta actin promoter comprises or consists of the nucleotide sequence in SEQ ID NO: 3.

[0019] Preferably, said chicken beta actin promoter comprises or consists of the nucleotide sequence in SEQ ID NO: 28.

[0020] In a preferred embodiment of the invention said transcription cassette comprises or consists of the nucleotide sequence in SEQ ID NO: 9.

[0021] A polymorphic sequence variant is a sequence that varies from a reference sequence by one or more nucleotides bases, for example, 2, 3, 4, 5 or more bases.

[0022] In a preferred embodiment of the invention said expression cassette comprises a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of:

• • [0023] i) a nucleotide sequence, or polymorphic sequence variant, as set forth in SEQ ID NO: 15 (AP4B1);
  • [0024] ii) a nucleotide sequence wherein said sequence is degenerate as a result of the genetic code to the nucleotide sequence defined in (i);
  • [0025] iii) a nucleic acid molecule the complementary strand of which hybridizes under stringent hybridization conditions to the sequence in SEQ ID NO: 15 (AP4B1) wherein said nucleic acid molecule encodes a polypeptide that forms a complex with polypeptides comprising the AP-4 complex;
  • [0026] iv) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 16 (AP4B1);
  • [0027] v) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence wherein said amino acid sequence is modified by addition deletion or substitution of at least one amino acid residue as represented in iv) wherein said polypeptide forms a complex with polypeptides comprising the AP-4 complex.

[0028] Hybridization of a nucleic acid molecule occurs when two complementary nucleic acid molecules undergo an amount of hydrogen bonding to each other. The stringency of hybridization can vary according to the environmental conditions surrounding the nucleic acids, the nature of the hybridization method, and the composition and length of the nucleic acid molecules used. Calculations regarding hybridization conditions required for attaining particular degrees of stringency are discussed in Sambrook et al., Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2001); and Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes Part I, Chapter 2 (Elsevier, New York, 1993). The Tm is the temperature at which 50% of a given strand of a nucleic acid molecule is hybridized to its complementary strand. The following is an exemplary set of hybridization conditions and is not limiting:

[0029] Very High Stringency (allows sequences that share at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to hybridize)

• • [0030] Hybridization: 5×SSC at 65° C. for 16 hours
  • [0031] Wash twice: 2×SSC at room temperature (RT) for 15 minutes each
  • [0032] Wash twice: 0.5×SSC at 65° C. for 20 minutes each

[0033] High Stringency (allows sequences that share at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89% identity to hybridize)

• • [0034] Hybridization: 5×-6×SSC at 65° C.-70° C. for 16-20 hours
  • [0035] Wash twice: 2×SSC at RT for 5-20 minutes each
  • [0036] Wash twice: 1×SSC at 55° C.-70° C. for 30 minutes each

[0037] Low Stringency (allows sequences that share at least 50%, 55%, 60%, 65%, 70% or 75% identity to hybridize)

• • [0038] Hybridization: 6×SSC at RT to 55° C. for 16-20 hours
  • [0039] Wash at least twice: 2×-3×SSC at RT to 55° C. for 20-30 minutes each.

[0040] In a preferred embodiment of the invention said expression cassette comprises a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of:

• • [0041] i) a nucleotide sequence, or polymorphic sequence variant, as set forth in SEQ ID NO: 17 (AP4E1);
  • [0042] a nucleotide sequence wherein said sequence is degenerate as a result of the genetic code to the nucleotide sequence defined in (i);
  • [0043] iii) a nucleic acid molecule the complementary strand of which hybridizes under stringent hybridization conditions to the sequence in SEQ ID NO: 17 (AP4E1);
  • [0044] wherein said nucleic acid molecule encodes a polypeptide that forms a complex with polypeptides comprising the AP-4 complex;
  • [0045] iv) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 18 (AP4E1);
  • [0046] v) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence wherein said amino acid sequence is modified by addition deletion or substitution of at least one amino acid residue as represented in iv) wherein said polypeptide forms a complex with polypeptides comprising the AP-4 complex.

[0047] In a preferred embodiment of the invention said expression cassette comprises a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of:

• • [0048] i) a nucleotide sequence, or polymorphic sequence variant, as set forth in SEQ ID NO: 19 (AP4M1);
  • [0049] ii) a nucleotide sequence wherein said sequence is degenerate as a result of the genetic code to the nucleotide sequence defined in (i);
  • [0050] iii) a nucleic acid molecule the complementary strand of which hybridizes under stringent hybridization conditions to the sequence in SEQ ID NO: 19 (AP4M1);
  • [0051] wherein said nucleic acid molecule encodes a polypeptide that forms a complex with polypeptides comprising the AP-4 complex;
  • [0052] iv) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 20 (AP4M1);
  • [0053] v) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence wherein said amino acid sequence is modified by addition deletion or substitution of at least one amino acid residue as represented in iv) wherein said polypeptide forms a complex with polypeptides comprising the AP-4 complex.

[0054] In a preferred embodiment of the invention said expression cassette comprises a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of:

• • [0055] i) a nucleotide sequence, or polymorphic sequence variant, as set forth in SEQ ID NO: 21 (AP4S1);
  • [0056] ii) a nucleotide sequence wherein said sequence is degenerate as a result of the genetic code to the nucleotide sequence defined in (i);
  • [0057] iii) a nucleic acid molecule the complementary strand of which hybridizes under stringent hybridization conditions to the sequence in SEQ ID NO: 21 (AP4S1);
  • [0058] wherein said nucleic acid molecule encodes a polypeptide that forms a complex with polypeptides comprising the AP-4 complex;
  • [0059] iv) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 22 (AP4S1);
  • [0060] a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence wherein said amino acid sequence is modified by addition deletion or substitution of at least one amino acid residue as represented in iv) wherein said polypeptide forms a complex with polypeptides comprising the AP-4 complex.

[0061] In a preferred embodiment of the invention said cassette is adapted for expression in a motor neurone.

[0062] In a preferred embodiment of the invention said nucleic acid molecule comprises or consists of a nucleotide sequence as represented in SEQ ID NO: 15, or polymorphic sequence variant thereof.

[0063] In a preferred embodiment of the invention there is provided a nucleotide sequence or polymorphic sequence variant thereof, that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 16.

[0064] In a preferred embodiment of the invention said nucleic acid molecule comprises or consists of a nucleotide sequence as represented in SEQ ID NO: 17, or polymorphic sequence variant thereof.

[0065] In a preferred embodiment of the invention there is provided a nucleotide sequence or polymorphic sequence variant thereof that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 18.

[0066] In a preferred embodiment of the invention said nucleic acid molecule comprises or consists of a nucleotide sequence as represented in SEQ ID NO: 19, or polymorphic sequence variant thereof.

[0067] In a preferred embodiment of the invention there is provided a nucleotide sequence or polymorphic sequence variant thereof that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 20.

[0068] In a preferred embodiment of the invention said nucleic acid molecule comprises or consists of a nucleotide sequence as represented in SEQ ID NO: 21, or polymorphic sequence variant thereof.

[0069] In a preferred embodiment of the invention there is provided a nucleotide sequence or polymorphic sequence variant thereof, that encodes a polypeptide comprising an amino acid sequence as represented in SEQ ID NO: 22.

[0070] A polypeptide as herein disclosed may differ in amino acid sequence by one or more substitutions, additions, deletions, truncations that may be present in any combination. Among preferred variants are those that vary from a reference polypeptide by conservative amino acid substitutions. Such substitutions are those that substitute a given amino acid by another amino acid of like characteristics. The following non-limiting list of amino acids are considered conservative replacements (similar): a) alanine, serine, and threonine; b) glutamic acid and aspartic acid; c) asparagine and glutamine d) arginine and lysine; e) isoleucine, leucine, methionine and valine and f) phenylalanine, tyrosine and tryptophan. Most highly preferred are variants that retain or enhance the same biological function and activity as the reference polypeptide from which it varies. In one embodiment, the polypeptides have at least 70% identity, even more preferably at least 75% identity, still more preferably at least 80%, 85%, 90%, 95% identity, and at least 99% identity the full-length amino acid sequence or nucleotide sequence illustrated herein.

[0071] In an alternative preferred embodiment of the invention said promoter is a constitutive promoter.

[0072] In a further alternative embodiment of the invention said promoter is a regulated promoter, for example an inducible or cell specific promoter.

[0073] In a preferred embodiment of the invention said promoter is selected from the group consisting of: chicken beta actin (CBA) promoter, chicken beta actin hybrid (CBh) promoter, CAG promoter, JeT promoter, neuronal and glial specific promoters including synapsin 1, Hb9, MeP229 and GFAP promoter sequences, as well as AP-4 subunit specific promoter regions including AP4B1, AP4E1, AP4M1 and AP4S1.

[0074] In a preferred embodiment of the invention said promoter is chicken beta actin hybrid (CBh) promoter as set forth in SEQ ID NO: 9.

[0075] In an alternative preferred embodiment of the invention said promoter is chicken beta actin hybrid (CBh) promoter as set forth in SEQ ID NO: 28.

[0076] In an alternative preferred embodiment of the invention said promoter is the JeT promoter comprising or consisting of the nucleotide sequence in SEQ ID NO: 5.

[0077] In an alternative preferred embodiment of the invention said promoter is the hSyn promoter comprising or consisting of the nucleotide sequence in SEQ ID NO: 6.

[0078] In an alternative preferred embodiment of the invention said promoter is the MeP229 promoter comprising or consisting of the nucleotide sequence in SEQ ID NO: 7.

[0079] In an alternative preferred embodiment of the invention said promoter is the AP4B1 promoter comprising or consisting of the nucleotide sequence in SEQ ID NO: 8.

[0080] “Promoter” or “transcription promoter” are art recognised and, for the sake of clarity, includes the following features which are provided by example only, and not by way of limitation. Enhancer elements are cis acting nucleic acid sequences often found 5′ to the transcription initiation site of a gene (enhancers can also be found 3′ to a gene sequence or even located in intronic sequences). Enhancers, for example CMV enhancers, function to increase the rate of transcription of the gene to which the enhancer is linked. Enhancer activity is responsive to trans acting transcription factors (polypeptides) which have been shown to bind specifically to enhancer elements. The binding/activity of transcription factors (please see Eukaryotic Transcription Factors, by David S Latchman, Academic Press Ltd, San Diego) is responsive to several physiological/environmental cues and can be constitutive or regulatable and also cell/tissue specific. Promoter elements also include so called TATA box and RNA polymerase initiation selection (RIS) sequences which function to select a site of transcription initiation. These sequences also bind polypeptides which function, inter alia, to facilitate transcription initiation selection by RNA polymerase.

[0081] As used herein, first nucleic acid comprising a promoter sequence and second nucleotide sequence encoding a polypeptide are said to be “operably” linked when they are covalently linked in such a way as to place the expression or transcription of the second nucleic acid molecule under the control of the first nucleic acid molecule comprising regulatory sequences. If it is desired that the coding sequences be translated into a functional protein, two DNA sequences are said to be operably linked if induction of a promoter in the 5′ regulatory sequences result in the transcription of the coding sequence and production of mRNA. Thus, a promoter region would be operably linked to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript IS translated into the desired protein or polypeptide.

[0082] According to a further aspect of the invention there is provided an expression vector comprising a transcription cassette according to the invention.

[0083] Viruses are commonly used as vectors for the delivery of exogenous genes. Commonly employed vectors include recombinantly modified enveloped or non-enveloped DNA and RNA viruses, for example baculoviridiae, parvoviridiae, picornoviridiae, herpesveridiae, poxviridae, adenoviridiae, picornaviridae or retroviridae e.g., lentivirus. Chimeric vectors may also be employed which exploit advantageous elements of each of the parent vector properties (See e.g., Feng, et al (1997) Nature Biotechnology 15:866-870). Such viral vectors may be wild-type or may be modified by recombinant DNA techniques to be replication deficient, conditionally replicating or replication competent. Conditionally replicating viral vectors are used to achieve selective expression in particular cell types while avoiding untoward broad-spectrum infection. Examples of conditionally replicating vectors are described in Pennisi, E. (1996) Science 274:342-343; Russell, and S. J. (1994) Eur. J. of Cancer 30A (8): 1165-1171.

[0084] Preferred vectors are derived from the adenoviral, adeno-associated viral or retroviral genomes.

[0085] In a preferred embodiment of the invention said expression vector is a viral based expression vector.

[0086] In a preferred embodiment of the invention said viral based vector is an adeno-associated virus [AAV].

[0087] In a preferred embodiment said viral based vector is selected from the group consisting of: AAV2, AAV3, AAV6, AAV13; AAV1, AAV4, AAV5, AAV6, AAV9 and rhAAV10.

[0088] In a preferred embodiment of the invention said viral based vector is AAV9.

[0089] In a preferred embodiment of the invention said viral based vector is an enhanced AAV9 vector, for example a PHP-b vector.

[0090] In a preferred embodiment of the invention said AAV vector is based on a single stranded AAV virus.

[0091] In an alternative embodiment of the invention said AAV vector is based on a self-complementary AAV virus.

[0092] Naturally occurring AAV serotypes typically comprise a single stranded genome which during natural infection is replicated to form a double stranded AAV viral genome. This is a rate limiting step in AAV replication and expression. A recombinant form of AAV is referred to as self-complementary AAV which comprise both a sense and antisense genomic strands that are adapted for immediate expression and replication. The viral based vector can comprise the gene encoding kanamycin resistance or for therapy can lack the gene encoding kanamycin resistance.

[0093] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 10.

[0094] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 11.

[0095] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 12.

[0096] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 13.

[0097] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 14.

[0098] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 23.

[0099] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 24.

[0100] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 25.

[0101] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 26.

[0102] In a preferred embodiment of the invention said viral based vector comprises the nucleotide sequence set forth in SEQ ID NO: 27.

[0103] Preferably, said viral based vector sequence selected from the group consisting of SEQ ID NO 10-14 and 23-27 lacks the kanamycin resistance gene and is flanked by 5′ and 3′ Inverted Terminal Repeat (ITR) sequences. As known in the prior art, only the sequences between the ITRs are packaged into the clinical viral vector and delivered to patients. The ITR flanked transgene encoded within the recombinant AAV persists subsequently as an episome in the nucleus of the transduced cell such as non-dividing neuronal cells and providing long term expression.

[0104] In an alternative preferred embodiment of the invention said viral based vector is a lentiviral vector.

[0105] According to a further aspect of the invention there is provided a pharmaceutical composition comprising an expression vector according to the invention and an excipient or carrier.

[0106] The expression vector compositions of the present invention are administered in pharmaceutically acceptable preparations. Such preparations may routinely contain pharmaceutically acceptable concentrations of salt, buffering agents, preservatives, compatible carriers and supplementary therapeutic agents. The expression vector compositions of the invention can be administered by any conventional route, including injection or by gradual infusion over time.

[0107] The expression vector compositions of the invention are administered in effective amounts. An “effective amount” is that amount of the expression vector that alone, or together with further doses, produces the desired response. In the case of treating a disease, the desired response is inhibiting the progression of the disease. This may involve only slowing the progression of the disease temporarily, although more preferably, it involves halting the progression of the disease permanently. This can be monitored by routine methods. Such amounts will depend, of course, on the particular condition being treated, the severity of the condition, the individual patient parameters including age, physical condition, size and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner.

[0108] These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.

[0109] The expression vector compositions used in the foregoing methods preferably are sterile and contain an effective amount of expression vector according to the invention for producing the desired response in a unit of weight or volume suitable for administration to a patient. The doses of vector administered to a subject can be chosen in accordance with different parameters, in particular in accordance with the mode of administration used and the state of the subject. Other factors include the desired period of treatment. If a response in a subject is insufficient at the initial doses applied, higher doses (or effectively higher doses by a different, more localized delivery route) may be employed to the extent that patient tolerance permits. Other protocols for the administration of vector compositions will be known to one of ordinary skill in the art, in which the dose amount, schedule of injections, sites of injections, mode of administration and the like vary from the foregoing. The administration of compositions to mammals other than humans, (e.g., for testing purposes or veterinary therapeutic purposes), is carried out under substantially the same conditions as described above. A subject, as used herein, is a mammal, preferably a human, and including a non-human primate, cow, horse, pig, sheep, goat, dog, cat or rodent.

[0110] When administered, the expression vector compositions of the invention are applied in pharmaceutically acceptable amounts and in pharmaceutically acceptable compositions. The term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active agent. Such preparations may routinely contain salts, buffering agents, preservatives, compatible carriers, and optionally other therapeutic agents' (e.g., those typically used in the treatment of the specific disease indication). When used in medicine, the salts should be pharmaceutically acceptable, but non-pharmaceutically acceptable salts may conveniently be used to prepare pharmaceutically acceptable salts thereof and are not excluded from the scope of the invention. Such pharmacologically and pharmaceutically acceptable salts include, but are not limited to, those prepared from the following acids: hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, maleic, acetic, salicylic, citric, formic, malonic, succinic, and the like. Also, pharmaceutically acceptable salts can be prepared as alkaline metal or alkaline earth salts, such as sodium, potassium or calcium salts.

[0111] The pharmaceutical compositions containing the expression vectors according to the invention may contain suitable buffering agents, including acetic acid in a salt; citric acid in a salt; boric acid in a salt; and phosphoric acid in a salt. The pharmaceutical compositions also may contain, optionally, suitable preservatives, such as: benzalkonium chloride; chlorobutanol; parabens and thimerosal.

[0112] The expression vector compositions may conveniently be presented in unit dosage form and may be prepared by any of the methods well-known in the art of pharmacy. All methods include the step of bringing the active agent into association with a vector which constitutes one or more accessory ingredients. The preparation may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example, as a solution in 1, 3-butanediol.

[0113] Among the acceptable solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil may be employed including synthetic mono- or di-glycerides. In addition, fatty acids such as oleic acid may be used in the preparation of injectables. Carrier formulation suitable for oral, subcutaneous, intravenous, intramuscular, etc. administrations can be found in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA.

[0114] According to a further aspect of the invention there is provided an expression vector according to the invention for use as a medicament.

[0115] According to a further aspect of the invention there is provided an expression vector according to the invention for use in the treatment of AP-4 Hereditary Spastic Paraplegias in a subject.

[0116] Preferably, said subject is a paediatric subject.

[0117] Paediatric subjects include neonates (0-28 days old), infants (1-24 months old), young children (2-6 years old) and prepubescent [7-14 years old].

[0118] In a preferred embodiment of the invention said AP-4-HSP is SPG47

[0119] In a preferred embodiment of the invention said AP-4-HSP is SPG50.

[0120] In a preferred embodiment of the invention said AP-4-HSP is SPG51.

[0121] In a preferred embodiment of the invention said AP-4-HSP is SPG52.

[0122] Spastic Paraplegia (SPG) is used interchangeably with Hereditary Spastic Paraplegia (HSP), thus SPG47 is HSP47, SPG50 is HSP50, SPG51 is HSP51 and SPG52 is HSP52.

[0123] According to a further aspect of the invention there is provided a cell transfected with an expression vector according to the invention.

[0124] In a preferred embodiment of the invention said cell is a neurone.

[0125] In a preferred embodiment of the invention said neurone is a motor neurone.

[0126] According to a further aspect of the invention there is provided a method to treat or prevent AP-4 Hereditary Spastic Paraplegias comprising administering a therapeutically effective amount of an expression vector according to the invention to prevent and/or treat Hereditary Spastic Paraplegias.

[0127] In a preferred method of the invention said AP-4-HSP is Spastic Paraplegia type 47 (SPG47).

[0128] In a preferred method of the invention said AP-4 HSP is Spastic Paraplegia type 50 (SPG50).

[0129] In a preferred method of the invention said AP-4 HSP is Spastic Paraplegia type 51 (SPG51). In a preferred method of the invention said AP-4 HSP is Spastic Paraplegia type 52 (SPG52).

[0130] According to a further aspect of the invention there is provide a method for measuring the efficacy of the treatment of hereditary spastic paraplegia in a subject wherein said subject is treated with an expression vector or the pharmaceutical composition according to the invention, said method comprising:

• • [0131] a) measuring the level of neurofilament L (NFL) in a biological sample obtained from the subject suffering from hereditary spastic paraplegia prior to administration of the expression vector according or the pharmaceutical composition according to the invention, and
  • [0132] b) comparing said levels to the levels of NFL in a biological sample obtained from the subject suffering from hereditary spastic paraplegia after the administration of the expression vector or the pharmaceutical composition according to the invention, and wherein
  • [0133] i) if the NFL levels are lower when compared to the levels obtained in step a) the treatment with the expression vector or composition is paused, or
  • [0134] ii) if the levels are substantially the same as the levels in step a) the treatment with the expression vector or composition according to the invention is continued.

[0135] In a preferred method of the invention said expression vector is selected from a group consisting of SEQ ID NO 10, 11, 12, 13, 14, 23, 24, 25, 26 and 27.

[0136] In a preferred method of the invention said sample under b) is obtained between 1, 2, 3, 4, 5 or 6 days or 1, 2, 3 or-4 weeks after administration.

[0137] According to a further aspect of the invention there is provided a method for measuring the efficacy of the treatment of hereditary spastic paraplegia in a subject suffering from hereditary spastic paraplegia wherein said subject is treated with an expression vector or pharmaceutical composition according to the invention, said method comprising:

• • [0138] a) measuring the level of neurofilament L (NFL) in a biological sample obtained from the subject suffering from hereditary spastic paraplegia and treated with said expression vector or composition, and
  • [0139] b) comparing said level with that of control subjects.

[0140] In a preferred method according to the invention, said expression vector is selected from a group consisting of SEQ ID NO 10, 11, 12, 13, 14, 23, 24, 25, 26 and 27.

[0141] In a preferred method of the invention said sample under a) is obtained between 1, 2, 3, 4, 5 or 6 days or 1, 2, 3 or-4 weeks after the treatment with the expression vector or pharmaceutical composition according to the invention

[0142] In a preferred method of the invention said method further comprises step c) wherein when said levels in a biological sample obtained from the subject suffering from hereditary spastic paraplegia are the same or lower than the NFL levels in a biological sample obtained from the control subject the treatment is effective and paused.

[0143] In a preferred method of the invention said method further comprises step c) wherein when said levels in a biological sample obtained from the subject suffering from hereditary spastic paraplegia are higher than the NFL levels in a biological sample obtained from the control subject the treatment is ineffective and the treatment with an expression vector or the pharmaceutical composition according to the invention is continued.

[0144] Throughout the description and claims of this specification, the words “comprise” and “contain” and variations of the words, for example “comprising” and “comprises”, means “including but not limited to”, and is not intended to (and does not) exclude other moieties, additives, components, integers or steps. “Consisting essentially” means having the essential integers but including integers which do not materially affect the function of the essential integers.

[0145] Throughout the description and claims of this specification, the singular encompasses the plural unless the context otherwise requires. Where the indefinite article is used, the specification is to be understood as contemplating plurality as well as singularity, unless the context requires otherwise.

[0146] Features, integers, characteristics, compounds, chemical moieties or groups described in conjunction with a particular aspect, embodiment or example of the invention are to be understood to be applicable to any other aspect, embodiment or example described herein unless incompatible therewith.

[0147] An embodiment of the invention will now be described by example only and with reference to the following figures:

[0168] All animal in vivo experiments were approved by the University of Sheffield Ethical Review Sub-Committee, the UK Animal Procedures Committee (London, UK) and performed according to the Animal (Scientific Procedures) Act 1986, under the Project License 40/3739. C57BL/6J-Ap4b1^em5Lutzy/J mice and non-transgenic C57BL/6J mice were maintained in a controlled facility in a 12h dark/12h light photocycle (on at 7 am/off at 7 pm) with free access to food and water. The ARRIVE guidelines have been followed in reporting this study.

[0169] The lead clinical vector pAAV-CBh-hAP4B1-Kan (SEQ ID NO 11) was synthesised by Genewiz. Briefly, a CBh promoter (SEQ ID NO 9), the gene of interest (hAP4B1 SEQ ID 15) and a human growth hormone (hGH) poly(A) signal (SEQ ID NO 4), were cloned into a Genewiz plasmid backbone between two AAV2 inverted terminal repeats (ITRs). The CBh promoter was initially designed and described by Grey S J, et al. 2011 as a novel, enhanced, hybrid form of the chicken beta actin (CBA) promoter. CBh is able to provide high level, ubiquitous neuronal expression, including in motor neurons (Gray et al 2011). The CBh promoter is comprised of three parts: a CMV enhancer (SEQ ID NO 1), a chicken beta actin promoter (SEQ ID 3), and a hybrid intron (SEQ ID NO 2) formed from the CBA intron 1 and the minute virus of mice (MVM) VP intron. The CMV enhancer detailed in SEQ ID NO 1 contains an 18 bp deletion compared to the standard CMV enhancer. There are short linker sequences between the 5′ ITR and the CBh promoter, the CBh promoter and hAP4B1, hAP4B1 and the hGH poly(A) signal, and the hGH poly(A) signal and the 3′ ITR. The plasmid backbone also contains an f1 bacteriophage origin of replication downstream of the 3′ITR, a kanamycin resistance gene downstream of this, and a high copy number (pUC) origin of replication immediately upstream of the 5′ ITR. The complete plasmid comprises of 6443 bp with the region to be packaged into AAV9 comprising 3895 bp.

[0170] Post-natal day 1 (P1) wildtype C57BI/6J mice were anaesthetised by isoflurane. Induction occurred in a chamber at 5% isoflurane, 3 L O2/minute. Anaesthesia was maintained via a mask at 1-2% isoflurane, 0.3L O2/minute for approximately 5 minutes during injection. The cisterna magna was located using a Wee-Sight transilluminator vein finder (Phillips). Viral vectors were injected directly into the cisterna magna of P1 mice (n=15 per group), using stereotaxic apparatus containing a 33-gauge Hamilton syringe with automated perfusion pump. The solution was administered at a flow-rate of 1 μL per minute; the maximum volume of solution administered was 5 μL per animal. Animals each received a maximum dose of 5×10¹⁰ total vector genomes. The experimental timeline proceeded as follows:

[0171] Day 1-Postnatal day 0, day of birth (PO)-Footpad tattoos applied for identification purposes Day 2-Postnatal day 1 (P1)-Injection of up to 5 L of viral vector or vehicle solution into the cisterna magna, under isoflurane anaesthesia.

[0172] Day 29 (or Day 170)-Postnatal day 28 (P28) or P168 (6 months post-injection)-Animals were perfused under terminal anaesthesia, and tissue samples collected for analysis.

[0173] A study to assess the ability of our therapeutic viral vector to mediate transgene expression in the central nervous system (CNS) of transgenic mice lacking endogenous Ap4b1 (KO C57BL/6J-Ap4b1^em5Lutzy/J) after injection via the cisterna magna, was followed. Mice were injected via the cisterna magna as in the previously described safety study. Two viral vectors were used; an AAV9 expressing a full length copy of the human AP4B1 (SPG47) gene and, an AAV9 expressing a V5 tag with no additional coding sequence as a viral control. Mice receiving AAV9-hAP4B1 viral vector were injected with two different doses (a low dose of 2×10¹⁰ vector genomes and a high dose of 4×10¹⁰ vector genomes, respectively), whereas mice receiving AAV9-V5 were injected with a high dose (4×10¹⁰ vector genomes) only. Two more groups were included in the study; untreated KO C57BL/6J-Ap4b1^em5Lutzy/J and untreated WT C57BL/6J-Ap4b1^em5Lutzy/J. Rescue of the phenotype was assessed by improvements in behavioural parameters, that will be described in details below, in the treated mice compared with untreated.

[0174] C57BL/6J-Ap4b1^em5Lutzy/J mice were generated by Jackson Labs using CRISPR-Cas9 mediated deletion of a 76 bp region within Exon 1 of the murine Ap4b1 gene. Deletion of this region generated a frameshift mutation and a truncated mRNA transcript. WT Sequence (deletions in lower case): TTGGCGACGATGCCATAccttggctctgaggacgtggtgaaggaactgaagaaggctctgtgtaaccctcatattcag gctgataggctgcgcTACCGGAATGTCATCCAGCGAGTTATTAGGTATCACCAACCTACCATAG AA.

[0175] Genotyping of mice was performed based on the protocol optimised by Charles River Laboratories. Mouse genotyping was performed on genomic DNA extracted from tail or ear tissue by the addition of 20 μl QuickExtract™ DNA Extraction Solution (Lucigen) and incubation on a thermocycler for 15 minutes at 65° C. followed by 2 minutes at 98° C. Genotyping PCRs were performed in a 20 μl volume reaction as separate reactions for WT and KO alleles. Reactions consisted of 5 μl 5×FIREPol® Master Mix Ready to Load with 7.5 mM MgCl₂ (Solis Biodyne), 500 nM each of genotyping primers-P1+P2 for WT allele amplification and P1+P3 for KO allele amplification-(P1: 5′-TCGCCCGAGGACCCAAGAA-3′ (SEQ ID NO 29); P2: 5′-CCTATCAGCCTGAATATGAGGGTTACA-3′ (SEQ ID NO 30); P3: 5′-GCTGGATGACATTCCGGTATATG-3′ (SEQ ID NO 31)) and 1 μl genomic DNA from the QuickExtract™ protocol. Touchdown PCR was performed according to the thermal profile shown in Table 1. Following PCR and agarose gel electrophoresis (2% agarose gel in Tris-acetate-EDTA buffer), WT and KO allele PCR products were visualised at ˜254 bp and ˜203 bp respectively.

[0176] Heterozygous mice were bred together to produce homozygous WT (Ap4b1+/+), KO (Ap4b1−/−) and heterozygous (Ap4b1+/−) littermates.

TABLE 1
Touchdown PCR conditions for C57BL/6J-Ap4b1em5Lutzy/J genotyping
PCR conditions
step	temp [° C.]	time [sec]
1) Initial denaturation	94	120
2) Denaturation	94	60	Cycle no. (2-4) × 10
3) Annealing	TD 58-54	60
4) Elongation	72	60
5) Denaturation	94	60	Cycle no. (5-7) × 25
6) Annealing	54	60
7) Elongation	72	60
8) Final elongation	72	300

[0177] RT-qPCR was carried out using 2 μl total RNA diluted to a concentration of 10 ng/μl in nuclease free water, 5 μl 2×QuantiFast SYBR Green RT-PCR Master Mix (Qiagen®), hAP4B1 (Forward: 5′-CTGGTGAACGATGAGAATGT-3′ (SEQ ID No 32); Reverse: 5′-GACCCAGCAACTCTGTTAAA-3′ (SEQ ID No 33), mAp4b1 (Forward: 5′-CTGTGCTAGGCTCCCACATC-3′24 (SEQ ID NO 34); Reverse: 5′-TGGCACTGGCCTTTACCATT-3′ (SEQ ID NO 35) and 18S (forward: 5′ GTAACCCGTTGAACCCCAT 3′ (SEQ ID NO 36); reverse: 5′ CCATCCAATCGGTAGTAGCG 3′ (SEQ ID NO 37) primers (all 1 μM concentration), 0.1 μl QuantiFast RT mix and H₂O to a final volume of 10 μl. Following an initial reverse transcription step at 50° C. for 10 min and a 5 min denaturation step at 95° C., cDNA was amplified by 39 cycles of 95° C. for 10 sec followed by a combined annealing/extension step at 60° C. for 10 sec. This was followed by one cycle at 65° C. for 31 sec, before subsequent melt curve analysis. All RT-qPCR was performed on a Bio-Rad C1000 Touch™ Thermal Cycler. Bio-Rad CFX Manager software was used to analyse signal intensity and relative gene expression values were determined using the ΔΔCt method, with 18S rRNA used as a reference gene.

[0178] Open field analysis was performed on mice at ages 6, 9 and 12 months. The protocol followed that performed by Herranz-Martin and colleagues 8. Mice were placed in a translucent box with dimensions 60 cm×40 cm×25 cm. The underside of the box was marked with permanent ink outlining a 5×3 grid of squares. Activity was measured as the number of grid lines crossed by each mouse over a 10 minute period. For a crossing to be recorded, all four paws of the animal were required to cross the grid line. The assessment was carried out in minimal lighting conditions and the apparatus was cleaned with 70% ethanol between each animal. One run was recorded for each animal at each timepoint.

[0179] Ugo Basile 7650 accelerating rotarod (set to accelerate from 3-37 rpm over 300 seconds) was used to measure motor function. Rotarod training was performed over 3 consecutive days, with two trials per day. Subsequently, this test was performed at bi-weekly intervals (characterisation study) or monthly (Proof-of-concept study) in the late morning. For each evaluation, the mice were tested twice, with a minimum rest period of 5 minutes between runs.

[0180] The best performance, measured as latency to fall in seconds, was used for analysis. The minimum threshold for recording rotarod activity was 3 seconds.

[0181] The CatWalk™ gait analysis system version 7.1 was used to assess gait parameters in Ap4b1-KO and WT mice. Mice were tested at 3, 6, 9 and 12 months of age. Mice were placed on the apparatus in complete darkness and their gait patterns recorded. Six unforced runs were recorded for each mouse and three selected for analysis. The runs to be analysed were selected based on the absence of behavioural anomalies-such as sniffing, exploration and rearing—and where mouse locomotion was consistent and without noticeable accelerations, decelerations or deviations from a straight line. Processing of gait data was performed with the Noldus software. Limbs were assigned manually, and gait parameters were calculated automatically. Parameter values were transferred to GraphPad Prism for statistical analysis.

[0182] Primary antibodies used in this study were mouse anti-α-tubulin (1:5000; Sigma), mouse anti-GAPDH (1:10,000; Millipore), rabbit anti-V5 (1:1000; Abcam), rabbit anti-β4 (in-house non-commercial antibody provided by J. Hirst) (1:400), rabbit anti-ATG9A (1:1000; Abcam), sheep anti-TGN46 (Bio-Rad), anti-MAP2.

[0183] Tissue was harvested from mice under terminal anaesthesia and snap frozen in liquid nitrogen. Tissue was homogenised using a dounce homogeniser in ice-cold RIPA buffer (50 mM Tris-HCL PH 7.4; 1% v/v NP-40; 0.5% w/v sodium deoxycholate; 0.1% v/v SDS; 150 mM NaCl; 2 mM EDTA) containing 1×protease inhibitor cocktail (Sigma-Aldrich). Lysate protein concentrations were determined using the BCA assay (Thermo Scientific Pierce™). 40 μg of protein lysate was denatured by heating to 100° C. for 5 minutes in the presence of 4×loading buffer (10 ml buffer contained: 240 mM Tris-HCL pH 6.8; 8% w/v SDS; 40% glycerol; 0.01% bromophenol blue; 10% β-mercaptoethanol). Lysates that were intended to be used for quantification of ATG9A protein levels were heated to 50° C., as boiling leads to aggregation of ATG9A and loss of signal. Lysates were then loaded onto 4-20% gradient mini-PROTEAN® TGX™ precast polyacrylamide gels (Bio-Rad). Gels were run at 180V in running buffer (25 mM Tris, 192 mM glycine, 0.1% SDS, pH 8.3) for approximately 50 minutes or until the dye front reached the bottom of the gel. Separated proteins were transferred by electrophoresis to an Immobilon-P PVDF membrane (Millipore) that had been pre-soaked in methanol. Protein transfer was carried out at 250 mA for 1.5 hours or 40 mA overnight in transfer buffer (25 mM Tris, 192 mM glycine, 5% v/v methanol). Membranes were blocked for 1 hour in 5% milk/TBS-T. Primary antibodies were diluted in 5% milk/TBS-T or 5% BSA/TBS-T and incubated with the membrane overnight at 4° C. After primary antibody incubation, the membrane was washed for 3×15 min each in TBS-T buffer. Secondary antibodies anti-mouse HRP (1:3000) and anti-rabbit HRP (1:3000) were diluted in 5% milk/TBS-T and incubated with the membrane for 2 hours at room temperature. After secondary antibody incubation, the membrane was washed for 3×15 min each in TBS-T buffer followed by a final 15 min wash in PBS. Protein bands were visualised using ECL Prime Western Blotting Detection Reagent (Amersham) and the G-Box imaging system (Syngene). Densitometric analysis of protein bands was carried out using Image J software.

[0184] Western blotting was generated using the following protocol: Cell lysates were extracted as above. 40 μg protein was loaded per lane on 10-well 4-12% Bis-Tris precast gel. The gel was run in 2-(N-morpholino) ethanesulfonic acid (MES) buffer and wet transferred to a nitrocellulose membrane (100 mA constant amps overnight). The membrane was blocked in 5% milk/TBS-T for 1 hour. Primary antibodies were added for 2 hours at room temperature (anti-AP4B1 1:400 in 5% BSA), followed by 4×15-minute washes in PBS-T.

[0185] Secondary antibodies were added for 30 mins at room temperature in 5% milk-TBS-T. The membrane was washed 5×5 minutes in PBS-T followed by a 30-minute-long wash in PBS. The membrane was developed with ECL Prime

[0186] Human Embryonic Kidney (HEK) 293T cells, HeLa-M/HeLa-AP4B1−/−cells (a gift from Dr J. Hirst) and human fibroblast cell lines were cultured at 37° C., 5% CO₂ in growth media consisting of Dulbecco's Modified Eagle's Medium (DMEM, Sigma) supplemented with 10% v/v Fetal Bovine Serum (FBS, Sigma, MI, US) and 1% v/v penicillin (100U/ml) and streptomycin (100U/ml) (Lonza, Basel, Switzerland).

[0187] For primary cortical neuron culture, E18 non-transgenic rat embryos and E16 mouse embryos were harvested from wild type and C57BL/6J-Ap4b1^em5Lutzy/J pregnant mice, essentially as described by (Krichevsky et al., 2001). Very briefly, the cortices were dissected and digested in 0.25% trypsin in HBSS without calcium or magnesium (GIBCO) at 37° C. for 15 minutes and dissociated manually in triturating medium by using three fire-burnt Pasteur pipettes with successively smaller openings. Dissociated cortical neurons were then plated on poly-D-lysine (SIGMA) coated plates and maintained in Neurobasal medium (Life Technologies) supplemented with 2% B27 (Life Technologies), 0.5 mM GlutaMax (Life Technologies) and 100 U/ml of penicillin and 100 μg/ml streptomycin (Lonza).

[0188] AP4B1 knockout Hela cells (HeLa-AP4B1^−/−) were provided by Dr J. Hirst, the generation of which is described in ⁹.

[0189] The AP4B1 deficient human fibroblasts from SPG47 patients, heterozygous family members, and age-matched homozygous wild type controls were gifted by Dr Henry Houlden and Dr Ivy Pin-Fang Chen.

[0190] AAV2-ITR transgene transfer plasmids-created as described above-were amplified in NEB Stable E. coli cells (New England Biolabs) and purified using Qiagen Plasmid Plus kits. Adenoviral helper genes (pHelper) and Rep-Cap genes (pAAV2/9) were supplied in trans and were obtained commercially through Plasmid Factory. Pseudotyped AAV9 viral vector was produced in-house following the protocol described in ⁶.

[0191] The size of the human AP4B1 cDNA open reading frame (2,800 bp) means that a simple gene replacement option is technically feasible and amenable to typical viral delivery approaches such as using a single-stranded adeno-associated virus (AAV) which has an insertion limit of ˜4,000 bp. We designed AAV vectors to achieve therapeutic level of transgene expression (FIG. 2A): 1) An expression cassette was developed involving the 0.8 kb CBh promoter and 130 bp SV40 poly A to drive expression of the human AP4B1. The CBh promoter has been reported to mediate efficient transgene expression in rodents and non-human primates; 2) A vector expressing an N-terminal V5 viral epitope-tagged human AP4B1 cDNA allowing in vitro and in vivo detection of AP4B1 restoration in the absence of suitable anti-AP4B1 antibodies; 3) A V5-tagged AP4B1 construct expressed from a lentiviral vector enabling in vitro validation of efficacy in cell types that are not efficiently transduced by AAV9 (e.g. fibroblasts). All constructs have been shown to efficiently express their viral cargos upon transfection or transduction in Hela cells (FIG. 2B,C), primary rat cortical neurons (FIG. 2D), and human fibroblasts (FIG. 2E) as determined by western blotting, RT-qPCR and immunocytochemistry. The viral constructs efficiently restore expression of the AP4B1 protein in both a CRISPR generated AP4B1-knockout HeLa cell line and fibroblasts from SPG47 patients lacking endogenous AP4B1 (FIG. 2 B,C,E). Expression of V5-tagged AP4B1 in SPG47 patient fibroblasts also rescues both overexpression and mis localisation of ATG9A (FIG. 3).

[0192] To select the appropriate route of delivery for optimal efficacy of the AAV9-CBh-hAP4B1 therapy in the AP4B1^−/− mouse model, we designed an in vivo experiment to test the two main delivery paradigms of gene therapies for Central Nervous System (CNS) diseases (FIG. 4): intra-CSF vs intravenous delivery. Indeed, AAV9 has been shown to cross the Blood-Brain Barrier (BBB), particularly when administered in neonates, and it has been delivered intravenously in successful pre-clinical (Valori et al., 2010) and clinical (Mendell et al., 2017) studies of CNS diseases, achieving robust therapeutical potential from this minimally invasive delivery route. However, intra-cerebrospinal fluid (CSF) delivery provides an immediate access to the CNS, therefore increasing the chance of reaching disease-target cells, for which reason it has also been used to deliver gene therapy treatments in pre-clinical (Iannitti et al., 2018) and clinical (Miller et al., 2020; Mueller et al., 2020) studies attempting to treat neurodegenerative diseases.

[0193] Based on this, we set out to assess the therapeutic efficacy of AAV9-hAP4B1 either delivered into the CSF, through injection in the cisterna magna (Intra-cisterna magna, ICM), or intravenously through injection in the facial vein (intravenous, IV), in AP4B1^−/−P2/P3. As viral control groups, we injected AAV9-V5 only (lacking the hAP4B1 transgene but containing the same CBh promoter, a V5 tag and a poly-A signal) using the same delivery routes, and we also kept wild type (WT) as well as homozygous untreated animals. Considering that our in-house characterisation of the AP4B1^−/−mouse model determined that male homozygous have a stronger disease phenotype, we decided to focus our resources by performing this experiment in males only. The following viral vectors used in this experiment were either produced in-house or outsourced to a CRO (VectorBuilder): AAV9-V5 only; AAV9-V5-hAP4B1; and AAV9-untagged hAP4B1. FIG. 4B summarizes the number of pups recruited and sacrificed for this experiment.

[0194] Upon perfusion with PBS, tissue was either processed for biochemical or histological analysis.

[0195] For biochemical tests, CNS tissue was divided into cerebrum, cerebellum and spinal cord, for a better appreciation of the therapeutic potential of the treatment in distinct and well-defined regions.

[0196] We started by tracking the viral biodistribution in the CNS of treated mice by performing qPCR on tissue-extracted genomic DNA with primers binding in the poly-A sequence, with results summarised in FIG. 4C. As determined by qPCR, cisterna magna delivery of AAV9-V5 only and AAV9-V5-hAP4B1 was far superior in transducing all the studied areas of the CNS than intravenous delivery, despite the injections having been done in neonates and AAV9 being able to cross the BBB.

[0197] Following biodistribution, we used RT-qPCR on tissue-extracted RNA with primers binding to the hAP4B1 transgene, to assess mRNA expression of the hAP4B1 transgene in the studied tissue, with results summarised in FIG. 5. In line with the results obtained from viral genome biodistribution, cisterna magna injection of AAV9-CBh-hAP4B1 was considerably superior in inducing mRNA expression of hAP4B1 in all CNS regions analysed.

[0198] A loss-of-function hypothesis for SPG47 is backed by substantial evidence, as mutations in all the other 3 subunits of the AP4 complex (AP4M1; AP4S1 and AP4E1) disrupt the normal function of the tetrameric protein and cause a very similar clinical presentation to that of SPG47. Therefore, the loss of any of its subunits appears to cause an AP4 deficiency disease, with an early onset progressive spastic paraplegia and intellectual disability as its main characteristics. To investigate whether ICM or IV delivery had restored functionality of the AP-4 complex, we extracted protein from CNS tissue and did Western blot to detect protein expression levels of another AP-4 subunit, AP4E1. Results are summarised in FIG. 7. AP4E1 expression is absent in AP4B1^−/−Homozygous untreated mice and animals treated with AAV9-V5 only, but ICM administration of AAV9-V5-hAP4B1 was successful in restoring AP4E1 protein levels in all regions of the CNS analysed, with efficiencies of ˜25% (cerebrum), ˜16% (cerebellum), and ˜36% (spinal cord) of WT levels. Intravenous delivery of AAV9-V5-hAP4B1 did not induce detectable rescue of AP4E1 expression in the cerebrum and cerebellum, whilst inducing a smaller rescue in the spinal cord than ICM injection.

[0199] Having collected substantial data from biochemical analysis of the tissue, we proceeded to do some histological analysis, namely, to check the impact of AAV9-hAP4B1 on corpus callosum thickness and enlargement of lateral ventricles in coronal sections of AP4B1-brains, other important hallmark of SPG47 (FIG. 8). Results summarised in FIG. 9 clearly demonstrate that AP4B1 gene replacement led to the rescue of corpus callosum thickness and enlargement of lateral ventricles.

[0200] We then proceeded to investigate whether AAV9-hAP4B1 would correct ATG9A mislocalisation, a well-established molecular hallmark of AP-4 neurodegenerative diseases. Immunofluorescence labelling was done on brain sections using anti-ATG9A, results summarised in FIG. 10. As expected, ATG9A shows mislocalisation in homozygous mice when comparing to WT littermates, across all CNS regions analysed. ICM delivery of AAV9-hAP4B1 was successful in correcting this phenotype in the cerebellum and brainstem (FIG. 10). Gene replacement approach was tested using CBh and Synapsin promoters.

[0201] Interestingly, our gene therapy approach led to the correction of clasping phenotype observed in Ap4b1−/−mouse model. The data are summarised in FIG. 11.

[0202] Dose response study investigating the AAV9_CBh_hAP4B1 gene treatment in SPG47 mouse model. SPG47 KO mice (ap4b1−/−) were treated with AAV9_CBh_hAP4B1 or AAV9_CBh_V5_empty vectors around P60 with cisterna magna delivery. 3 different doses of AAV9_CBh_hAP4B1 were delivered—a low-dose (6×10E10 vg), a mid-dose (8×10E10 vg) and a high-dose (1×10E11 vg). Mice are sacrificed at 2 months and 4 months of age. Mice weight and clasping phenotype was assessed weekly, and tissues were taking at 2 months for biochemical analysis and brains were fixed at 4 months for anatomical analysis (corpus callosum and lateral vertical size) and ATG9A accumulation analysis (Table 1).

TABLE 1
			Number	Number
			of mice 2	of mice 4
		Route of	months	months
Group	Treatment	delivery	timepoint	timepoint
Wildtype	Untreated	3	9
Ap4b1−/−	AAV9-Empty	Cisterna Magna	3	9
Ap4b1−/−	AAV9-CBh-	Cisterna Magna	3	9
	hAP4B1
	(dose 1 low)
Ap4b1−/−	AAV9-CBh-	Cisterna Magna	3	9
	hAP4B1
	(dose 2 mid)
Ap4b1−/−	AAV9-CBh-	Cisterna Magna	3	9
	hAP4B1
	(dose 3 high)

[0203] Treated mice show no adverse effect on weight gain (see FIG. 15). Clasping data displays a progression of hind limb clasping severity over time in SPG47 mice untreated and V5-ony treated (control). Wildtype mice do not show a clasping phenotype with age. Treatment with all 3 doses show a reduction in hind limb clasping severity progression over time (see FIG. 16). Low-dose treatment gives a 86% rescue of hind limb clasping severity at the 120 day timepoint. 76% rescue for mid-dose and a 55% rescue at high-dose treatment.

[0204] Data on rotarod performance at 6 months of age (4 months post injection). This data displays a possible rescue of this phenotype with both the mid- and high-dose treatments. See FIG. 17.

[0205] Here we have measured brain weight immediately after dissection of the sacrificed mice. Treated mice (V5-only) have significantly reduce brain weight compared to that of the wildtypes in females at 2 months post treatment. This data suggests a rescue of this brain weight phenotype when treated of all 3 doses (see FIG. 18A); 98% rescue at the low-dose, 85% rescue at the mid-dose and 96% rescue at high-dose treatment. Brain weight measured in males at 4 months post injection show data of a similar pattern. (see FIG. 18B).

[0206] Corpus callosum measurements were taken over 8 consistent positions within the brains of treated mice. Corpus callosum thickness varies over these positions. SPG47 control treated mice (V5-only) show a reduced corpus callosum thickness (orange data set) compared to wildtype (blue data set). AAV9_Cbh_hAP4B1 high dose treated mice displays a rescue of the corpus callosum thickness to wild type levels (see FIG. 19).

[0207] Impact of AAV9-AP4B1 gene replacement on neurofilament L (NFL) levels in cerebrospinal fluid (CSF) and Plasma. As shown in FIG. 19 Ap4b1−/−mice treated with AAV9-CBh-AP4B1 and AAV9-Synapsin 1-AP4B1 vector showed reduction of NFL levels in mice to similar levels seen in wildtype both in CSF and Plasma. The intreated mice shown increased levels when compared to wild type. This indicates that the vector can effectively reduce neurofilament levels in patients lacking AP4B1.

• [0208] 1 Harvard SPG47 registry, managed by Dr Darius Ebrahimi-Fakhari, accessed October 2020.
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