BACKGROUND OF THE INVENTION

1. TECHNICAL FIELD

[0001] The present invention relates to methods of performing clinical trials with the purpose of determining safety and tolerability while obtaining confirmation of mechanism-of-action and further obtaining dosing information to guide the design of subsequent clinical trials. More specifically, the present invention relates to methods of performing clinical trials with gene therapeutics.

2. BACKGROUND ART

[0002] Clinical trials with human participants are required by the Federal Drug Administration (FDA) in order for it to approve the safety and effectiveness of a medical treatment. Clinical trials are required for all new drugs, biologies, gene therapies, dietary supplements, and medical devices. Generally, a small pilot study is performed first and subsequently larger studies are performed. The human participants usually are suffering from some medical condition that the new treatment is designed to remedy. If it is found that the benefits of the new treatment outweigh the risks, the FDA will approve the new treatment for its intended use.

[0003] To date, no gene therapeutics have been approved by the FDA, although many are being studied in clinical trials. The first clinical trial for a CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats) has just recently been approved to begin in order to determine whether CRISPR is safe to use in humans. CRISPR-Cas9 is a gene editing system derived from microbial organisms that can be used to insert, delete, or otherwise mutate an organism's genome by the use of nucleases. Three types (l-lll) of CRISPR systems have been identified. CRISPR clusters contain spacers, the sequences complementary to antecedent mobile elements. CRISPR clusters are transcribed and processed into mature CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) RNA (crRNA). The CRISPR-associated endonuclease, Cas9, belongs to the type II CRISPR/Cas system and has strong endonuclease activity permitting the cutting of target DNA. Cas9 is guided by a mature crRNA that contains about 20 base pairs (bp) of unique target sequence (called spacer) and a trans-activated small RNA (tracrRNA) that serves as a guide for ribonuclease Ill-aided processing of pre-crRNA. The crRNA:tracrRNA duplex directs Cas9 to target DNA via complementary base pairing between the spacer on the crRNA and the complementary sequence (called protospacer) on the target DNA. Cas9 recognizes a trinucleotide (NGG) protospacer adjacent motif (PAM) to specify the cut site (the 3rd nucleotide from PAM). The crRNA and tracrRNA can be expressed separately or can be engineered into an artificial fusion small guide RNA (sgRNA) via a synthetic stem loop (AGAAAU) in order to mimic the natural crRNA/tracrRNA duplex. Such sgRNA, like shRNA, can be synthesized or can be transcribed in vitro for direct RNA transfection or can be expressed from a U6 or Hl-promoted RNA expression vector, although cleavage efficiencies of the artificial sgRNA are lower than those for systems with the crRNA and tracrRNA expressed separately. Other companies pursuing CRISPR and CRISPR-like technologies, including CRISPR Inc. (Basel, Switzerland), Editas (Cambridge MA), and Caribou (Berkeley CA) are utilizing these technologies to create specific gene edits or block gene expression as opposed to deleting large segments of a viral genome.

[0004] CRISPR can be used in treating many different viruses by inactivating the viruses or by deleting the viral genome from the host's DNA. For example, U.S. Patent Application No. 14/838,057 to Khalili, et al. discloses a method of inactivating a proviral DNA integrated into the genome of a host cell latently infected with a retrovirus, including the steps of: treating the host cell with a composition comprising a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated endonuclease, and two or more different guide RNAs (gRNAs), wherein each of the at least two gRNAs is complementary to a different target nucleic acid sequence in a long terminal repeat (LTR) of the proviral DNA; and inactivating the proviral DNA. Preferably, the proviral DNA being inactivated is human immunodeficiency virus (HIV).

[0005] There remains a need for a clinical trial design for CRISPR gene editing systems, especially as a treatment for HIV.

SUMMARY OF THE INVENTION

[0006] The present invention provides for a method of performing a clinical trial for a gene editing or gene excising system for treating HIV in humans, by recruiting HIV infected individuals currently receiving highly active antiretroviral therapy (HAART) that is effective in lowering viral load, administering the gene editing or gene excising system treatment to the individuals in Phase la, Phase lb, and Phase lc, and performing assays to confirm HIV viral genome excision from the individuals' cells.

DETAILED DESCRIPTION OF THE INVENTION

[0007] The present invention provides for methods of performing a clinical trial for a gene editing or gene excising system to treat HIV in humans. The method includes recruiting HIV infected individuals currently receiving and responding well to highly active antiretroviral therapy (HAART) (i.e. it is effective in lowering viral load), administering the gene editing or gene excising system treatment to the individuals in Phase la, Phase lb, and Phase lc, and performing assays to confirm HIV viral genome excision from the individuals' cells.

[0008] Preferably, (but not limited to) the gene editing or gene excising system is a CRISPR system or Argonaute system and effectively excises the entire genome of HIV from the host cells. Most preferably, the treatment is EBT101 (CRISPR-Cas9 system using at least two gRNAs targeting the U3 region of the 3' and 5' LTR (long terminal repeat sequence)), and the Gag and Pol genes of the HIV- 1 pro and non-integrated virus.

[0009] "Nuclease" as used herein, refers to an enzyme that is able to cleave the phosphodiester bonds between nucleotide subunits of nucleic acids.

[00010] The CRISPR system can use a Cas nuclease (such as Cas9) or a Cpfl nuclease, or any other suitable nuclease that is able to target DNA or RNA and make additions, deletions, mutations, and preferably excisions of entire genes or gene clusters.

[00011] The Argonaute system is an RNA-guided or DNA-guided endonuclease enzyme that is able to cleave any sequence complementary to guide RNA or guide DNA. Argonaute proteins are proteins of the PIWI protein superfamily that contain a PIWI (P element-induced wimpy testis) domain, a MID (middle) domain, a PAZ (Piwi-Argonaute-Zwille) domain and an N-terminal domain. Argonaute proteins are capable of binding small RNAs, such as microRNAs, small interfering RNAs (siRNAs), and Piwi-interacting RNAs. Argonaute proteins can be guided to target sequences with these RNAs in order to cleave mRNA, inhibit translation, or induce mRNA degradation in the target sequence. Natronobacterium gregoryi Argonaute (NgAgo) is a DNA-guided endonuclease suitable for genome editing in human cells.

[00012] The method extends through the end of Phase 1 to establish safety, tolerability, and effective excision/deletion Mechanism-of-Action by way of existing standard PCR assays and ELISA assays used in current clinical studies. A biochemical metabolomics based Mass Spectrometry/NMR diagnostics assay can be used in parallel with the standard PCR assays and ELISA assays to validate the metabolomics assays increased sensitivity, specificity, selectivity, robustness and precision for future use as an independent companion diagnostic. This assay is further described below.

[00013] These trials can recruit HIV infected individuals who are responding well to HAART (highly active antiretroviral therapy) (i.e. the HAART treatments are effective) as measured by (1) no viral replication, (2) no viral load, and (3) healthy CD4 T cell counts. The HAART treatments which the individuals are currently taking can be nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, protease inhibitors, fusion inhibitors, integrase inhibitors, CCR5 antagonists, or combinations thereof.

[00014] Phase la includes 6-18 individuals treated with up to three different doses of the treatment (EBT101). Endpoints for this Phase la trial include (i) safety and tolerability and (ii) efficacy and accuracy of viral DNA excision as indexed by molecular biomarker analysis (PCR assays). The molecular assay provides information relating to the efficacy of the CRISPR therapeutic in a nonclinical phenotype-dependent manner. This efficacy data will be used to guide the design of the Phase lb trial.

[00015] Phase lb includes up to 32 individuals treated in four equal cohorts: (i) single low dose, (ii) single high dose (0.5 to 1 log above low dose), (iii) two doses with a separation in time of 1-5 days, and (iv) placebo. As before, safety and tolerability are the primary endpoints and blood leukapheresis samples can be tested for the proper excision of the HIV genome using the PCR assay. An optimal dose can be determined by these trials. Phase lc tests EBT101 in 24-32 individuals in three cohorts: (1) 12-16 placebo, (2) 6-8 optimal dose (from Phase lb) and (3) 6-8 at a 0.5log higher dose than the Phase lb optimal dose. As before, safety and tolerability are the primary endpoints. Blood leukapheresis samples can be tested for the proper excision of the HIV genome using the PCR assay.

In an analysis of the effectiveness of the gene editing or gene excising treatment, various assays can be performed to confirm HIV viral genome excision from the cells of the individuals in the trial. Gl tract mucosal lymph node biopsies can be taken to test for HIV genome excision (molecular determination to be made in 1-2 days). Blood leukapheresis can be performed to test circulating T cells for HIV genome excision (molecular determination to be made in 1-2 days).

[00016] The assays as described above in Phases la-lc can include using a diagnostic panel to determine the effectiveness of the gene editing or excising treatment, as described in U.S. Provisional Patent Application No. 62/340,624. The diagnostic panel is able to detect biomarkers or metabolites indicative of the presence of a virus (HIV) that currently used PCR and ELISA assays in clinical trials are not able to detect. A sample can be taken from the individuals in the clinical trial at any point during the trial as necessary, the sample is applied to the diagnostic panel including at least one biomarker indicative of HIV, detecting the presence of at least one biomarker, comparing levels of the biomarker to a baseline, and determining if the treatment (EBTlOl) is working to reverse or prevent the HIV. The diagnostic panel can confirm that the HIV genome has been excised from the individuals' cells in the clinical trial. A baseline of healthy individuals can be chosen to compare to metabolite levels in individuals in the clinical trial. The metabolites can be measured in individuals having HIV in the clinical trial that are on HAART both before treatment begins and after treatment (at any point in the trial) to determine if the treatment is working.

[00017] The biomarkers are preferably metabolites that are indicative of the presence of a disease, and especially a virus (HIV). Metabolites are those chemicals (generally less than 1,000 Da) that are involved in cellular reactions for energy production, growth, development, signaling and reproduction, and can be taken up, or released from cells according to cellular needs. These chemicals include sugars, amino acids, organic acids, as well as xenobiotic compounds. Metabolomics (or metabonomics as it is sometimes referred), is dedicated to the study of all metabolites in a cell or system and changes that might result from an internal or external stress such as an infection, disease state, or exposure to a toxin. Metabolic changes can result from changes in the chemical reactions that use these metabolites (i.e. metabolic pathways), or the transporters that take up or release these metabolites. Infection of a person by a virus or bacterium causes major changes both at the cellular level (the site of infection), and systemically (through the innate immune response). These responses include, but are not limited to, signaling of specific immune cells, signaling of apoptosis, changes in transporters, as well as changes in mitochondrial function and energy production - changes that can be observed as changes in metabolite concentrations at the cellular level, and systemically in the blood or urine.

[00018] The metabolites can include, but are not limited to, 1,3-dimethylurate, levoglucosan, 1- methylnicotinamide, metabolite 1, 2-hydroxyisobutyrate, 2-oxoglutarate, 3-aminoisobutyrate, 3- hydroxybutyrate, 3-hydroxyisovalerate, 3-indoxylsulfate, 4-hydroxyphenylacetate, 4- hydroxyphenyllactate, 4-pyridoxate, acetate, acetoacetate, acetone, adipate, alanine, allantoin, asparagine, betaine, carnitine, citrate, creatine, creatinine, dimethylamine, ethanolamine, formate, fucose, fumarate, glucose, glutamine, glycine, metabolite 2, metabolite 3, hippurate, histidine, hypoxanthine, isoleucine, lactate, leucine, lysine, mannitol, metabolite 4, metabolite 5 (which may be methylamine), metabolite 6 (which may be methylguanidine), Ν,Ν-dimethylglycine, O-acetylcarnitine, pantothenate, propylene glycol, pyroglutamate, pyruvate, quinolinate, serine, succinate, sucrose, metabolite 7 (which may be tartrate), taurine, threonine, trigonelline, trimethylamine-N-oxide, tryptophan, tyrosine, uracil, urea, valine, xylose, cis-aconitate, myo-inositol, trans-aconitate, 1- methylhistidine, 3-methylhistidine, ascorbate, phenylacetylglutamine, 4-hydroxyproline, gluconate, galactose, galactitol, galactonate, lactose, phenylalanine, proline betaine, trimethylamine, butyrate, propionate, isopropanol, mannose, 3-methylxanthine, ethanol, benzoate, glutamate, or glycerol.

[00019] The metabolite can also be any from the following metabolic cycles:

[00020] Polypurine: guanosine, guanine, xanthine, uric acid, adenosine, inosine, inosinic acid, hypoxanthine, xanthine, C02, H20, urea, N-carboamoyl- -alanine, beta-alanine, ammonia, and β- aminoisobutyrate.

[00021] Polyamines: putrescine, spermidine, spermine, methionine, S-adenosylmethionine, decarboxylated S-adenosylmethionine, arginine, ornithine, putrescine, Nl-acetylspermidine, Nl- acetylspermine, elF5A(Lys), elF5A(Dhp), elF5A(Hpu), NlN2-diacetylspermine, 3-aminopropanal, 3- acetylaminopropanal, acrolein, and FDP-lysine protein.

[00022] KREBS/TCA cycle: threo-Ds-isocitrate, oxalo-succinate, 2-oxo-glutarate, oxalo-acetate, L- glutamate, 2-hydroxy-glutarate, pyruvate, acetyl-CoA, cis-Aconitate, D-isocitrate, a-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, glycine, citrate, carnitine, (-)O-acetyl-carnitine, cis- aconitate, itaconate, glycolate, glyoxylate, oxalate, oxalyl-CoA, formate, formyl-CoA, and C0 ₂ .

[00023] Glycolysis and gluconeogenesis: glucose, glucose 6-phosphate (G6P), fructose 6- phosphate (F6P), fructose 1,6-biphosphate (F1,6BP), glyceraldehyde 3-phosphate (GADP), dihydroxyacetone phosphate (DHAP), 1,3-bisphosphoglyceric acid (1,3BPG), 3-phosphoglyceric acid (3PG), 2-phosphoglyceric acid (2PG), phosphoenolpyruvic acid (PEP), pyruvate, D-glucose, D-glucono- 1,5-lactone, D-gluconate, oc-D-mannose 6-P, D-mannose, D-fructose, D-sorbitol, glycerone-P, sn- glycerol-3P, glycerol, D-glyceraldehyde, 1,2 propane-diol, 2-hydroxypropionaldehyde, 3-P-serine, 3-P- hydroxypyruvate, D-glycerate, hydroxypyruvate, L-alanine, L-alanyl-tRNA, L-glutamate, 2-oxoglutarate, L-lactate, and D-lactate. [00024] Oxidative phosphorylation: adenosine triphosphate (ATP), adenosine diphosphate (ADP), H+, succinate, fumarate, H ₂ 0, 0 ₂ , NADH, and NAD+.

[00025] Pentose phosphate: glucose-6-phosphate, NADP+, NADPH, 6-phosphogluconolatone, H ₂ 0, H+, 6-phosphogluconate, C0 ₂ , ribulose-5-phosphate, ribose-5-phosphate, xylulose-5-phosphate, glyceraldehyde 3-phosphate, sedoheptulose 7-phosphate, fructose 6-phosphate, erythrose 4- phosphate, and xylulose 5-phosphate, D-ribulose, D-ribitol, D-ribose, L-ribulose, sedoheptulose 1,7P ₂ , 3-oxo-6-P-hexulose.

[00026] Urea cycle: L-ornithine, carbamoyl phosphate, L-citrulline, argininosuccinate, fumarate, L-arginine, urea, L-aspartate, adenosine diphosphate (ADP), adenosine monophosphate (AMP), and pyrophosphate.

[00027] Fatty acid β-oxidation: trans-A ² -enoyl-CoA, L^-hydroxyacyl CoA, β-ketoacyl CoA,

FADH2, NADH, acetyl-CoA, acyl-CoA, propionyl-CoA, and succinyl-CoA.

[00028] Nucleotide metabolism: AMP, inosine monophosphate (IMP), xanthosine monophosphate (XMP), guanosine monophosphate (GMP), ribose-5-phosphate, adenosine, inosine, hypoxanthine, xanthosine, xanthine, guanosine, guanine, uric acid, fumarate, adenylosuccinate, uridine, uridine monophosphate (UMP), ADP, thymidine, thymine, deoxyribose-l-phosphate, deoxythymidine monophosphate (dTMP), deoxycytidine, ATP, and deoxycytidine monophosphate (dCMP).

[00029] Cofactors and vitamins: retinyl palmitate, palmitate, palmityl-CoA, retinoate, β- glucuronide, retinal, β-carotene, retinoic acid, calcidiol, 25-hydroyergocalciferol, calcitriol, methylcobalamin, 5'-deoxyadenosylcobalamin, -CECH, NAD+, NADH, ADP, and ATP.

[00030] Amino acid metabolism: glutamate, NH4+, a-ketoglutarate, pyruvate, oxaloacetate, glutamate γ-semialdehyde, A ¹ -pyrroline-5-carboxylate, citrulline, arginine, urea, ornithine, glycine, C02, NH3, N ⁵ ,N ¹⁰ -methyleneTHF, 3-phosphoglycerate, a-ketobutyrate, propionyl-CoA, succinyl-CoA, acetyl-CoA, serine, a-amino- -ketobutyrate, aminoacetone, cysteine sulfinate, β-sulfinylpyruvate, bisulfite, sulfite, sulfate, alanine, glutathione, taurine, hypotaurine, adenosine 5'-phosphosulfate, 3'- phosphoadenosine 5'-phosphosulfate, homocysteine, oc-keto-P-methylvalerate, a-ketoisocaproate, oc- ketoisovalerate, a-methylbutyryl-CoA, tiglyl-CoA, 3-methyl-3-hydroxybutyryl-CoA, 2- methylacetoacetyl-CoA, isovaleryl-CoA, 3-methylcrotonyl-CoA, 3-methylglutaconyl-CoA, 3-hydroxy-3- methylglutaryl-CoA, acetoacetate, isobutyryl CoA, methacrylyl-CoA, 3-hydroxyisobutyryl-CoA, methylmalonic semialdehyde, tyrosine, p-hydroxyphenylpyruvate, homogentisate, 4- maleylacetoacetate, 4-fumarylacetoacetate, fumarate, 3-hydroxytrimethyllysine, 4-N- trimethylaminobutyraldehyde, γ-butyrobetaine, carnitine, urocanate, 4-imidazolone-5-propionate, N- formimidoyl-L-glutamate, N ⁵ -formimino-tetrahydrofolate, histamine, N-formyl-kynurenine, kynurenine, kynurenate, 3-hydroxykynurenine, anthranilate, 3-hydroxyanthranilate, quinolinate, glutaryl-CoA, and acetoacetyl-CoA.

[00031] A single metabolite can be used, as well as any combination of metabolites in determining disease state.

[00032] Various methods can be used to detect the presence of the biomarkers, such as, but not limited to, liquid chromatography, gas chromatography, liquid chromatography - mass spectrometry, gas chromatography - mass spectrometry, high performance liquid chromatography - mass spectrometry, capillary electrophoresis - mass spectrometry, nuclear magnetic resonance spectrometry (NMR), raman spectroscopy, or infrared spectroscopy.

[00033] A 15-day to 6-month (preferably 30-day) follow-up can be performed for safety and tolerability. Also, individuals will not be weaned from anti-viral (HAART) therapy that they are currently taking and can remain on the HAART throughout the clinical trial.

[00034] Throughout this application, various publications, including United States patents, are referenced by author and year and patents by number. Full citations for the publications are listed below. The disclosures of these publications and patents in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.

[00035] The invention has been described in an illustrative manner, and it is to be understood that the terminology, which has been used is intended to be in the nature of words of description rather than of limitation.

[00036] Obviously, many modifications and variations of the present invention are possible in light of the above teachings. It is, therefore, to be understood that within the scope of the appended claims, the invention can be practiced otherwise than as specifically described.