Systemic RNAi Therapuetics for the Treatment of HIV-1 Prof. John J. Rossi

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1 Systemic RNA Interference (RNAi) Therapeutics for the of HIV-1 John J. Rossi, Professor and chairman Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope Duarte California 1 2 Typical Course of HIV infection 3 1

2 Why do we need new HIV drugs? HIV infection is chronic and lifelong treatment required Increasing number of patients with drug resistant virus few if any options Toxicities of current chemotherapy agents (in Highly Active Anti-Retroviral Therapy cocktail) Difficult dosing regimens for patients, and drugs must be taken daily Gene and/or systemic small RNA therapies could replace or be used as adjuvants for chemotherapy 4 Major goals of anti-hiv therapies Reduce viral load Use combination therapies to mitigate emergence of drug resistant viral mutants Prevent CD4 T-cell decline If possible, eradicate latent viral reservoirs 5 Combinatorial RNA based therapy for HIV Most efficacious drug therapy for HIV uses combination of two or three drugs targeting HIV RT and protease; Combinations prolong and sometimes prevent resistant viral variants We hypothesized that it should be possible to develop effective small RNA based combinatorial therapies 6 2

Applying RNAi for the treatment of human diseases Powerful mechanism for targeted inhibition of gene

Amenable to systemic delivery or a gene therapy approach 7 Challenge - treat HIV infection by systemic

RNA(-) PAMAM dendrimer (+) Cooperative electrostatic interactions 8 Nanoparticles for internalization

ligands (proteins, carbohydrates, other nucleic acids) with high affinities, similar to antibodies

3 Applying RNAi for the treatment of human diseases Powerful mechanism for targeted inhibition of gene expression Only a two dimensional design (Watson-Crick base pairing) is required for drug design Amenable to systemic delivery or a gene therapy approach 7 Challenge - treat HIV infection by systemic delivery of small RNAs sirna PAMAM dendrimers delivery RNA Ba Selective delivery Aptamer sirna (21 nt) RNA(-) PAMAM dendrimer (+) Cooperative electrostatic interactions 8 Nanoparticles for internalization RNA/dendrimer complex for scrna delivery Aptamers In vitro evolved nucleic acids that bind to selected ligands (proteins, carbohydrates, other nucleic acids) with high affinities, similar to antibodies Selection process involves use of libraries of random sequences to select tight binders out of as many as molecules 9 3

T7 PGGGAGGACGAUGCGG - N20-40 CAGACGACUCGCCCGA - Protein/RNA library mixture Random RNA library A New RNA library for next cycle F Protein/RNA 10-15 cycle B complex Aptamers Clone and sequence

HIV infection We evolved RNA aptamers that selectively bind to the HIV envelope protein gp 120; The binding neutralizes a broad range of viral isolates (Zhou et al.

4 T7 PGGGAGGACGAUGCGG - N20-40 CAGACGACUCGCCCGA - Protein/RNA library mixture Random RNA library A New RNA library for next cycle F Protein/RNA cycle B complex Aptamers Clone and sequence Nitrocellulose membrane Elute E Transcription Bound RNA (Aptamer) RT-PCR D 10 Nitrocellulose-based in vitro SELEX C Unbound RNA pool Targeted delivery using dual function Aptamer- sirna treatment of HIV infection We evolved RNA aptamers that selectively bind to the HIV envelope protein gp 120; The binding neutralizes a broad range of viral isolates (Zhou et al., NAR, 2009) The gp120 aptamer has also been developed as a delivery vehicle of anti-hiv sirnas to HIV infected cells expressing envelope at the cell surface (Zhou et al., Molecular Therapy, 2008, Nuc. Acids Res., 2009) making dual function inhibitors 11 Bound RNA (%) Gp 120 binding affinities of individual RNA aptamer Gel shift assay 80% A-1 70% B-68 A-28 50% A-12 40% A-9 30% A-5 20% 10% 0% Concentration of gp120 (nm) Figure 2 C: specific binding affinity Aptamer + HIV-1 Bal gp120 protein (nm) A-1 B Predicted secondary structures K D (nm) A-1 B ±7.02 nm K D (nm) ±18.77 nm 12 4

Chimeric-siRNA aptamer uptake into gp120 expressing cells CHO-WT gp160 + Cy3-labled Chimeras A-1 10 min 2 h 3 h 4 h 5 h CHO-EE control + Cy3-labled Chimeras A-1 10 min 2 h 3 h 4 h 5

secondary Ab Controls: infected plus tat/rev sirna-cy3; Uninfected plus aptamer-sirna-cy3 14 Brightfield Cy3 (red) HIV-1 p17 (FITC green) Nuclear (DAPI blue) HIV HIV-1 infected CEM

5 Chimeric-siRNA aptamer uptake into gp120 expressing cells CHO-WT gp160 + Cy3-labled Chimeras A-1 10 min 2 h 3 h 4 h 5 h CHO-EE control + Cy3-labled Chimeras A-1 10 min 2 h 3 h 4 h 5 h 13 Anti-gp120 aptamer - only taken up by HIV infected cells Infect CEM cells with NL4-3- Treat with aptamer-labeled with CY3 Treat cells with anti-p17 antibody-fitc labeled secondary Ab Controls: infected plus tat/rev sirna-cy3; Uninfected plus aptamer-sirna-cy3 14 Brightfield Cy3 (red) HIV-1 p17 (FITC green) Nuclear (DAPI blue) HIV HIV-1 infected CEM alone HIV+Apt. Merged (Cy3 and FITC) HIV-1 infected CEM + Cy3-A-1 HIV+ sirna only HIV-1 infected CEM + Cy3- Tat/rev DsiRNA Merged (Cy3 and DAPI) Apt, No HIV Un-infected CEM + Cy3-A

Aptamer-targeted RNA interference for HIV-1 therapy Amy Yan and Andrew Ellington, A Hitchhiker s Guide to HIV, vol. 16, 1356-1358, (2008) J. H. Zhou, H. T. Li, S. Li, J. Zaia, J.

, (2009) 16 Aptamer and aptamer chimera mediated inhibition of HIV-1 in PBMCs and Cultured T-lymphocytes HIV IIIB-CEM cells BaL-CD4 PBMC HIV-1 p24 expression (pg/ml) 1.3 10 6 7 days 1.0 10 6 7.

6 Aptamer-targeted RNA interference for HIV-1 therapy Amy Yan and Andrew Ellington, A Hitchhiker s Guide to HIV, vol. 16, , (2008) J. H. Zhou, H. T. Li, S. Li, J. Zaia, J. Rossi, Molecular Ther.,(2008) J. H. Zhou, C. P. Neff, P. Swiderski, H. T. Li, J. Zhang, R. Akkina, J. J. Rossi, Nucleic Acid Res., (2009) 16 Aptamer and aptamer chimera mediated inhibition of HIV-1 in PBMCs and Cultured T-lymphocytes HIV IIIB-CEM cells BaL-CD4 PBMC HIV-1 p24 expression (pg/ml) days HIV-1 p24 expression (pg/ml) days Small animal model for studying anti-hiv RNAi based therapies 18 Rag2 / γc / (RAG-hu) mice with a capacity for multilineage human hematopoietic cell engraftment P.W. Denton, J. V. Garcia, Novel humanized murine models for HIV research. Curr. HIV/AIDS Rep. 6, 13 19, 2009 HIV-1 infected RAG-hu mice can sustain chronic viremia lasting for more than a year HIV -1 infected animals display a continuous declining trend of CD4+ T cell levels, mirroring the main features of human HIV-1 infection Thus, the RAG-hu mouse model of HIV-1 infection is an excellent model for in vivo pathogenesis studies and the evaluation of new anti-hiv therapeutic strategies (Neff et al., Science Translational Medicine, 2011) 6

In vivo testing of aptamer-sirna chimera in humanized RAG-hu mice Rag2-/-gamma c-/- mouse 3-5 weeks HIV NL4-3 infection infection 3 to 5 weekly injections of aptamer, sirna Injection 5 Chimeras A-1

al., Science Translational Medicine,2011 Both aptamer and aptamer chimera inhibit HIV infection start end start end Viral load (RNA copies/ml plasma) Viral load (RNA copies/ml plasma) Time after

, STM, 2011 sirna enhances duration of anti-hiv activity over aptamer alone Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 1 1 1 1 1 1 1 1 1 1 1 1 J570

7 In vivo testing of aptamer-sirna chimera in humanized RAG-hu mice Rag2-/-gamma c-/- mouse 3-5 weeks HIV NL4-3 infection infection 3 to 5 weekly injections of aptamer, sirna Injection 5 Chimeras A-1 th week 6 th week 7 th week 8 th week Control RNAs 1 th week infection Untreated 19 The humanized Rag2-/-γc-/- mice (RAG-hu) engrafted with CD34 hematopoietic progenitor cells were infected with HIV-1 NL4.3 virus intraperitonially One injection of 10 μg experimental RNA per week 1-9 weeks samples for viral loading test monitored by real-time PCR 5 th week sample for sirna and Tat/rev detection Neff et al., Science Translational Medicine,2011 Both aptamer and aptamer chimera inhibit HIV infection start end start end Viral load (RNA copies/ml plasma) Viral load (RNA copies/ml plasma) Time after infection with HIV (week) Time after infection with HIV (week) 20 Neff et al., STM, 2011 sirna enhances duration of anti-hiv activity over aptamer alone Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week J570 Uninfected J Control J Average Nontreated Mutant Chimera A-5 Aptamer A-1 Chimera A-1 J J J Average J J J Average J J J Average J J J Average

22 Aptamer and chimeric aptamer-sirna prevent

T cell ratio (%) CD4-CD3 T cell ratio (%) Time

Infection with HIV (week) 23 Neff et al.

aptamer - that allows separate synthesis of

used for multiplexing sirnas Internalization

8 22 Aptamer and chimeric aptamer-sirna prevent CD4+ cell decline start end start end CD4-CD3 T cell ratio (%) CD4-CD3 T cell ratio (%) Time after Infection with HIV (week) Time after Infection with HIV (week) 23 Neff et al., STM, 2011 Modular chemically synthesized aptamer - that allows separate synthesis of aptamer and dicer substrate sirnas; Can be used for multiplexing sirnas Internalization in CHO-gp160 cells of aptamer-stick-sirna 10 min incubation Before nuclear staining Overnight incubation Before nuclear staining After nuclear staining 24 8

9 Multiplexed aptamer-dsirnas down regulate multiplexed targets in humanized mouse model RNA knockdown in PBMCs after second round of injection in individual mice 150% 120% Tat/rev expression CD4 expression TNPO3 expression Relative expression 90% 30% 25 0% J472 J473 J474 J481 J484 J432 J433 J434 J435 No RT Aptamer-stick-cocktailed sirna Naked sirna Control 1.00E E+05 HIV-1 viral loads Log averages Five injections *1 *2 1.00E+04 *3 Copy number 1.00E E+02 Five injections *11 *14 *14.5 *15 *16 * E+01 Reinjections E+00 Non-infected Non-treatment Naked sirna Aptamer-stick-cocktailed sirna One injection of 0.25 nmol (10 μg) experimental RNA per week Five injections were performed from 1 week to 5 week Two more injections were performed at *12.5 week and *13.5 week (re-treatment: aptamer-cocktail sirnas) Can aptamer deliver cytotoxic sirnas to kill HIV infected cells? ELAC-tRNAse 3 target Relative Abs. at 490 nm MTS assay (PBMCs and NL4-3) 3 days, 400 nm 120% 7 days, 400 nm 100% 80% 40% 20% 5 0% ELAC2 DsiRNA A (25/27-mer) Sense Antisense ELAC2 DsiRNA B (27/25-mer) Sense Antisense A-1-ELAC2 site 2 25/27-mer sirna Bluntchimera A U8 linker Sense UUUUUUUU 3 Dicer 5 Antisense 21 nt A-1-ELAC2 site 2 25/27-mer sirna OVH chimera B U2 linker Sense 27 5 UU Antisense 21 nt 3 5 Dicer 9

28 Summary of aptamer studies Once a week intravenous injections of 10 μg/animal of anti-gp120 aptamer-sirna chimeras provided long term inhibition of HIV-1 replication in a humanized mouse model of

target knockdown and inhibition of HIV in the humanized mice The aptamer approach presents the possibility of purging HIV infected cells via selective delivery of cyto-toxic sirnas to HIV infected

10 28 Summary of aptamer studies Once a week intravenous injections of 10 μg/animal of anti-gp120 aptamer-sirna chimeras provided long term inhibition of HIV-1 replication in a humanized mouse model of HIV infection Aptamer-siRNA chimeras provide dual function inhibition A synthetic version of the anti-gp120 aptamer with a stickybridge sequence allowed mixing of a cocktail of sirnas for effective target knockdown and inhibition of HIV in the humanized mice The aptamer approach presents the possibility of purging HIV infected cells via selective delivery of cyto-toxic sirnas to HIV infected cells Flexible PAMAM dendrimers with a triethanolamine core (for clarity, G3 dendrimer as an example) 29 Dendrimers plus sirnas form nanoparticles, protect sirna from degradation and deliver sirnas to T-lymphocytes Formation of G5-siRNA complexes gel shift assay G5 + sirna complex TEM image of G5-siRNA nanoparticles N/P ratio 100 nm RNase resistance of G5-siRNA complexes sirna stability Cy3 sirna into T-lymphocytes G5-siRNA complex (N/P ratio of 5) 30 Zhou et al., Molecular Therapy,2011. and unpublished 10

11 Relative expression (%) 120% 100% 80% 40% 20% 0% CD4 expression (PBMCs) G5 dendrimer delivered sirnas down regulate target mrnas in vitro Tat/rev expression (HIV-1 infected CEM cells) Relative expression (%) 120% 100% 80% 40% 20% 0% 31 15min 24h In vivo distribution and cryosection observation of G5 dendrimer-cy5 sirna complexes 1h 36h 4h 48h Yuanyu Huang, Quan Du, and Zicai Liang, Institute of Molecular Medicine, Peking University Zhou et al., Molecular Therapy, Multiplex sirnas for HIV-1 treatment Anti-HIV tat/rev sirna The Tat and Rev regulatory proteins encoded by HIV-1 are both expressed early in the viral life cycle and are both essential for viral replication Anti-CD4 sirna Primary receptor required for HIV entry Anti-TNPO3 sirna TNPO3 is required for nuclear import of the HIV-1 preintegration complex (PIC) 33 11

12 In vivo analyses of G5 dendrimer delivered sirnas Cocktail of three (TNPO3, tat/rev, CD4) Dendrimer-tat/rev alone Dendrimer-mutant non-functional tat/rev sirna Uncomplexed combination of sirnas Dendrimer alone 34 Humanized Rag2-/-γc-/- mice (RAG-hu), injected with human CD34+ hematopoietic progenitor cells-differentiate in T-cells, macrophages, monocytes, dendritic cells Dendrimer-siRNAs injection HIV NL4-3 infection 3 weeks infection 1 st week injection Naked sirna 2nd week 1st week 3rd week 4th week 2nd week 1 st week infection Untreated 5th week 4th week HIV-1 infection 1 st injection 2 nd 3 rd 4 rd 5 th Re-treatment at *12.5 and *13.5 week -2 week -3 week 0 week 1 week 2 week 3 week 4 week -1 week 5 week *1 week *2 week *19 week Collect samples for assay mg/kg injected per animal Targeted mrna reductions in Dendrimer/siRNA treated animals following second and third injections 140% Second week Relative expression % 100% 80% 40% 20% 0% Tat/rev expression CD4 expression TNPO3 expression Zhou et al., Molecular Therapy,2011 Relative expression 120% 100% 80% 40% 20% 0% Third week 12

Reductions in HIV loads following dendrimer sirna injections

complexes protect HIV infected RAG-hu mice from CD4 T cell loss

First injection Last injection -8-3 -2 1 3 5 *2 *4 *6 *11 Weeks

13 Reductions in HIV loads following dendrimer sirna injections Start injection End injection Plasma Viral RNA (copies/ml) 37 Zhou et al., Molecular Therapy,2011 Week of post infection Dendrimer-siRNA complexes protect HIV infected RAG-hu mice from CD4 T cell loss 110% CD4 level Ratio of CD4 and CD3 100% 90% 80% 70% 50% 40% First injection Last injection *2 *4 *6 *11 Weeks of treatment Naked sirna G5+ tat/rev sirna G5+cocktail sirna 38 Non-infected Non-treatment Bio distribution of G5 dendrimer sirnas 39 13

No type I IFN induction or liver toxicities 5.0 IFN response INF-a expression (ng/ml) 4.0 2 hours ) 24 hours ) 3.0 ) 2.0 0.5 0.4 0.3 0.2 0.1 0.

$vehicles for dsirnas/sirnas Effective in vivo delivery to lymphocytes which are normally refractory to most delivery vehicles These dendrimers are candidates for delivery of cocktails of therapeutic$

14 No type I IFN induction or liver toxicities 5.0 IFN response INF-a expression (ng/ml) hours ) 24 hours ) 3.0 ) J745 J746 J700 J701 J702 J703 J712 J713 J714 J715 J721 J722 J723 J724 J741 J742 J743 J744 J745 J754 J766 J767 J Summary of dendrimer studies PAMAM dendrimers are safe and effective delivery vehicles for dsirnas/sirnas Effective in vivo delivery to lymphocytes which are normally refractory to most delivery vehicles These dendrimers are candidates for delivery of cocktails of therapeutic dsirnas/sirnas in HIV infected patients who have HAART resistant virus 41 Aptamers: Jiehua Zhou, Haitang Li, Jane Zhang, Piotr Swiderski David Smith Beckman Research Institute, City of Hope Acknowledgments Dendrimer: Ling Peng-Tracy Liu Centre Interdisciplinaire de Nanoscience de Marseille, CNRS Yuanyu Huang, Quan Du, Zicai Liang Institute of Molecular Medicine, Peking University, Beijing RAG-hu mice: Ramesh Akkina and Preston Neff 42 Colorado State University Jiehua Zhou, Haitang Li Funding NIH NIAID,NHLBI 14

15 43 15

A phase I pilot study of safety and feasibility of stem cell therapy for AIDS lymphoma using stem cells treated with a lentivirus vector encoding

A phase I pilot study of safety and feasibility of stem cell therapy for AIDS lymphoma using stem cells treated with a lentivirus vector encoding multiple anti-hiv RNAs John A. Zaia, M.D. John J. Rossi,