Matt Gethers/20.380 HIV Project/Design Ideas/Seven Ideas

Seven Ideas

These are the 7 ideas that everyone likes and the assignments to do further research:

1. Cellular Trap/Modulating Membrane Permeability (Jessie)
2. Zombie HIV (Courtney)
3. Induce Latency (Matt)
4. Premature Viral Fusion (David)
5. Anti-John (Stephanie)
6. Engineered T-Cell (Rob)
7. Lethal Gene (Yi)

It would be best to outline the idea, talk about what would need to be done, potential pitfalls, etc. I've written a small description of the idea as it was presented in our meeting, but feel free to modify.

Cellular Trap/Modulating Membrane Permeability

Prevent virions from escaping into extracellular environments by modulating membrane permeability.

1. Vpu crucial in overcoming tetherin's hold on virus particles pmid=19244337
2. Bst2 restricts viron release, downregulated by Vpu pmid=18342597

Zombie HIV

Trick HIV into thinking it's in one part of the body when it's in the other with the hopes of cultivating a non-pathogenic strain.

Brain-derived HIV-1 is unable to infect T-cells, but is BETTER at infecting macrophages. Cells are basically either good at infecting T-cells or macrophages, some can do both. Depends on which coreceptor they bind to. In short, HIV targets a combination of CCR5, CXCR4, and CD4 receptors.

The macrophage infection is due to V1,V2, V3 sequence changes in the envelope protein. Patients who get AIDS related dementia tend to release more neurotoxins from the destroyed macrophage.

I think this is a bad idea to follow. Reasons:

We don't want the cells to act like brain-HIV, because brain-HIV causes dementia! Bad idea.

Because the difference between brain-HIV and the stuff in the rest of the body is related to fusion (receptors and envelope proteins) - affecting this tends to just be mutated around by HIV. However, affecting this could be developed as part of an additional treatment with RT inhibitors, etc.

Induce Latency

Make all virus quiet and non-pathogenic.

The mechanism(s) for HIV-latency are not well-known. The two main theories are that CD4+ cells become infected with HIV and, if they survive, they progress to quiescence. This quiescent state is characterized by a down-regulation of transcription within the cell that limits the reproductive capabilities of the virus. The other mechanism is that the virus also has a tropism for naive CD4 cells which are also characterized by a down-regulation of transcription within the cell.

Latency is overcome when the T-cell in question is activated, thus up-regulating transcription within the cell and making viral transcription possible.

To induce a clinical "latency", we would have to trick T-cells into being quiescent or at least convince the integrated virus that the T-Cell is quiescent. As this stage appears to be defined by a global down-regulation of transcription, it would be hard to achieve quiescence without also causing someone to be immunocompromised.

Feelings: challenging, not well enough understood to continue

Premature Viral Fusion

Promote fusion of viral capsules in the blood stream (or wherever) before fusion with CD4+ cells.

• CD4/gp120 binding is necessary first step in fusion
• One idea would be to have soluble forms of CD4 and/or the co-receptors floating around in the bloodstream to compete with receptors on T-cells for HIV binding
• This is a really old idea, dating back to the 1980's (1)
• Can't find anything that directly says this doesn't work, but time seems to be against this idea working
• One article says this worked in vitro with laboratory-adapted strains, but not in vivo (2)
• Possibly problematic is that this could actually increase fusion - study done with SIV (not sure if same mechanism) found it increased HIV infection in CD(-) cells because CD4 binding induces binding to CCR5 (3)
• Summary: probably not good idea, also not very innovative
• Possibly other ways of doing same thing?

1. Smith DH, Byrn RA, Marsters SA, Gregory T, Groopman JE, and Capon DJ. Blocking of HIV-1 infectivity by a soluble, secreted form of the CD4 antigen. Science. 1987 Dec 18;238(4834):1704-7. DOI:10.1126/science.3500514 |
2. Chan DC and Kim PS. HIV entry and its inhibition. Cell. 1998 May 29;93(5):681-4. DOI:10.1016/s0092-8674(00)81430-0 |
3. Schenten D, Marcon L, Karlsson GB, Parolin C, Kodama T, Gerard N, and Sodroski J. Effects of soluble CD4 on simian immunodeficiency virus infection of CD4-positive and CD4-negative cells. J Virol. 1999 Jul;73(7):5373-80. DOI:10.1128/JVI.73.7.5373-5380.1999 |

Feelings:

• old, probably won't work
  • didn't work in vivo
  • actually increased infection of CD4-
  • possibly new if we combine with coreceptor on a vesicle

Anti-John

Slow the rate of mutation of HIV so it can be managed with one drug (that targets something that is usually prone to mutation).

Feelings:

• RNase H will need to be knocked out before we can add proofreading
  • could introduce new RT
  • could just target RNase H
    • not well exploited

Engineered T-Cell

Pimp out a T-cell so it dominates the virus.

Genes to be added

• HIV-1 siRNAs?
• Overexpressed protease?
• gag-pol of another virus? (then our T-cells could produce virons which target CD4+ cells while still silencing HIV genes)

Genes to be removed

• MHCs (avoid immunity all together, are they really necessary?)
• T-cell receptor (don't want it to actually have immune system functions)

Papers

4. Tamhane M and Akkina R. Stable gene transfer of CCR5 and CXCR4 siRNAs by sleeping beauty transposon system to confer HIV-1 resistance. AIDS Res Ther. 2008 Jul 30;5:16. DOI:10.1186/1742-6405-5-16 |
5. ter Brake O, Konstantinova P, Ceylan M, and Berkhout B. Silencing of HIV-1 with RNA interference: a multiple shRNA approach. Mol Ther. 2006 Dec;14(6):883-92. DOI:10.1016/j.ymthe.2006.07.007 |
6. ter Brake O, 't Hooft K, Liu YP, Centlivre M, von Eije KJ, and Berkhout B. Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition. Mol Ther. 2008 Mar;16(3):557-64. DOI:10.1038/sj.mt.6300382 |
7. Steidl S, Schüle S, Mühlebach MD, Stitz J, Boller K, Cichutek K, and Schweizer M. Genetic engineering of onco/lentivirus hybrids results in formation of infectious but not of replication-competent viruses. J Gen Virol. 2004 Mar;85(Pt 3):665-678. DOI:10.1099/vir.0.19479-0 |

Lethal Gene

Encode a viral defense specific to HIV and place it in all human cells.

Wild Card: Utilizing the HIV Superinfection prevention mechanism

"Infect" cells with an HIV-like virus that carries the superinfection prevention mechanism to T-Cells. This will prevent infection of HIV at later times. There are instances of superinfection prevention that don't involve down-regulation of key surface proteins (Levy, 56-57, Taddeo, and Federico).

Is it OK to temporarily down-regulate CD4 expression on surface and then reverse?

8. Federico M, Taddeo B, Carlini F, Nappi F, Verani P, and Rossi GB. A recombinant retrovirus carrying a non-producer human immunodeficiency virus (HIV) type 1 variant induces resistance to superinfecting HIV. J Gen Virol. 1993 Oct;74 ( Pt 10):2099-110. DOI:10.1099/0022-1317-74-10-2099 |
9. Federico M, Nappi F, Ferrari G, Chelucci C, Mavilio F, and Verani P. A nonproducer, interfering human immunodeficiency virus (HIV) type 1 provirus can be transduced through a murine leukemia virus-based retroviral vector: recovery of an anti-HIV mouse/human pseudotype retrovirus. J Virol. 1995 Nov;69(11):6618-26. DOI:10.1128/JVI.69.11.6618-6626.1995 |
10. Nethe M, Berkhout B, and van der Kuyl AC. Retroviral superinfection resistance. Retrovirology. 2005 Aug 18;2:52. DOI:10.1186/1742-4690-2-52 |
11. Taddeo B, Federico M, Titti F, Rossi GB, and Verani P. Homologous superinfection of both producer and nonproducer HIV-infected cells is blocked at a late retrotranscription step. Virology. 1993 Jun;194(2):441-52. DOI:10.1006/viro.1993.1283 |
12. Wildum S, Schindler M, Münch J, and Kirchhoff F. Contribution of Vpu, Env, and Nef to CD4 down-modulation and resistance of human immunodeficiency virus type 1-infected T cells to superinfection. J Virol. 2006 Aug;80(16):8047-59. DOI:10.1128/JVI.00252-06 |

Biblio

13. Amado RG, Mitsuyasu RT, and Zack JA. Gene therapy for the treatment of AIDS: animal models and human clinical experience. Front Biosci. 1999 May 15;4:D468-75. DOI:10.2741/amado |
14. Bagasra O. A unified concept of HIV latency. Expert Opin Biol Ther. 2006 Nov;6(11):1135-49. DOI:10.1517/14712598.6.11.1135 |
15. Brooks DG, Hamer DH, Arlen PA, Gao L, Bristol G, Kitchen CM, Berger EA, and Zack JA. Molecular characterization, reactivation, and depletion of latent HIV. Immunity. 2003 Sep;19(3):413-23. DOI:10.1016/s1074-7613(03)00236-x |
16. Brooks DG, Kitchen SG, Kitchen CM, Scripture-Adams DD, and Zack JA. Generation of HIV latency during thymopoiesis. Nat Med. 2001 Apr;7(4):459-64. DOI:10.1038/86531 |
17. Cann AJ. Stable and safe HIV provirus clones. Nucleic Acids Res. 1990 Oct 25;18(20):6153-4. DOI:10.1093/nar/18.20.6153 |
18. Cheng-Mayer C and Levy JA. Distinct biological and serological properties of human immunodeficiency viruses from the brain. Ann Neurol. 1988;23 Suppl:S58-61. DOI:10.1002/ana.410230716 |
19. Cheng-Mayer C and Levy JA. Human immunodeficiency virus infection of the CNS: characterization of "neurotropic" strains. Curr Top Microbiol Immunol. 1990;160:145-56. DOI:10.1007/978-3-642-75267-4_9 |
20. Cheng-Mayer C, Weiss C, Seto D, and Levy JA. Isolates of human immunodeficiency virus type 1 from the brain may constitute a special group of the AIDS virus. Proc Natl Acad Sci U S A. 1989 Nov;86(21):8575-9. DOI:10.1073/pnas.86.21.8575 |
21. Cheng-Mayer C. Biological and molecular features of HIV-1 related to tissue tropism. AIDS. 1990;4 Suppl 1:S49-56.
22. Chun TW, Finzi D, Margolick J, Chadwick K, Schwartz D, and Siliciano RF. In vivo fate of HIV-1-infected T cells: quantitative analysis of the transition to stable latency. Nat Med. 1995 Dec;1(12):1284-90. DOI:10.1038/nm1295-1284 |
23. Chun TW, Justement JS, Lempicki RA, Yang J, Dennis G Jr, Hallahan CW, Sanford C, Pandya P, Liu S, McLaughlin M, Ehler LA, Moir S, and Fauci AS. Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1908-13. DOI:10.1073/pnas.0437640100 |
24. Han Y, Wind-Rotolo M, Yang HC, Siliciano JD, and Siliciano RF. Experimental approaches to the study of HIV-1 latency. Nat Rev Microbiol. 2007 Feb;5(2):95-106. DOI:10.1038/nrmicro1580 |
25. Hermankova M, Siliciano JD, Zhou Y, Monie D, Chadwick K, Margolick JB, Quinn TC, and Siliciano RF. Analysis of human immunodeficiency virus type 1 gene expression in latently infected resting CD4+ T lymphocytes in vivo. J Virol. 2003 Jul;77(13):7383-92. DOI:10.1128/jvi.77.13.7383-7392.2003 |
26. Jeeninga RE, Westerhout EM, van Gerven ML, and Berkhout B. HIV-1 latency in actively dividing human T cell lines. Retrovirology. 2008 Apr 25;5:37. DOI:10.1186/1742-4690-5-37 |
27. Lassen K, Han Y, Zhou Y, Siliciano J, and Siliciano RF. The multifactorial nature of HIV-1 latency. Trends Mol Med. 2004 Nov;10(11):525-31. DOI:10.1016/j.molmed.2004.09.006 |
28. Li XD, Moore B, and Cloyd MW. Gradual shutdown of virus production resulting in latency is the norm during the chronic phase of human immunodeficiency virus replication and differential rates and mechanisms of shutdown are determined by viral sequences. Virology. 1996 Nov 1;225(1):196-212. DOI:10.1006/viro.1996.0588 |
29. Marcello A. Latency: the hidden HIV-1 challenge. Retrovirology. 2006 Jan 16;3:7. DOI:10.1186/1742-4690-3-7 |
30. Williams SA and Greene WC. Regulation of HIV-1 latency by T-cell activation. Cytokine. 2007 Jul;39(1):63-74. DOI:10.1016/j.cyto.2007.05.017 |