Skip to main content

Advertisement

SpringerLink
Log in

Quantitative Evaluation and Optimization of Co-drugging to Improve Anti-HIV Latency Therapy

  • Published:
Cellular and Molecular Bioengineering Aims and scope Submit manuscript

Abstract

Human immunodeficiency virus 1 (HIV) latency remains a significant obstacle to curing infected patients. One promising therapeutic strategy is to purge the latent cellular reservoir by activating latent HIV with latency-reversing agents (LRAs). In some cases, co-drugging with multiple LRAs is necessary to activate latent infections, but few studies have established quantitative criteria for determining when co-drugging is required. Here we systematically quantified drug interactions between histone deacetylase inhibitors and transcriptional activators of HIV and found that the need for co-drugging is determined by the proximity of latent infections to the chromatin-regulated viral gene activation threshold at the viral promoter. Our results suggest two classes of latent viral integrations: those far from the activation threshold that benefit from co-drugging, and those close to the threshold that are efficiently activated by a single drug. Using a primary T cell model of latency, we further demonstrated that the requirement for co-drugging was donor dependent, suggesting that the host may set the level of repression of latent infections. Finally, we showed that single drug or co-drugging doses could be optimized, via repeat stimulations, to minimize unwanted side effects while maintaining robust viral activation. Our results motivate further study of patient-specific latency-reversing strategies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7

Similar content being viewed by others

References

  1. Archin, N. M., A. L. Liberty, A. D. Kashuba, S. K. Choudhary, J. D. Kuruc, et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature 487:482–485, 2012.

    Article  Google Scholar 

  2. Barboric, M., J. H. N. Yik, N. Czudnochowski, Z. Yang, R. Chen, et al. Tat competes with HEXIM1 to increase the active pool of P-TEFb for HIV-1 transcription. Nucleic Acids Res. 35:2003–2012, 2007.

    Article  Google Scholar 

  3. Blazkova, J., K. Trejbalova, F. Gondois-Rey, P. Halfon, P. Philibert, et al. CpG Methylation Controls Reactivation of HIV from Latency. PLoS Pathog. 5:e1000554, 2009.

    Article  Google Scholar 

  4. Bliss, C. I. The calculation of microbial assays. Bacteriol. Rev. 20:243–258, 1956.

    Google Scholar 

  5. Böhnlein, E., J. W. Lowenthal, M. Siekevitz, D. W. Ballard, B. R. Franza, et al. The same inducible nuclear proteins regulates mitogen activation of both the interleukin-2 receptor-alpha gene and type 1 HIV. Cell 53:827–836, 1988.

    Article  Google Scholar 

  6. Bosque, A., and V. Planelles. Induction of HIV-1 latency and reactivation in primary memory CD4+ T cells. Blood 113:58–65, 2009.

    Article  Google Scholar 

  7. Bosque, A., and V. Planelles. Studies of HIV-1 latency in an ex vivo model that uses primary central memory T cells. Methods 53:54–61, 2011.

    Article  Google Scholar 

  8. Bullen, C. K., G. M. Laird, C. M. Durand, J. D. Siliciano, and R. F. Siliciano. New ex vivo approaches distinguish effective and ineffective single agents for reversing HIV-1 latency in vivo. Nat. Med. 20:425–429, 2014.

    Article  Google Scholar 

  9. Burnett, J. C., K.-I. Lim, A. Calafi, J. J. Rossi, D. V. Schaffer, et al. Combinatorial latency reactivation for HIV-1 subtypes and variants. J. Virol. 84:5958–5974, 2010.

    Article  Google Scholar 

  10. Burnett, J. C., K. Miller-Jensen, P. S. Shah, A. P. Arkin, and D. V. Schaffer. Control of stochastic gene expression by host factors at the HIV promoter. PLoS Pathog. 5:e1000260, 2009.

    Article  Google Scholar 

  11. Choudhary, S. K., N. M. Archin, and D. M. Margolis. Hexamethylbisacetamide and disruption of human immunodeficiency virus type 1 latency in CD4(+) T cells. J. Infect. Dis. 197:1162–1170, 2008.

    Article  Google Scholar 

  12. Contreras, X., M. Barboric, T. Lenasi, and B. M. Peterlin. HMBA releases P-TEFb from HEXIM1 and 7SK snRNA via PI3K/Akt and activates HIV transcription. PLoS Pathog. 3:1459–1469, 2007.

    Article  Google Scholar 

  13. Contreras, X., M. Schweneker, C. S. Chen, J. M. McCune, S. G. Deeks, et al. Suberoylanilide hydroxamic acid reactivates HIV from latently infected cells. J. Biol. Chem. 284:6782–6789, 2009.

    Article  Google Scholar 

  14. Coull, J. J., F. Romerio, J. M. Sun, J. L. Volker, K. M. Galvin, et al. The human factors YY1 and LSF repress the human immunodeficiency virus type 1 long terminal repeat via recruitment of histone deacetylase 1. J. Virol. 74:6790–6799, 2000.

    Article  Google Scholar 

  15. Duh, E. J., W. J. Maury, T. M. Folks, A. S. Fauci, and A. B. Rabson. Tumor necrosis factor alpha activates human immunodeficiency virus type 1 through induction of nuclear factor binding to the NF-kappa B sites in the long terminal repeat. Proc Natl Acad Sci USA 86:5974–5978, 1989.

    Article  Google Scholar 

  16. Durand, C. M., J. N. Blankson, and R. F. Siliciano. Developing strategies for HIV-1 eradication. Trends Immunol. 33:554–562, 2012.

    Article  Google Scholar 

  17. Emiliani, S., C. Van Lint, W. Fischle, P. Paras, Jr., M. Ott, et al. A point mutation in the HIV-1 Tat responsive element is associated with postintegration latency. Proc. Natl. Acad. Sci. USA 93:6377–6381, 1996.

    Article  Google Scholar 

  18. Fernandez, G., and S. L. Zeichner. Cell line-dependent variability in HIV activation employing DNMT inhibitors. Virol. J. 7:266, 2010.

    Article  Google Scholar 

  19. Finzi, D., J. Blankson, J. D. Siliciano, J. B. Margolick, K. Chadwick, et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat. Med. 5:512–517, 1999.

    Article  Google Scholar 

  20. Finzi, D., M. Hermankova, T. Pierson, L. M. Carruth, C. Buck, et al. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278:1295–1300, 1997.

    Article  Google Scholar 

  21. Fitzgerald, J. B., B. Schoeberl, U. B. Nielsen, and P. K. Sorger. Systems biology and combination therapy in the quest for clinical efficacy. Nat. Chem. Biol. 2:458–466, 2006.

    Article  Google Scholar 

  22. Ganesh, L., E. Burstein, A. Guha-Niyogi, M. K. Louder, J. R. Mascola, et al. The gene product Murr1 restricts HIV-1 replication in resting CD4+ lymphocytes. Nature 426:853–857, 2003.

    Article  Google Scholar 

  23. Han, Y., K. Lassen, D. Monie, A. R. Sedaghat, S. Shimoji, et al. Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J. Virol. 78:6122–6133, 2004.

    Article  Google Scholar 

  24. Ho, Y. C., L. Shan, N. N. Hosmane, J. Wang, S. B. Laskey, et al. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 155:540–551, 2013.

    Article  Google Scholar 

  25. Jiang, G., A. Espeseth, D. J. Hazuda, and D. M. Margolis. c-Myc and Sp1 contribute to proviral latency by recruiting histone deacetylase 1 to the human immunodeficiency virus type 1 promoter. J. Virol. 81:10914–10923, 2007.

    Article  Google Scholar 

  26. Jordan, A., D. Bisgrove, and E. Verdin. HIV reproducibly establishes a latent infection after acute infection of T cells in vitro. EMBO J. 22:1868–1877, 2003.

    Article  Google Scholar 

  27. Kao, S. Y., A. F. Calman, P. A. Luciw, and B. M. Peterlin. Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product. Nature 330:489–493, 1987.

    Article  Google Scholar 

  28. Kasowski, M., S. Kyriazopoulou-Panagiotopoulou, F. Grubert, J. B. Zaugg, A. Kundaje, et al. Extensive variation in chromatin states across humans. Science 342:750–752, 2013.

    Article  Google Scholar 

  29. Kauder, S. E., A. Bosque, A. Lindqvist, V. Planelles, and E. Verdin. Epigenetic regulation of HIV-1 latency by cytosine methylation. PLoS Pathog. 5:e1000495, 2009.

    Article  Google Scholar 

  30. Kim, Y. K., C. F. Bourgeois, R. Pearson, M. Tyagi, M. J. West, et al. Recruitment of TFIIH to the HIV LTR is a rate-limiting step in the emergence of HIV from latency. EMBO J. 25:1–9, 2006.

    Article  Google Scholar 

  31. Kinoshita, S., L. Su, M. Amano, L. A. Timmerman, H. Kaneshima, et al. The T cell activation factor NF-ATc positively regulates HIV-1 replication and gene expression in T cells. Immunity 6:235–244, 1997.

    Article  Google Scholar 

  32. Miller-Jensen, K., S. S. Dey, N. Pham, J. E. Foley, A. P. Arkin, et al. Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-kappaB mediated viral gene expression. Integr. Biol. (Camb.) 4:661–671, 2012.

    Article  Google Scholar 

  33. Miller-Jensen, K., R. Skupsky, P. S. Shah, A. P. Arkin, and D. V. Schaffer. Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression. PLoS Comput. Biol. 9:e1003135, 2013.

    Article  Google Scholar 

  34. Nabel, G., and D. Baltimore. An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature 326:711–713, 1987.

    Article  Google Scholar 

  35. Ott, M., M. Geyer, and Q. Zhou. The control of HIV transcription: keeping RNA polymerase II on track. Cell Host Microbe 10:426–435, 2011.

    Article  Google Scholar 

  36. Quivy, V., E. Adam, Y. Collette, D. Demonte, A. Chariot, et al. Synergistic activation of human immunodeficiency virus type 1 promoter activity by NF-kappaB and inhibitors of deacetylases: potential perspectives for the development of therapeutic strategies. J. Virol. 76:11091–11103, 2002.

    Article  Google Scholar 

  37. Reuse, S., M. Calao, K. Kabeya, A. Guiguen, J.-S. Gatot, et al. Synergistic activation of HIV-1 expression by deacetylase inhibitors and prostratin: implications for treatment of latent infection. PLoS ONE 4:e6093, 2009.

    Article  Google Scholar 

  38. Richman, D. D., D. M. Margolis, M. Delaney, W. C. Greene, D. Hazuda, et al. The challenge of finding a cure for HIV infection. Science 323:1304–1307, 2009.

    Article  Google Scholar 

  39. Rowinsky, E. K., D. S. Ettinger, L. B. Grochow, R. B. Brundrett, A. E. Cates, et al. Phase I and pharmacologic study of hexamethylene bisacetamide in patients with advanced cancer. J. Clin. Oncol. 4:1835–1844, 1986.

    Google Scholar 

  40. Selby, M. J., and B. M. Peterlin. Trans-activation by HIV-1 Tat via a heterologous RNA binding protein. Cell 62:769–776, 1990.

    Article  Google Scholar 

  41. Tyagi, M., and J. Karn. CBF-1 promotes transcriptional silencing during the establishment of HIV-1 latency. EMBO J. 26:4985–4995, 2007.

    Article  Google Scholar 

  42. Tyagi, M., R. J. Pearson, and J. Karn. Establishment of HIV latency in primary CD4+ cells is due to epigenetic transcriptional silencing and P-TEFb restriction. J. Virol. 84:6425–6437, 2010.

    Article  Google Scholar 

  43. Weinberger, L. S., J. C. Burnett, J. E. Toettcher, A. P. Arkin, and D. V. Schaffer. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122:169–182, 2005.

    Article  Google Scholar 

  44. Williams, S. A., L.-F. Chen, H. Kwon, C. M. Ruiz-Jarabo, E. Verdin, et al. NF-κB p50 promotes HIV latency through HDAC recruitment and repression of transcriptional initiation. EMBO J. 25:139–149, 2006.

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by the Bill and Melinda Gates Foundation’s Grand Challenges Explorations (Round 7 to K.M.J.) and the National Science Foundation (NSF CBET-1264246 to K.M.J.). V.C.W. was supported by a National Institutes of Health Predoctoral Training Grant in Genetics (2T32GM007499-36, 5T32GM007499-34, 5T32GM007499-35).

Conflict of interest

V.C.W., L.E.F., N.M.A., Q.X., S.S.D., and K.M.J. declare that they have no conflicts of interest.

Ethical Standards

No human studies or animal studies were carried out by the authors for this article.

Author information

Author notes

  1. Siddharth S. Dey

    Present address: Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands

Authors and Affiliations

  1. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA

    Victor C. Wong & Kathryn Miller-Jensen

  2. Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA

    Linda E. Fong, Nicholas M. Adams, Qiong Xue & Kathryn Miller-Jensen

  3. California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA

    Siddharth S. Dey

Authors
  1. Victor C. Wong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Linda E. Fong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nicholas M. Adams
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qiong Xue
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Siddharth S. Dey
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kathryn Miller-Jensen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kathryn Miller-Jensen.

Additional information

Associate Editor David Schaffer oversaw the review of this article.

This paper is part of the 2014 Young Innovators Issue.

Kathryn Miller-Jensen is an Assistant Professor of Biomedical Engineering and Molecular, Cellular, and Developmental Biology at Yale University. Her lab uses experimental and computational approaches to study signaling and transcriptional regulation in response to pathogens, with a focus on activation of latent HIV, as well as innate immune signaling. Her work is funded by the National Institutes of Health, the National Science Foundation, and the Bill and Melinda Gates Foundation. Kathryn was an NIH NSRA Postdoctoral Fellow at the University of California at Berkeley and she holds a Ph.D. in Chemical Engineering from the Massachusetts Institute of Technology and A.B. and B.E. degrees in Engineering Sciences from Dartmouth College. She is a member of the Biomedical Engineering Society and a former Christine Mirzayan Science and Technology Policy Fellow at the National Academies in Washington, DC.

figure b

Victor C. Wong and Linda E. Fong have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 1951 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wong, V.C., Fong, L.E., Adams, N.M. et al. Quantitative Evaluation and Optimization of Co-drugging to Improve Anti-HIV Latency Therapy. Cel. Mol. Bioeng. 7, 320–333 (2014). https://doi.org/10.1007/s12195-014-0336-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12195-014-0336-9

Keywords

Search

Navigation