Modeling the kinetics of an HIV cure

From the Schiffer group, Vaccine and Infectious Disease Division

Continual use of antiretrovial therapies successfully suppresses HIV viral load below detection, butcomplete HIV eradication within infected individuals has so far been thwarted by latent reservoirs of long-lived, HIV-infected cells. Therefore, curative strategies are targeted towards eliminating latently infected cells or permanently preventing latent viral reactivation after antiretroviral treatment interruption (ATI). Presently, the only two known cases of true HIV cure have been patients who, during treatment for blood cancers, received allogeneic hematopoietic stem cell (HPSC) transplants. In these instances, to simultaneously eliminate HIV, the patients received transplanted allogeneic donor CD4+ T cells containing mutation in CCR5, the primary host cell receptor used by HIV for infection. This replacement of endogenous CCR5-sufficent cells with CCR5-defiecient donor cells cured these patients of HIV by interrupting the infection cycle.

While this treatment ultimately eradicated HIV, the requisite total body irradiation (TBI) and immunosuppressive pre- and post-transplant therapies are highly toxic and not realistic for wide-spread use to eliminate HIV. A modified strategy that has been shown to be safe and effective in simian-HIV (SHIV) uses autologous transplantation of a patient’s own cells after they have undergone ex vivo inactivation of CCR5. This strategy eliminates the need for an allogeneic CCR5-negative donor and immunosuppressants to prevent graft-versus-host disease. However, current protocols have not achieved sufficient fractions of genetically-modified CCR5 cells to prevent HIV rebound.

In a recent eLife publication, Dr. Fabian Cardozo-Ojeda from the Schiffer group in the Vaccine and Infectious Disease Division, along with colleagues from Drs. Hans-Peter Kiem and Christopher Peterson asked a simple question: what percentage of CCR5-edited autologous HSPCs would be necessary to effectively cure a patient of HIV? To answer this, the team “developed a novel mathematical model to simulate the virus behavior and immune response during autologous transplantation of stem cells” during SHIV infection,” explained Dr. Cardozo-Ojeda. They divided their analysis into three parts, first focusing on using empirical data to model the kinetics of T cell reconstitution after autologous transplantation, and next modeling SHIV kinetics during acute infection and rebound following ATI. They then combined these analyses and applied the model to predict the frequency and dose of CCR5-edited cells and the level of SHIV-specific immunity needed to prevent viral rebound following ATI.

The authors first used empirical data from animals that were infected with SHIV and then received combination ART, total body irradiation, and transplantation of autologous HSPCs with or without CCR5 gene editing. Half of these animals underwent ATI one year post-ART initiation, while the remaining were analyzed pre-ATI. Peripheral blood T cell frequencies from these studies was used to model the kinetics of CD4+ and CD8+ T cell rebound, and found that CCR5-edited cells recovered more slowly than their unedited counterparts.

Mathematical model of HIV and T cell dynamics.
Mathematical model of HIV and T cell dynamics. Image from publication.

Secondly, the team built a mathematical model of virus dynamics, comparing the viral loads of animals at three stages: pre-ART, after ART treatment, and after ATI. They found that in the control group, viral loads post-ATI were lower than pre-ART. However, in the transplanted animals, those with unedited CCR5 transplant had very high viral loads post-ATI compared to pre-ART, while CCR5-edited recipient animals had slightly lower but still elevated viral loads. These results suggest that transplantation affects the host response against SHIV, but that CCR5 deletion partially rescues this effect.

Next, the two model components were combined into a second-stage model that recapitulates viral and T cell dynamics from animals that received autologous HSPC transplantation. Together, the model showed that transplantation reduces anti-SHIV T cell immunity, resulting in higher viral load. However, transplantation of CCR5-deficient cells may recover partial anti-SHIV immunity. To further investigate the threshold of CCR5-edited HSPC needed to prevent viral rebound post-ATI, the authors ran many versions of the model, adjusting the parameters in each iteration. In summary, the model predicted that post-ATI viral control following transplantation is successful when the HSPC dose is significantly higher than the residual, endogenous CCR5-sufficient HSPCs that survive TBI, and when the fraction of CCR5-deficient HSPCs in the transplant is high enough to outcompete CCR5-sufficient cells to disrupt ongoing viral replication. Importantly, the model demonstrated that post-rebound viral control was most successful after CCR5-deficient T cells achieve steady state around one year post-transplantation. This suggests that transplantation of autologous CCR5-edited T cells, administered in sufficiently high doses, may successfully disrupt viral replication, but that delay of ATI to at least of year post-transplantation may increase the likelihood of success. 

Dr. Cardozo-Ojeada, the lead author on this study, summarized their findings: “The mathematical model predicts that for the animals to be free of HIV viremia in the absence of any treatment, the transplantation requires that at least 75-94% of the stem cells in it have to be genetically modified. The model also requires that the amount of stem cells transplanted have to be sufficiently higher than the stem cells in the animal." These discoveries have important implications for the HIV cure field, “since the needed conditions for CCR5 edition are too high for the current gene-edition technology,” Dr. Cardozo-Ojeda said. “New questions arise regarding how complementary gene technologies can be optimally used to boost the immune system besides protecting stem cells by CCR5 edition. One of these technologies is the chimeric antigen receptor (CAR) T cells, which are genetically modified to target virus-infected cells. The Kiem lab has been developing this technology for the last few years,” Dr. Cardozo-Ojeda continued. Going forward, the authors are “developing mathematical models to understand the mechanisms of action of these CAR T cells, and to investigate the optimal way in which they can be used for HIV cure,” said Dr. Cardozo-Ojeda.

This work was supported by the National Institutes of Health, the National Institute of Allergy and Infectious Diseases, the National Center for Advancing Translational Sciences, the Washington Research Foundation, and the Center for AIDS Research.

UW/Fred Hutch Cancer Consortium members Josh Schiffer and Hans-Peter Kiem contributed to this work.

Cardozo-Ojeda EF, Duke ER, Peterson CW, Reeves DB, Mayer BT, Kiem HP, Schiffer JT. Thresholds for post-rebound SHIV control after CCR5 gene-edited autologous hematopoietic cell transplantation. eLife. 2021 Jan 12;10:e57646. doi: 10.7554/eLife.57646.