Chronic inflammation and immune dysfunction play a key role in the development of non-AIDS related comorbidities. The aim of our study was to characterize the functional phenotype of immune cells in people living with HIV (PLHIV). We enrolled a cross-sectional cohort study of PLHIV on stable antiretroviral therapy and healthy controls. We assessed ex vivo cytokine production capacity and transcriptomics of monocytes and T-cells upon bacterial, fungal and viral stimulation. PLHIV exhibited an exacerbated pro-inflammatory profile in monocyte-derived cytokines, but not in lymphocyte-derived cytokines. Particularly, the production of the IL-1β to imiquimod, E. coli LPS and Mycobacterium tuberculosis was increased, and this production correlated with plasma concentrations of hsCRP and sCD14. This increase in monocyte responsiveness remained stable over time in subsequent blood sampling after >1year. Transcriptome analyses confirmed priming of the monocyte IL-1β pathway, consistent with a monocyte trained immunity phenotype. Increased plasma concentrations of β-glucan, a well-known inducer of trained immunity, were associated with increased innate cytokine responses. Monocytes of PLHIV exhibit a sustained pro-inflammatory immune phenotype with priming of the IL-1β pathway. Training of the innate immune system in PLHIV likely plays a role in long-term HIV complications and provides a promising therapeutic target for inflammation-related comorbidities.
Wouter A. van der Heijden, Lisa van de Wijer, Farid Keramati, Wim Trypsteen, Sofie Rutsaert, Rob ter Horst, Martin Jaeger, Hans J.P.M. Koenen, Hendrik G. Stunnenberg, Irma Joosten, Paul E. Verweij, Jan van Lunzen, Charles A. Dinarello, Leo A.B. Joosten, Linos Vandekerckhove, Mihai G. Netea, André J. van der Ven, Quirijn de Mast
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) with CCR5– donor cells is the only treatment known to cure HIV-1 in patients with underlying malignancy. This is likely due to a donor cell–mediated graft-versus-host effect targeting HIV reservoirs. Allo-HSCT would not be an acceptable therapy for most people living with HIV due to the transplant-related side effects. Chimeric antigen receptor (CAR) immunotherapies specifically traffic to malignant lymphoid tissues (lymphomas) and, in some settings, are able to replace allo-HSCT. Here, we quantified the engraftment of HSC-derived, virus-directed CAR T cells within HIV reservoirs in a macaque model of HIV infection, using potentially novel IHC assays. HSC-derived CAR cells trafficked to and displayed multilineage engraftment within tissue-associated viral reservoirs, persisting for nearly 2 years in lymphoid germinal centers, the brain, and the gastrointestinal tract. Our findings demonstrate that HSC-derived CAR+ cells reside long-term and proliferate in numerous tissues relevant for HIV infection and cancer.
Isaac M. Barber-Axthelm, Valerie Barber-Axthelm, Kai Yin Sze, Anjie Zhen, Gajendra W. Suryawanshi, Irvin S.Y. Chen, Jerome A. Zack, Scott G. Kitchen, Hans-Peter Kiem, Christopher W. Peterson
Antiretroviral therapies (ART) abrogate HIV replication; however, infection persists as long-lived reservoirs of infected cells with integrated proviruses, which re-seed replication if ART is interrupted. A central tenet of our current understanding of this persistence is that infected cells are shielded from immune recognition and elimination through a lack of antigen expression from proviruses. Efforts to cure HIV infection have therefore focused on reactivating latent proviruses to enable immune-mediated clearance, but these have yet to succeed in reducing viral reservoirs. Here, we revisited the question of whether HIV reservoirs are predominately immunologically silent from a new angle: by querying the dynamics of HIV-specific T-cell responses over long-term ART for evidence of ongoing recognition of HIV-infected cells. In longitudinal assessments, we show that the rates of change in persisting HIV Nef-specific responses, but not responses to other HIV gene products, were associated with residual frequencies of infected cells. These Nef-specific responses were highly stable over time, and disproportionately exhibited a cytotoxic, effector functional profile, indicative of recent in vivo recognition of HIV antigens. These results indicate substantial visibility of the HIV-infected cells to T-cells on stable ART, presenting both opportunities and challenges for the development of therapeutic approaches to curing infection.
Eva M. Stevenson, Adam R. Ward, Ronald Truong, Allison S. Thomas, Szu-Han Huang, Thomas R. Dilling, Sandra Terry, John K. Bui, Talia M. Mota, Ali Danesh, Guinevere Q. Lee, Andrea Gramatica, Pragya Khadka, Winiffer D. Conce Alberto, Rajesh T. Gandhi, Deborah K. McMahon, Christina M. Lalama, Ronald J. Bosch, Bernard J. Macatangay, Joshua C. Cyktor, Joseph J. Eron, John W. Mellors, R. Brad Jones
Although many HIV cure strategies seek to expand HIV-specific CD8+ T cells to control the virus, all are likely to fail if cellular exhaustion is not prevented. A loss in stem-like memory properties (i.e., the ability to proliferate and generate secondary effector cells) is a key feature of exhaustion; little is known, however, about how these properties are regulated in human virus-specific CD8+ T cells. We found that virus-specific CD8+ T cells from humans and non-human primates naturally controlling HIV/SIV infection express more of the transcription factor, TCF-1, than non-controllers. HIV-specific CD8+ T cell TCF-1 expression correlated with memory marker expression and expansion capacity and declined with antigenic stimulation. CRISPR-Cas9 editing of TCF-1 in human primary T cells demonstrated a direct role in regulating expansion capacity. Collectively, these data suggest that TCF-1 contributes to the regulation of the stem-like memory property of secondary expansion capacity of HIV-specific CD8+ T cells, and they provide a rationale for exploring the enhancement of this pathway in T cell-based therapeutic strategies for HIV.
Rachel L. Rutishauser, Christian Deo T. Deguit, Joseph Hiatt, Franziska Blaeschke, Theodore L. Roth, Lynn Wang, Kyle A. Raymond, Carly E. Starke, Joseph C. Mudd, Wenxuan Chen, Carolyn P. Smullin, Rodrigo Matus-Nicodemos, Rebecca Hoh, Melissa R. Krone, Frederick M. Hecht, Christopher D. Pilcher, Jeffrey N. Martin, Richard A. Koup, Daniel C. Douek, Jason M. Brenchley, Rafick-Pierre Sékaly, Satish K. Pillai, Alexander Marson, Steven G. Deeks, Joseph M. McCune, Peter W. Hunt
Despite the efficacy of antiretroviral therapy (ART), HIV persists in a latent form and remains a hurdle to eradication. CD4+ T lymphocytes harbor the majority of the HIV reservoir, but the role of individual subsets remains unclear. CD4+ T cells were sorted into central, transitional, effector memory, and naive T cells. We measured HIV DNA and performed proviral sequencing of more than 1900 proviruses in 2 subjects at 2 and 9 years after ART initiation to estimate the contribution of each subset to the reservoir. Although our study was limited to 2 subjects, we obtained comparable findings with publicly available sequences. While the HIV integration levels were lower in naive compared with memory T cells, naive cells were a major contributor to the intact proviral reservoir. Notably, proviral sequences isolated from naive cells appeared to be unique, while those retrieved from effector memory cells were mainly clonal. The number of clones increased as cells differentiated from a naive to an effector memory phenotype, suggesting naive cells repopulate the effector memory reservoir as previously shown for central memory cells. Naive T cells contribute substantially to the intact HIV reservoir and represent a significant hurdle for HIV eradication.
Emmanuele Venanzi Rullo, Marilia Rita Pinzone, LaMont Cannon, Sam Weissman, Manuela Ceccarelli, Ryan Zurakowski, Giuseppe Nunnari, Una O’Doherty
While the RV144 HIV vaccine trial lead to moderately reduced risk of HIV acquisition, emerging data from the repeat failure of the HVTN702 trial point to the critical need to re-examine the relationships between previously identified correlates of reduced risk of protection in the RV144 study. Specifically, the induction of V2-binding, non-IgA, IgG3 antibody responses with non-neutralizing functions were linked to reduced risk of infection in RV144 vaccinees. While each of these features was individually linked to reduced risk of infection, the relationships and interactions between these humoral immune signatures remain unclear. Thus, here we comprehensively profiled the humoral immune response in 300 RV144 vaccinees to specifically decipher the relationships between humoral biomarkers of protection and susceptibility. Here, we found that vaccine-specific IgG1, IgG3, and IgA were highly correlated. However, ratios of IgG1:IgG3:IgA provided new insights into subclass/isotype polyclonal functional regulation. For instance, in the absence of high IgG1 levels, IgG3 antibodies exhibited limited functional activity, pointing to IgG3 as a critical contributor, but not sole driver, of more effective antiviral humoral immunity. Moreover, in contrast to previous findings, higher IgA levels were linked to enhanced antibody effector function, including neutrophil phagocytosis (ADNP), complement deposition (ADCD) and NK degranulation (CD107a). Several IgA-associated functions were increased in infected vaccinees in a case:control dataset, suggesting that rather than blocking, IgA may have driven deleterious functions, thereby compromising immunity. These data highlight the interplay between IgG1, IgG3 and IgA, pointing to the critical need to deeply profile the relationships between subclass/isotype selection.
Stephanie Fischinger, Sepideh Dolatshahi, Madeleine F. Jennewein, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayaphan, Nelson L. Michael, Sandhya Vasan, Margaret E Ackerman, Hendrik Streeck, Galit Alter
The integration of HIV DNA into the host genome contributes to lifelong infection in most individuals. Few studies have examined integration in lymphoid tissue, where HIV predominantly persists before and after antiretroviral treatment (ART). Of particular interest is whether integration site distributions differ between infection stages with paired blood and tissue comparisons. Here, we profiled HIV integration site distributions in sorted memory, tissue resident, and/or follicular helper CD4+ T-cell subsets from paired blood and lymphoid tissue samples from acute, chronic, and ART-treated individuals (n=3 each). We observed minor differences in the frequency of non-intronic and non-distal intergenic sites varying with tissue and residency phenotypes during ART. Genomic and epigenetic annotations were generally similar. Clonal expansion of cells marked by identical integration sites was detected, with increased detection in chronic and ART-treated individuals. However, overlap between or within CD4+ T-cell subsets or tissue compartments was only observed in 8 unique sites out of 3,540 sites studied. Together, these findings suggest that shared integration sites between blood and tissue may, depending on the tissue site, be the exception rather than the rule, and indicate that additional studies are necessary to fully understand the heterogeneity of tissue sequestered HIV reservoirs.
Vincent H. Wu, Christopher L Nobles, Leticia Kuri-Cervantes, Kevin McCormick, John K. Everett, Son Nguyen, Perla M. del Río Estrada, Mauricio González-Navarro, Santiago Ávila-Ríos, Gustavo Reyes-Terán, Frederic D. Bushman, Michael R. Betts
African green monkeys (AGMs) are natural hosts of Simian immunodeficiency virus (SIV) that post-thymically down-regulate CD4 to maintain a large population of CD4-CD8aa+ virus-resistant cells with T-helper functionality, which can result in AGMs becoming apparently cured of SIVagm infection. To understand the mechanisms of this process we performed genome-wide transcriptional analysis on T cells induced to down-regulate CD4 in vitro from AGMs and closely-related Patas monkeys, and T cells that maintain CD4 expression from rhesus macaques. In T cells that down-regulated CD4, pathway analysis revealed an atypical regulation ofthe DNA methylation machinery, which was reversible when pharmacologically targeted with 5-aza-2deoxycytidine. This signature was driven largely by the dioxygenase TET3 that became down-regulated with loss of CD4 expression. CpG motifs within the AGM CD4 promoter region became methylated during CD4 downregulation in vitro and were stably imprinted in AGM CD4-CD8aa+ T cells sorted directly ex vivo. These results suggest AGMs employ epigenetic mechanisms to durably silence the CD4 gene. Manipulation of these mechanisms could provide avenues for modulating SIV and human immunodeficiency virus (HIV)-1 entry receptor expression in hosts that become progressively SIV-infected, which could lead to novel therapeutic interventions aimed to reduce HIV viremia in vivo.
Joseph C. Mudd, Stephen Lai, Sanjana Shah, Andrew R. Rahmberg, Jacob K. Flynn, Carly E. Starke, Molly R. Perkins, Amy Ransier, Samuel Darko, Daniel Douek, Vanessa Hirsch, Mark J. Cameron, Jason M. Brenchley
Nonalcoholic fatty liver disease (NAFLD) is a common comorbidity among people living with HIV with a more aggressive course than in the general population. In a recent randomized placebo-controlled trial, we demonstrated that the growth hormone-releasing hormone analogue tesamorelin reduced liver fat and prevented fibrosis progression in HIV-associated NAFLD over one year. As such, tesamorelin is the first strategy that has shown to be effective against NAFLD among the HIV population. The current study leveraged paired liver biopsy specimens from this trial to identify hepatic gene pathways that are differentially modulated by tesamorelin versus placebo. Using Gene Set Enrichment Analysis (GSEA), we found that tesamorelin increased hepatic expression of hallmark gene sets involved in oxidative phosphorylation and decreased hepatic expression of gene sets contributing to inflammation, tissue repair, and cell division. Tesamorelin also reciprocally up- and downregulated curated gene sets associated with favorable and poor hepatocellular carcinoma prognosis, respectively. Notably, among tesamorelin-treated participants, these changes in hepatic expression correlated with improved fibrosis-related gene score. Our findings inform our knowledge of the biology of growth hormone action on the liver and provide a mechanistic basis for the observed clinical effects of tesamorelin on the liver.
Lindsay T. Fourman, James M. Billingsley, George Agyapong, Shannan J. Ho Sui, Meghan N. Feldpausch, Julia Purdy, Isabel Zheng, Chelsea S. Pan, Kathleen E. Corey, Martin Torriani, David E. Kleiner, Colleen M. Hadigan, Takara L. Stanley, Raymond T. Chung, Steven K. Grinspoon
Type I IFN (IFN-I) production by plasmacytoid DCs (pDCs) occurs during acute HIV-1 infection in response to TLR7 stimulation, but the role of pDC-derived IFN-I in controlling or promoting HIV-1 infection is ambiguous. We report here a sex-biased interferogenic phenotype for a frequent single-nucleotide polymorphism of human TLR7, rs179008, displaying an impact on key parameters of acute HIV-1 infection. We show allele rs179008 T to determine lower TLR7 protein abundance in cells from women, specifically — likely by diminishing TLR7 mRNA translation efficiency through codon usage. The hypomorphic TLR7 phenotype is mirrored by decreased TLR7-driven IFN-I production by female pDCs. Among women from the French ANRS PRIMO cohort of acute HIV-1 patients, carriage of allele rs179008 T associated with lower viremia, cell-associated HIV-1 DNA, and CXCL10 (IP-10) plasma concentrations. RNA viral load was decreased by 0.85 log10 (95% CI, −1.51 to −0.18) among T/T homozygotes, who also exhibited a lower frequency of acute symptoms. TLR7 emerges as an important control locus for acute HIV-1 viremia, and the clinical phenotype for allele rs179008 T, carried by 30%–50% of European women, supports a beneficial effect of toning down TLR7-driven IFN-I production by pDCs during acute HIV-1 infection.
Pascal Azar, José Enrique Mejía, Claire Cenac, Arnoo Shaiykova, Ali Youness, Sophie Laffont, Asma Essat, Jacques Izopet, Caroline Passaes, Michaela Müller-Trutwin, Pierre Delobel, Laurence Meyer, Jean-Charles Guéry
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