Biology subjects

Michael, N. L.

Publications and source records attributed to Michael, N. L..

10 recordsLinked to original sources

bioRxiv2026

Unique CD8+ T Cell Populations Expand during ART and Predict Delayed HIV-1 Rebound

Antiretroviral therapy (ART) suppresses HIV-1 replication but does not eliminate the latent reservoir, resulting in viral rebound with variable kinetics after treatment interruption. How the immune cell states established during ART influences timing of rebound is not fully understood. In this study, we analyzed 111 participants across multiple cohorts, with 188 single-cell multiomic samples generated and integrated for joint analysis. Longitudinal profiling of peripheral blood mononuclear cells from individuals with acute HIV-1 infection on ART, spanning early infection through sustained therapy and pre-analytical treatment interruption, revealed that time to viral rebound was driven not by global changes in immune composition but by dynamic transcriptional programs within CD8+ T cells. During ART, there was a dramatic expansion of a unique cluster of poised naive CD8+ T cells, with a distinct immune state positioned upstream of stem-like memory CD8+ T cells along a cell differentiation continuum. The differential abundance of this poised naive CD8+ T cell population was enriched in participants with delayed rebound and showed strong predictive power for discriminating time to rebound. Mechanistically, the poised naive CD8+ T cells exhibited features of a precursor phenotype of stem-like memory CD8+ T cells, and showed activation of the TNF-NF-{kappa}B signaling pathway and increased chromatin accessibility at AP-1 motifs. Notably, both poised naive CD8+ T cells and stem-like memory CD8+ T cells were consistently enhanced during ART in both acute and chronic infection. In participants who received investigational therapeutic vaccination, the dominant predictive signal shifted downstream along the differentiation trajectory, with stem-like memory CD8+ T cells emerging as the primary determinant of delayed rebound. Together, these findings identify a dynamic CD8+ T cell state continuum as a central determinant of HIV-1 rebound, even in the absence of antigen-specificity, where ART establishes a predictive poised naive state that can be further leveraged by vaccination to enhance protective stem-like memory responses.

immunology↗

bioRxiv2025

Distinct memory CD4 subset tropism of two CCR5-tropic HIV-1 in a rapid progressor

CCR5 tropic HIV-1 mainly infect memory CD4+ T cells. Memory CD4+ T cells are heterogenous which comprise central memory (CM), transitional memory (TM) and effector memory (EM) subsets based on cell differentiation stages. Previous studies demonstrate that low viral burden in the CM subset correlates with long-term non-progressive HIV-1 infection (1, 2) and is a hallmark of non-pathogenetic SIV infection (3, 4). These findings indicate the importance of CD4 subset tropism of HIV/SIV in determining disease progression. However, an important, yet unanswered question is whether CCR5 HIV-1 variants have different memory CD4 subset preferences. Here, we demonstrate clear compartmentalization of two CCR5 HIV-1 in different memory CD4 subsets in vivo.

microbiology↗

bioRxiv2024

Single-cell analyses reveal that monocyte gene expression profiles influence HIV-1 reservoir size in acutely treated cohorts

Elimination of latent HIV-1 is a major goal of AIDS research but the host factors determining the size of these reservoirs are poorly understood. Here, we investigated whether differences in host gene expression modulate the size of the HIV-1 reservoir during suppressive ART. Peripheral blood mononuclear cells (PBMC) from fourteen individuals initiating ART during acute infection who demonstrated effective viral suppression but varying magnitude of total HIV-1 DNA were characterized by single-cell RNA sequencing (scRNA-seq). Differentially expressed genes and enriched pathways demonstrated increased monocyte activity in participants with undetectable HIV-1 reservoirs. IL1B expression in CD14+ monocytes showed the greatest fold difference. The inverse association of IL1B with reservoir size was validated in an independent cohort comprised of 38 participants with different genetic backgrounds and HIV-1 subtype infections, and further confirmed with intact proviral DNA assay (IPDA(R)) measurements of intact HIV-1 proviruses in a subset of the samples. Modeling interactions with cell population frequencies showed that monocyte IL1B expression associated inversely with reservoir size in the context of higher frequencies of central memory CD4+ T cells, implicating an indirect effect of IL1B via the cell type well established to be a reservoir for persistent HIV-1. Signatures consisting of co-expressed genes including IL1B were highly enriched in the "TNF signaling via NF-{kappa}B" geneset. Functional analyses in cell culture revealed that IL1B activates NF-{kappa}B, thereby promoting productive HIV-1 infection while simultaneously suppressing viral spread, suggesting a natural latency reversing activity to deplete the reservoir in ART treated individuals. Altogether, unbiased high throughput scRNA-seq analyses revealed that monocyte IL1B variation could decrease HIV-1 proviral reservoirs in individuals initiating ART during acute infection.

immunology↗

bioRxiv2023

Transmission of highly virulent CXCR4 tropic HIV-1 through the mucosal route in an individual with a wild-type CCR5 genotype

Nearly all transmitted/founder (T/F) HIV-1 are CCR5 (R5)-tropic. While previous evidence suggested that CXCR4 (X4)-tropic HIV-1 are transmissible, detection was not at the earliest stages of acute infection. Here, we identified an X4-tropic T/F HIV-1 in a participant in acute infection cohort. Coreceptor assays demonstrated that this T/F virus is strictly CXCR4 tropic. The participant experienced significantly faster CD4 depletion compared with R5 virus infected participants in the same cohort. Naive and central memory CD4 subsets declined faster than effector and transitional memory subsets. All CD4 subsets, including naive, were productively infected. Increased CD4+ T cell activation was observed over time. This X4-tropic T/F virus is resistant to broadly neutralizing antibodies (bNAbs) targeting V1/V2 and V3 regions. These findings demonstrate that X4-tropic HIV-1 is transmissible through the mucosal route in people with the wild-type CCR5 genotype and have implications for understanding the transmissibility and immunopathogenesis of X4-tropic HIV-1.

microbiology↗

bioRxiv2023

Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting

The CCR5 (R5) to CXCR4 (X4) coreceptor switch in natural HIV-1 infection is associated with faster progression to AIDS, but the underlying mechanisms remain unclear. The difficulty in capturing the earliest moment of coreceptor switch in vivo limits our understanding of this phenomenon. Here, by tracking the evolution of the transmitted/founder (T/F) HIV-1 in a prospective cohort of individuals at risk for HIV-1 infection identified very early in acute infection, we investigated this process with high resolution. The earliest X4 variants evolved from the R5 tropic T/F strains. Strong X4 usage can be conferred by a single mutation. The mutations responsible for coreceptor switch can confer escape to neutralization and drive X4 variants to replicate mainly in the central memory and naive CD4+ T cells. We propose a novel concept to explain the co-evolution of virus antigenicity and entry tropism termed "escape by shifting". This concept posits that for viruses with receptor or coreceptor flexibility, entry tropism alteration represents a mechanism of immune evasion in vivo.

microbiology↗

bioRxiv2021

Monocyte-derived transcriptome signature indicates antibody-dependent cellular 1 phagocytosis as the primary mechanism of vaccine-induced protection against HIV-1

A gene signature previously correlated with mosaic adenovirus 26 vaccine protection in simian immunodeficiency virus (SIV) and SHIV challenge models in non-human primates (NHP). In this report we investigated presence of this signature as a correlate of reduced risk in human clinical trials and potential mechanism for protection. The absence of this gene signature in the DNA/rAd5 human vaccine trial which did not show efficacy, strengthens our hypothesis that this signature is only enriched in studies that demonstrated protection. This gene signature was enriched in the partially effective RV144 human trial that administered the ALVAC/protein vaccine, and we find that the signature associates with both decreased risk of HIV-1 acquisition and increased vaccine efficacy. Total RNA-seq in a clinical trial that used the same vaccine regimen as the RV144 HIV vaccine implicated antibody-dependent cellular phagocytosis (ADCP) as a potential mechanism of vaccine protection. CITE-seq profiling of 53 surface markers and transcriptomes of 53,777 single cells from the same trial, showed that genes in this signature were primarily expressed in cells belonging to the myeloid lineage including monocytes, which are major effector cells for ADCP. The consistent association of this transcriptome signature with vaccine efficacy represents a tool both to identify potential mechanisms, as with ADCP here, and to screen novel approaches to accelerate development of new vaccine candidates.

systems biology↗

bioRxiv2021

A spike-ferritin nanoparticle vaccine induces robust innate immune activity and drives polyfunctional SARS-CoV-2-specific T cells

Potent cellular responses to viral infections are pivotal for long -lived protection. Evidence is growing that these responses are critical in SARS -CoV-2 immunity. Assessment of a SARS -CoV-2 spike ferritin nanoparticle (SpFN) immunogen paired with two distinct adjuvants, Alhydrogel(R) (AH) or Army Liposome Formulation containing QS-21 (ALFQ) demonstrated unique vaccine evoked immune signatures. SpFN+ALFQ enhanced recruitment of highly activated classical and non -classical antigen presenting cells (APCs) to the vaccine-draining lymph nodes of mice. The multifaceted APC response of SpFN+ALFQ vaccinated mice was associated with an increased frequency of polyfunctional spike -specific T cells with a bias towards TH1 responses and more robust SARS-CoV-2 spike-specific recall response. In addition, SpFN+ALFQ induced Kb spike(539-546)-specific memory CD8+ T cells with effective cytolytic function and distribution to the lungs. This epitope is also present in SARS-CoV, thus suggesting that generation of cross-reactive T cells may provide protection against other coronavirus strains. Our study reveals that a nanoparticle vaccine, combined with a potent adjuvant, generates effective SARS-CoV-2 specific innate and adaptive immune T cell responses that are key components to inducing long-lived immunity. One Sentence SummarySpFN vaccine generates multifactorial cellular immune responses.

immunology↗

bioRxiv2020

Dendritic cells focus CTL responses toward highly conserved and topologically important HIV epitopes

During early HIV Infection, immunodominant T cell responses to highly variable epitopes lead to the selection and expansion of immune escape variants. As a potential therapeutic strategy, we assessed a specialized type 1-polarized monocyte-derived DC dendritic cell (MDC1)-based approach to selectively elicit functional CD8+ cytotoxic T lymphocyte (CTL) responses against highly conserved and topologically important HIV epitopes. Cells were obtained from 10 HIV-infected individuals in the Thailand RV254/SEARH010 cohort who initiated suppressive anti-retroviral therapy (ART) during Fiebig stages I to IV of early infection. Autologous MDC1 were generated for use as peptide antigen presenting cells to induce ex vivo CTL responses against HIV Gag, Pol, Env and Nef. Ultra-conserved (Epigraph) or topologically important (Network) antigens were respectively identified using the Epigraph tool and a structure-based network analysis approach, and each compared to overlapping peptides spanning the entire Gag proteome. MDC1 loaded with either overlapping Gag, Epigraph, or Network 14-21mer peptide pools were consistently capable of activating and expanding HIV-specific T cells to epitopes identified at the 9-13mer peptide level. Some CTL responses occurred outside of known or expected HLA associations, providing evidence of new HLA-associated CTL epitopes. Comparative analyses of peptide pools demonstrated more sequence conservation among the Epigraph antigens, but statistically higher magnitude of CTL responses to Network and Gag peptide groups. Importantly, when select Gag antigens used to initiate the cultures were part of the Network peptide pool, CTL responses directed against these topologically important epitopes were enhanced as compared to when they were included within the complete pool of overlapping Gag peptides. Our study supports that MDC1 can be used to effectively focus CTL responses toward potentially fitness-constrained regions of HIV as a therapeutic strategy to prevent HIV immune escape and control viral replication. Author summaryA major hurdle in the development of a successful HIV immunotherapy is the capacity of the virus to evade the immune response by efficiently establishing epitope variants in response to selective pressure. While effective at suppressing viremia, current regimens of antiretroviral therapy (ART) are not curative. Therefore, achieving immune control of HIV upon cessation of ART as a functional cure, similar to that observed in elite controllers (EC), has been a major therapeutic goal. Such immune control is realized through the actions of antigen-specific cytotoxic T cell lymphocytes (CTL) capable of specifically targeting sequence-conserved epitopes in HIV. In this study, a specialized, antigen presenting, dendritic cell (DC)-based vaccine strategy was used to elicit HIV specific CTL responses in vitro against carefully selected, ultra-conserved and topologically important epitopes. This DC-based approach yielded broad responses against peptide epitopes of both known and unknown HLA-associations, the latter of which implies the uncovering of potentially novel epitopes. Importantly, we demonstrate that CTL responses can be re-directed or focused toward potentially more fitness-constrained regions of the virus, thus highlighting the potential for DC-based therapies to induce immune responses that circumvent the issue of viral escape.

immunology↗

bioRxiv2020

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Here we analyzed SARS-CoV-2 sequence diversity across 5,700 sequences sampled since December 2019. The Spike protein, which is the target immunogen of most vaccine candidates, showed 93 sites with shared polymorphisms; only one of these mutations was found in more than 1% of currently circulating sequences. The minimal diversity found among SARS-CoV-2 sequences can be explained by drift and bottleneck events as the virus spread away from its original epicenter in Wuhan, China. Importantly, there is little evidence that the virus has adapted to its human host since December 2019. Our findings suggest that a single vaccine should be efficacious against current global strains. One Sentence SummaryThe limited diversification of SARS-CoV-2 reflects drift and bottleneck events rather than adaptation to humans as the virus spread.

evolutionary biology↗

bioRxiv2020

A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein

SARS-CoV-2 is a zoonotic virus that has caused a pandemic of severe respiratory disease--COVID-19-- within several months of its initial identification. Comparable to the first SARS-CoV, this novel coronaviruss surface Spike (S) glycoprotein mediates cell entry via the human ACE-2 receptor, and, thus, is the principal target for the development of vaccines and immunotherapeutics. Molecular information on the SARS-CoV-2 S glycoprotein remains limited. Here we report the crystal structure of the SARS-CoV-2 S receptor-binding-domain (RBD) at a the highest resolution to date, of 1.95 [A]. We identified a set of SARS-reactive monoclonal antibodies with cross-reactivity to SARS-CoV-2 RBD and other betacoronavirus S glycoproteins. One of these antibodies, CR3022, was previously shown to synergize with antibodies that target the ACE-2 binding site on the SARS-CoV RBD and reduce viral escape capacity. We determined the structure of CR3022, in complex with the SARS-CoV-2 RBD, and defined a broadly reactive epitope that is highly conserved across betacoronaviruses. This epitope is inaccessible in the "closed" prefusion S structure, but is accessible in "open" conformations. This first-ever resolution of a human antibody in complex with SARS-CoV-2 and the broad reactivity of this set of antibodies to a conserved betacoronavirus epitope will allow antigenic assessment of vaccine candidates, and provide a framework for accelerated vaccine, immunotherapeutic and diagnostic strategies against SARS-CoV-2 and related betacoronaviruses. HIGHLIGHTSHigh resolution structure of the SARS-CoV-2 Receptor-Binding-Domain (RBD). Recognition of the SARS-CoV-2 RBD by SARS-CoV antibodies. Structure of the SARS-COV-2 RBD in complex with antibody CR3022. Identification of a cryptic site of vulnerability on the SARS-CoV-2 Spike.

immunology↗