Biology subjects

Noppe, Y.

Publications and source records attributed to Noppe, Y..

4 recordsLinked to original sources

bioRxiv2026

Broadly neutralizing antibody-secreting CAR-T cells elicit Fc-mediated effector functions in vitro and suppress HIV in humanized mice

Despite significant advances in antiretroviral therapy (ART) that have transformed human immunodeficiency virus (HIV) infection from a fatal diagnosis to a manageable chronic condition, the persistent viral reservoir necessitates lifelong treatment underscoring the critical need for curative interventions. Viral persistence within anatomically distinct reservoirs, coupled with HIV-associated immune dysregulation accentuates the need for innovative combination immunotherapies that can act through multiple mechanisms. We introduce the Hybrid chimeric antigen receptor (CAR) platform: a dual-function immunotherapy that combines the targeted cytotoxicity of CAR-T cells with the secretion of broadly neutralizing antibodies (bNAbs). This approach enables direct elimination of HIV-infected cells, neutralization of free virus and Fc-mediated effector recruitment. In vitro, Hybrid CAR-T cells eliminated HIV-infected CD4+ T cells while the secreted bNAbs neutralized HIV and mediated robust Fc-effector functions including antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). In humanized mice, Hybrid CAR-T treatment achieved more than a 9-fold reduction in plasma viremia, accompanied by a significant decrease in viral levels across tissues, with circulating bNAbs detected in plasma. Collectively, these findings highlight the potential of Hybrid CAR-T cells as a synergistic next-generation therapeutic that bridges cellular and humoral immunity, supporting their translational promise as a strategy toward functional HIV cure.

immunology↗

bioRxiv2023

HIV-PULSE: A long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization

A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1,308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11% vs 18%) and overall good concordance, though at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.

molecular biology↗

bioRxiv2021

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Clonal expansion of HIV-infected cells contributes to the long-term persistence of the HIV reservoir in ART-suppressed individuals. However, the contribution to plasma viremia from cell clones that harbor inducible proviruses is poorly understood. Here, we describe a single-cell approach to simultaneously sequence the TCR, integration sites and proviral genomes from translation-competent reservoir cells, called STIP-Seq. By applying this approach to blood samples from eight participants, we showed that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5-end of the genome, often involving the major splice donor site. TCR and integration site sequencing revealed that antigen-responsive cells can harbor inducible proviruses integrated into cancer-related genes. Furthermore, we found several matches between proviruses retrieved with STIP-Seq and plasma viruses obtained during ART and upon treatment interruption, showing that STIP-Seq can capture clones that are responsible for low-level viremia or viral rebound.

microbiology↗

bioRxiv2021

In-depth characterization of HIV-1 reservoirs reveals links to viral rebound during treatment interruption

The HIV-1 reservoir is composed of cells harboring latent proviruses that are capable of contributing to viremia upon antiretroviral treatment (ART) interruption. Although this reservoir is known to be maintained by clonal expansion, the contribution of large, infected cell clones to residual viremia and viral rebound remains underexplored. Here, we conducted an extensive analysis on four ART-treated individuals who underwent an analytical treatment interruption (ATI). We performed subgenomic (V1-V3 env), near full-length proviral and integration site sequencing, and used multiple displacement amplification to sequence both the integration site and provirus from single HIV-infected cells. We found eight proviruses that could phylogenetically be linked to plasma virus obtained before or during the ATI. This study highlights a role for HIV-infected cell clones in the maintenance of the replication-competent reservoir and suggests that infected cell clones can directly contribute to rebound viremia upon ATI.

microbiology↗