Biology subjects

Waickman, A.

Publications and source records attributed to Waickman, A..

8 recordsLinked to original sources

bioRxiv2026

Integrated single-cell analysis reveals interferon-driven immune signatures in a DENV1 human infection model.

Dengue virus infection triggers complex innate and adaptive immune responses, yet the molecular mechanisms that shape early antiviral immunity remain incompletely defined. We performed longitudinal single-cell multi-omics profiling of peripheral blood mononuclear cells from four flavivirus-naive adults experimentally infected with DENV-1, integrating 5' scRNA-seq with paired surface proteomics. Across 95,841 high-quality cells collected at baseline and on days 8 and 10 post-infection, we observed a strong interferon-driven transcriptional response accompanied by marked immune-cell redistribution, including expansion of monocytes and transient reductions in dendritic cells and double-negative T cells. Cytotoxic and helper lymphocyte populations, particularly naive, central memory, and effector memory CD8 T cells, showed extensive crosstalk with monocytes and NK cells, reflecting coordinated cytokine production and cytotoxic activation. Early B cell activation was evident through increased immunoglobulin gene expression. Innate sensing pathways, including RIG-I and Toll-like signaling, were activated across NK, T, and B cell subsets, while also demonstrating enrichment of antigen processing and apoptosis programs. Pro-inflammatory and cytotoxic signatures peaked at day 8, supported by broad upregulation of interferon-stimulated, pro-apoptotic, and regulatory genes. Together, these findings define a robust IFN-driven antiviral state and coordinated activation of immune cell subsets, providing new insights into the immune dynamics of primary dengue infection. ImportanceDengue virus infects millions of people each year, but the early immune events that shape disease outcomes are still unclear. Most studies measure average responses across all blood cells, which hides how individual cell types react. By tracking thousands of single immune cells from volunteers infected with dengue virus under controlled conditions, we show how the immune system rapidly reorganizes during the first days of infection. Many cell types activate antiviral programs, communicate with one another, and shift their behavior in a coordinated way, driven by strong interferon activity. These results provide a clearer view of how early immune responses unfold in humans and identify cellular processes that may influence who develops more severe illness.

microbiology↗

bioRxiv2026

Molecular and biophysical requirements for B cell receptor dependent enhancement of dengue virus infection

Dengue virus (DENV) is the causative agent of dengue, a mosquito-borne disease that represents a significant and growing public health burden around the world. A unique pathophysiological feature of dengue is immune-mediated enhancement, wherein preexisting immunity elicited by a primary infection can enhance the severity of a subsequent infection by a heterologous DENV serotype. A leading mechanistic explanation for this phenomenon is antibody dependent enhancement (ADE), where sub-neutralizing concentrations of DENV-specific IgG antibodies facilitate entry of DENV into Fc{gamma}R expressing cells. Accordingly, this model posits that phagocytic mononuclear cells are the primary reservoir of DENV. However, multiple independent groups have shown that B cells are the largest reservoir of virally infected cells in circulation during acute dengue, representing a disconnect in our understanding of immune-mediated DENV tropism. In response to this persistent knowledge gap, our team has previously identified a novel mechanism of immune-mediated enhancement we have termed BCR-dependent enhancement (BDE) of DENV infection. In this study, we show that DENV infection of DENV-reactive B cells is highly sensitive to BCR/DENV envelope (E) protein interactions. DENV entry into this subset of B cells is dynamin-mediated and requires proximal BCR signaling. Finally, we show that DENV-reactive B cells are productively infected by live DENV, capable of supporting active viral replication and dissemination. We propose that BDE provides an additional layer of pathogen-specific immune-mediated infection risk that complements existing models of ADE and offers additional insight into potential mechanisms of DENV immunopathogenesis.

immunology↗

bioRxiv2025

Antibody response to Aedes aegypti D7L1+2 salivary proteins as marker of aggregate vector exposure and correlate of dengue virus susceptibility

Aedes aegypti mosquitoes transmit several arboviruses of public health importance. Among these is dengue virus (DENV), a flavivirus whose global infection rates continue to rise each year. With limited options available for preventing or treating DENV infections, mosquito control remains the most widely implemented strategy to combat DENV transmission. Due to the global distribution of DENV, which infects an estimated 400 million people per year, vector suppression practices vary drastically by country and/or region and even small differences in microenvironment can significantly impact vector abundance. There remains a significant need to better understand vector exposure rates at an individual level to disentangle vector exposure and arboviral infection rates. To this end, we have optimized a serologic assay to assess the abundance of antibodies directed against the mosquito salivary proteins AeD7L1+2 as a surrogate metric of vector exposure. Utilizing this assay, we found that anti-D7L1+2 IgG levels were unable to identify low levels of Aedes exposure in individuals with limited prior Aedes exposure, indicating they are unreliable markers of an individuals recent exposure to low levels of these vectors. However, antibody levels against D7L1+2 were robust in plasma samples from individuals living in Aedes endemic regions. These antibody levels reflected seasonal changes in Aedes abundance and exposure, indicating their potential for use as an aggregate marker of vector exposure. Additionally, we found that there were slight negative associations with anti-D7L1+2 IgG levels and age in our cohort. Interestingly, we also found that lower titers of anti-AeD7L1+2 IgG correlated with higher infection burden in households. This finding has implications for the potential interaction between AeD7 proteins and DENV during infection events that will require further study.

immunology↗

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↗

bioRxiv2024

HSV-1 Infection Alters MAPT Splicing and Promotes Tau Pathology in Neural Models of Alzheimer's Disease

INTRODUCTIONHerpes simplex virus 1 (HSV-1) infection alters critical markers of Alzheimers Disease (AD) in neurons. One key marker of AD is the hyperphosphorylation of Tau, accompanied by altered levels of Tau isoforms. However, an imbalance in these Tau splice variants, specifically resulting from altered 3R to 4R MAPT splicing of exon 10, has yet to be directly associated with HSV-1 infection METHODSTo this end, we infected 2D and 3D human neural models with HSV-1 and monitored MAPT splicing and Tau phosphorylation. Further, we transduced SH-SY5Y-neurons with HSV-1 ICP27 which alters RNA splicing to analyze if ICP27 alone is sufficient to induce altered MAPT exon 10 splicing. RESULTSWe show that HSV-1 infection induces altered splicing of MAPT exon 10, increasing 4R-Tau protein levels, Tau hyperphosphorylation, and Tau oligomerization. DISCUSSIONOur experiments reveal a novel link between HSV-1 infection and the development of cytopathic phenotypes linked with AD progression. HIGHLIGHTSO_LIHSV-1 infection in forebrain organoids reduces the neurite length of MAP2-positive neurons. C_LIO_LIHSV-1 infection increases Tau hyperphosphorylation in both two-month-old and four-month-old forebrain organoids. C_LIO_LIHSV-1 infection increases Exon 10 containing (4R) MAPT mRNA and 4R-Tau protein expression in both forebrain organoids and human SH-SY5Y-neurons. C_LIO_LIHSV-1 ICP27 is both necessary and sufficient to induce increased 4R MAPT mRNA and 4R-Tau protein expression in SH-SY5Y-neurons. C_LIO_LIHSV-1 infection increases Tau oligomerization in both forebrain organoids and SH-SY5Y-neurons. C_LI

microbiology↗

bioRxiv2024

Antibody-dependent DENV infection induces distinct transcriptomic responses in infected and bystander human macrophages

Dengue virus (DENV) is a mosquito-borne flavivirus which coexists as four genetically and immunologically distinct serotypes (DENV1-4). In secondary heterologous DENV infection, pre-existing immunity is believed to contribute to severe disease through antibody dependent enhancement (ADE). Although the elevated pathology observed in ADE conditions has been described, the cell intrinsic mechanisms governing this process remain unclear. Using scRNAseq, we investigated the transcriptomic profiles of human monocyte-derived macrophages infected by DENV via ADE compared to conventional infection conditions. Unsupervised analysis of scRNAseq data enabled the identification and differentiation of infected and bystander/uninfected cells in a heterogeneous cell culture. Differential gene expression and Ingenuity Pathway analyses revealed a number of significantly up- and down-regulated genes and gene networks between cells infected by ADE compared to conventional infection. Specifically, these pathways indicated mechanisms such as suppressed interferon signaling and inflammatory chemokine transcription in cells infected via ADE. Further analysis revealed that transcriptomic changes were independent of viral RNA within infected cells, suggesting that the observed changes are reflective of cell-intrinsic responses and not simply a function of per-cell viral burden. Bystander cells in ADE conditions also demonstrated distinct profiles, indicating an immunologically activated phenotype enriched for the expression of gene networks involved with protein translation, cytokine production, and antigen presentation. Together, these findings support the concept that DENV infection via ADE induces a qualitatively different transcriptomic response in infected and bystander cells, contributing to our understanding of ADE as a mechanistic driver of disease and pathogenesis. IMPORTANCEDengue virus (DENV) is a mosquito-borne human pathogen with a significant and growing global health burden. Although correlates of severe dengue disease are poorly understood, pre-existing immunity to DENV has been associated with severe disease risk and known to contribute to an alternative route of viral entry termed antibody-dependent enhancement (ADE). Using single cell RNA sequencing, we identified distinct transcriptomic processes involved in antibody-mediated DENV entry compared to conventional receptor mediated entry. These data provide meaningful insight into the discrete processes contributing to DENV pathogenesis in ADE conditions.

immunology↗

bioRxiv2020

Temporally integrated single cell RNA sequencing analysis of controlled and natural primary human DENV-1 infections

Controlled dengue human infection studies present an opportunity to address many longstanding questions in the field of flavivirus biology. However, limited data are available on how the immunological and transcriptional response elicited by an attenuated challenge virus compares to that associated with a wild-type DENV infection. To bridge this knowledge gap, we utilized scRNAseq to analyze PBMC from individuals enrolled in a DENV-1 controlled human challenge study and from individuals experiencing a natural primary DENV-1 infection. While both controlled and natural DENV infection resulted in overlapping patterns of inflammatory gene upregulation, natural DENV infection was accompanied with a more pronounced suppression in gene products associated with protein translation and mitochondrial function, principally in monocytes. This suggests that the immune response elicited by controlled and natural primary DENV infection are similar, but that natural DENV infection has a more pronounced impact on basic cellular processes to induce a multi-layered anti-viral state

immunology↗

bioRxiv2020

Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

Dengue is one of the most widespread vector-borne viral diseases in the world. However, the size, heterogeneity, and temporal dynamics of the cell-associated viral reservoir during acute dengue virus (DENV) infection remains unclear. In this study, we analyzed cells infected in vitro with DENV and PBMC from an individual experiencing a natural DENV infection utilizing 5 capture single cell RNA sequencing (scRNAseq). Both positive- and negative-sense DENV RNA was detected in reactions containing either an oligo(dT) primer alone, or in reactions supplemented with a DENV-specific primer. The addition of a DENV-specific primer did not increase the total amount of DENV RNA captured or the fraction of cells identified as containing DENV RNA. However, inclusion of a DENV-specific cDNA primer did increase the viral genome coverage immediately 5 to the primer binding site. Furthermore, while the majority of intracellular DENV sequence captured in this analysis mapped to the 5 end of the viral genome, distinct patterns of enhanced coverage within the DENV polyprotein coding region were observed. The 5 capture scRNAseq analysis of PBMC not only recapitulated previously published reports by detecting virally infected memory and naive B cells, but also identified cell-associated genomic variants not observed in contemporaneous serum samples. These results demonstrate that oligo(dT) primed 5 capture scRNAseq can detect DENV RNA and quantify virus-infected cells in physiologically relevant conditions, and provides insight into viral sequence variability within infected cells. IMPORTANCEDengue is one of the most widespread vector-borne viral diseases in the world. However, it is still unclear which cells harbor virus during DENV infection, and how viral reservoirs in serum and infected cells are related. These results demonstrate for the first time that intracellular DENV RNA can be identified and infected cells quantified by 5 capture scRNAseq. This strategy provides a significantly greater throughput and higher sensitivity than previously published methods and has the potential to provide additional information on the genomic heterogeneity of intracellular DENV RNA.

microbiology↗