Biology subjects

Feeney, M. E.

Publications and source records attributed to Feeney, M. E..

12 recordsLinked to original sources

bioRxiv2026

Circulating T-follicular helper and type I regulatory T cells have overlapping phenotypes in P. falciparum malaria and are maintained by parasite exposure.

Immunity to P. falciparum malaria develops slowly, requiring repeated infection in areas of high transmission, and wanes rapidly in the absence of parasite exposure. Key to this immunity, is the development of antibodies which is supported by CD4 T follicular helper (Tfh) cells that drive robust germinal centre responses. However, in malaria, the malaria-specific CD4 T cell compartment in peripheral blood is dominated by Type 1 regulatory T cells (Tr1), which produce high levels of IL-10 in response to parasites. Tr1-like Tfh cells (Tfh10) have been reported in several settings of repeated antigen stimulation but have not been investigated in malaria. Here we used single-cell RNA sequencing and multiparameter flow cytometry to characterise malaria-specific Tfh and Tr1 cells in a longitudinal cohort of highly exposed individuals and assessed their persistence after transmission interruption. Malaria-specific Tfh and Tr1 cells shared overlapping profiles, and Tr1 cell-like transcriptional signatures and phenotypes were detectable within the Tfh cell compartment. Tfh10 cell subsets were the dominant phenotype of malaria-specific Tfh cells. Following disruption of malaria transmission, the frequencies of malaria-specific Tr1 and Tfh10 cells declined. These findings highlight a close relationship between Tfh and Tr1 cells and show that the Tfh cell compartment in malaria is dominated by Tfh10 cells. The rapid waning of these cells in the absence of continuous exposure is consistent with requirements of persistent antigen in maintaining regulatory CD4 T cell phenotypes.

immunology↗

bioRxiv2026

Maternal malaria and early-life infections shape humoral immunity to P. falciparum in infants

Placental malaria may negatively impact acquisition of immunity to malaria in infants. To study the effect of maternal antibodies on early-life infections, a birth cohort of infants were enrolled in a prospective observational study in Busia, Uganda. We measured P. falciparum-specific antibody responses to 19 P. falciparum antigens and tetanus toxoid in 183 infants using a Luminex multiplex bead array. We also assessed the frequency and phenotype of peripheral T follicular helper cells and B cells using flow cytometry. Placental malaria and lower gestational age adversely impacted antibody transfer overall. Maternal antibodies present in cord blood were not associated with protection in the first year of life, and neither was maternal malaria status. Infants generated antibodies against P. falciparum antigens in response to infection, but these were also not associated with protection, only exposure. Interestingly, infections in the first six months of life correlated with decreased levels of antibodies to P. falciparum antigen at one year of age. Early-life infections were not clearly associated with circulating follicular T cell or B cell phenotypic composition. These data suggest the infant antibody response has little, if any, impact on preventing clinical malaria or patent parasitemia in the first year of life.

immunology↗

bioRxiv2025

Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors

Gamma delta T cells ({gamma}{delta} T cells) emerge early during human gestation and are uniquely equipped to protect the fetus and infant following in utero infection with viruses such as cytomegalovirus (CMV). Previous research showed that fetal {gamma}{delta} T cells in early gestation are transcriptionally pre-programmed for effector functions in the thymus. Infants with congenital CMV infection (cCMV) exhibit expansions of {gamma}{delta} T cells with CMV-reactive TCRs; however, the functional and transcriptional programming of these innate-like effector cells has not been characterized. Here, we analyzed cord blood mononuclear cells from cCMV+ and uninfected neonates in Uganda using flow cytometry and single-cell RNA and TCR sequencing. We find that {gamma}{delta} T cells in cCMV+ neonates are more differentiated, activated, cytotoxic, and proliferative. TCR repertoires of cCMV+ infants exhibit oligoclonal expansions with an enrichment of {gamma}{delta}TCRs that possess shorter CDR3 lengths and fewer N additions, which suggest they arise from early fetal progenitor cells. These expanded {gamma}{delta} T cell clonotypes in cCMV+ infants are more frequently public and exhibit cytotoxic transcriptional programming. These findings demonstrate that cCMV infection drives an oligoclonal expansion of highly cytotoxic effector {gamma}{delta} T cells with fetal-like TCR features, underscoring their specialized roles in early-life immunity.

immunology↗

bioRxiv2025

Inhibitory NK receptors regulate the γδ T cell response to malaria

Gamma delta ({gamma}{delta}) T cells are important mediators of the immune response to childhood malaria infection. Human V{gamma}9+V{delta}2+ T cells possess intrinsic, HLA-independent responsiveness to Plasmodium falciparum phosphoantigens produced in the blood stage of malaria infection. Engagement of the {gamma}{delta} T cell receptor (TCR) by phosphoantigen-bound butyrophilin molecules results in V{gamma}9+V{delta}2+ T cell expansion, pro-inflammatory cytokine production, and release of cytotoxic granules that mediate parasite killing. Repeated malaria infection, however, leads to a reduction in circulating V{gamma}9+V{delta}2+ T cells and upregulation of immunomodulatory molecules, including NK receptors, that correlates with less severe symptoms upon infection. We explore phenotypic and functional differences of {gamma}{delta} T cells in Ugandan children with high versus low malaria exposure, utilizing high-parameter spectral flow cytometry analysis of PBMCs. We observed significant differences in expression of inhibitory NK receptors - KIR2DL1, KIR2DL2/3, KIR3DL1, LILRB1, and NKG2A - on {gamma}{delta} T cell subsets, with V{gamma}9+V{delta}2+ T cells exhibiting a divergent mechanism of control compared to other subsets. We found that NKG2A and KIR3DL1 expression associated with potent V{gamma}9+V{delta}2+ T cell responses to TCR- and Fc receptor (FcR)-mediated stimulation while KIR2DL1, KIR2DL2/3 and LILRB1 associated with reduced degranulation and cytokine production. These results identify a new role for inhibitory NK receptors expressed on {gamma}{delta} T cells, exerting a finely tuned balance of activating and inhibitory signals to regulate the response to malaria-related antigens. AUTHOR SUMMARYMalaria remains one of the deadliest infectious diseases, disproportionately affecting young children in sub-Saharan Africa who succumb to sequelae of Plasmodium falciparum infection. However, children living in highly endemic areas experience repeated malaria infection and develop naturally acquired-but not sterilizing-immunity which leads to an asymptomatic reinfection pattern. The immune factors that determine the balance of inflammatory and tolerogenic functions seen in non-sterilizing malaria immunity are yet to be fully understood. Here, we focus on the phenotypic and functional differences in one cell type between children with a history of low versus high malaria exposure. We identified a group of inhibitory surface receptors that improved the antimalarial function of this cell, and another group that worsened their function. Our study clarifies the immune landscape in highly malaria-exposed individuals and illuminates one potential system of regulating the cellular response to repeat infection.

immunology↗

bioRxiv2025

Learned Geometry, Predicted Binding: Structurally-BasedPrediction of Peptide:MHC Binding Using AlphaFold 3 EnablesCD4 T Cell Epitope Prediction

The accurate prediction of T cell epitope peptides within proteins of interest has a wide range of applications, but is complicated by the multiple determinants of antigenicity, the polymorphism of the Major Histocompatibility Complex (MHC) locus, and the great diversity of possible peptide antigens. Leading in silico methods use a variety of statistical approaches to learn from sequences identified through both in vitro MHC binding and peptide elution studies, but their performance remains imperfect, particularly for MHC II-restricted responses. Here we present MHCIIFold-GNN, an entirely orthogonal solution to this problem that combines three new elements: (i) a highly-multiplexed peptide:MHCII binding assay, (ii) generalizable structural modeling using AlphaFold3, and (iii) transfer learning with a Graph-based Neural Network. Trained exclusively on newly-generated in vitro binders, we show that MHCIIFold-GNN enables state-of-the-art prediction of CD4 T cell epitopes presented by diverse MHC II proteins, on par with non-structural methods that rely on much larger datasets including naturally-processed ligands. Moreover, when MHCIIFold-GNN and a leading non-structural method are combined, we observe unparalleled performance on a held-out test set (11 % boost), underscoring the orthogonality of the methods. These results highlight the power of a new class of structure-informed approaches to the CD4 T cell epitope prediction problem.

bioinformatics↗

bioRxiv2024

Differences in phenotype between long-lived memory B cells against Plasmodium falciparum merozoite antigens and variant surface antigens

Plasmodium falciparum infections elicit strong humoral immune responses to two main groups of antigens expressed by blood-stage parasites: merozoite antigens that are involved in the erythrocyte invasion process and variant surface antigens that mediate endothelial sequestration of infected erythrocytes. Long-lived B cells against both antigen classes can be detected in the circulation for years after exposure, but have not been directly compared. Here, we studied the phenotype of long-lived memory and atypical B cells to merozoite antigens (MSP1 and AMA1) and variant surface antigens (the CIDR1 domain of PfEMP1) in Ugandan adults before and after local reduction of P. falciparum transmission. After a median of 1.7 years without P. falciparum infections, the percentage of antigen-specific activated B cells declined, but long-lived antigen-specific B cells were still detectable in all individuals. The majority of MSP1/AMA1-specific B cells were CD95+CD11c+ memory B cells, which are primed for rapid differentiation into antibody-secreting cells, and FcRL5-T-bet- atypical B cells. On the other hand, most CIDR1-specific B cells were CD95-CD11c- memory B cells. CIDR1-specific B cells were also enriched among a subset of atypical B cells that seem poised for antigen presentation. These results point to differences in how these antigens are recognized or processed by the immune system and how P. falciparum-specific B cells will respond upon re-infection.

immunology↗

bioRxiv2024

Broadly inhibitory antibodies against severe malaria virulence proteins

Plasmodium falciparum pathology is driven by the accumulation of parasite-infected erythrocytes in microvessels. This process is mediated by the parasites polymorphic erythrocyte membrane protein 1 (PfEMP1) adhesion proteins. A subset of PfEMP1 variants that bind human endothelial protein C receptor (EPCR) through their CIDR1 domains is responsible for severe malaria pathogenesis. A longstanding question is whether individual antibodies can recognize the large repertoire of circulating PfEMP1 variants. Here, we describe two broadly reactive and binding-inhibitory human monoclonal antibodies against CIDR1. The antibodies isolated from two different individuals exhibited a similar and consistent EPCR-binding inhibition of 34 CIDR1 domains, representing five of the six subclasses of CIDR1. Both antibodies inhibited EPCR binding of both recombinant full-length and native PfEMP1 proteins as well as parasite sequestration in bioengineered 3D brain microvessels under physiologically relevant flow conditions. Structural analyses of the two antibodies in complex with two different CIDR1 antigen variants reveal similar binding mechanisms that depend on interactions with three highly conserved amino acid residues of the EPCR-binding site in CIDR1. These broadly reactive antibodies likely represent a common mechanism of acquired immunity to severe malaria and offer novel insights for the design of a vaccine or treatment targeting severe malaria.

immunology↗

bioRxiv2023

Distinct transcriptional profiles of maternal and fetal placental macrophages at term are associated with gravidity

Maternal intervillous monocytes (MIMs) and fetal Hofbauer cells (HBCs) are myeloid-derived immune cells at the maternal-fetal interface. Little is known regarding the molecular phenotypes and roles of these distinct monocyte/macrophage populations. Here, we used RNA sequencing to investigate the transcriptional profiles of MIMs and HBCs in six normal term pregnancies. Our analyses revealed distinct transcriptomes of MIMs and HBCs. Genes involved in differentiation and cell organization pathways were more highly expressed in MIMs vs. HBCs. In contrast, HBCs had higher expression of genes involved in inflammatory responses and cell surface receptor signaling. Maternal gravidity influenced monocyte programming, as expression of pro-inflammatory molecules was significantly higher in MIMs from multigravidas compared to primigravidas. In HBCs, multigravidas displayed enrichment of gene pathways involved in cell-cell signaling and differentiation. In summary, our results demonstrated that MIMs and HBCs have highly divergent transcriptional signatures, reflecting their distinct origins, locations, functions, and roles in inflammatory responses. Our data further suggested that maternal gravidity influences the gene signatures of MIMs and HBCs, potentially modulating the interplay between tolerance and trained immunity. The phenomenon of reproductive immune memory may play a novel role in the differential susceptibility of primigravidas to pregnancy complications.

immunology↗

bioRxiv2023

Disease Tolerance Acquired Through Repeated Plasmodium Infection Involves Epigenetic Reprogramming of Innate Immune Cells

The regulation of inflammation is a critical aspect of disease tolerance and naturally acquired immunity to malaria. Here, we demonstrate using RNA sequencing and epigenetic landscape profiling by cytometry by Time-Of-Flight (EpiTOF), that the regulation of inflammatory pathways during asymptomatic parasitemia occurs downstream of pathogen sensing--at the epigenetic level. The abundance of certain epigenetic markers (methylation of H3K27 and dimethylation of arginine residues) and decreased prevalence of histone variant H3.3 correlated with suppressed cytokine responses among monocytes of Ugandan children. Such an epigenetic signature was observed across diverse immune cell populations and not only characterized active asymptomatic parasitemia but also predicted long-term future disease tolerance when observed in uninfected children. This broad methylated signature likely develops gradually and was associated with age and recent parasite exposure. Our data support a model whereby exposure to Plasmodium falciparum induces epigenetic changes that regulate excessive inflammation and contribute to naturally acquired immunity to malaria.

immunology↗

bioRxiv2022

Single-cell sequencing identifies novel atypical B cell subsets with distinct effector functions

Atypical B cells are a population of activated B cells that are commonly enriched in individuals with chronic immune activation, but are also part of a normal immune response to infection or vaccination. Prior studies to determine the function of these cells have yielded conflicting results, possibly due to functional heterogeneity among this B cell population. To better define the role(s) of atypical B cells in the host adaptive immune response, we performed single-cell sequencing of transcriptomes, cell surface markers, and B cell receptors in individuals with chronic Plasmodium falciparum exposure, a condition known to lead to accumulation of circulating atypical B cells. Our studies identified three previously uncharacterized populations of atypical B cells with distinct transcriptional and functional profiles, that separate into two differentiation pathways. We identified a set of cell surface markers to distinguish these atypical B cell subsets and confirmed their presence in malaria-experienced children and adults using flow cytometry. Plasmodium falciparum-specific cells were present in equal proportions within each of these atypical B cell populations, indicating that all three subsets develop in response to antigen stimulation. However, we observed marked differences among the three subsets in their ability to produce IgG upon T-cell-dependent activation. Collectively, our findings help explain the conflicting observations in prior studies on the functions of atypical B cells and provide a better understanding of their role in the adaptive immune response in chronic inflammatory conditions. One sentence summaryAtypical B cells consist of three subsets that may play distinct roles in the host adaptive immune response.

immunology↗

bioRxiv2022

In Utero Activation of NK Cells in Congenital CMV Infection

BackgroundCongenital cytomegalovirus (CMV) infection is the most common infectious cause of birth defects and neurological damage in newborns. Despite a well-established role for NK cells in control of CMV infection in older children and adults, it remains unknown whether fetal NK cells can sense and respond to CMV infection acquired in utero. MethodsHere, we investigate the impact of congenital CMV infection on the neonatal NK cell repertoire by assessing the frequency, phenotype, and functional profile of NK cells in cord blood samples from newborns with congenital CMV and from uninfected controls enrolled in a birth cohort of Ugandan mothers and infants. ResultsWe find that neonatal NK cells from congenitally CMV infected newborns show increased expression of cytotoxic mediators, signs of maturation and activation, and an expansion of mature CD56-negative NK cells, an NK cell subset associated with chronic viral infections in adults. Activation was particularly prominent in NK cell subsets expressing the Fc{gamma} receptor CD16, indicating a role for antibody-mediated immunity against CMV in utero. ConclusionThese findings demonstrate that NK cells can be activated in utero and suggest that NK cells may be an important component of the fetal and infant immune response against CMV.

immunology↗

bioRxiv2021

Distinct cellular immune signatures in acute Zika virus infection are associated withhigh or low persisting neutralizing antibody titers

Although the formation of a durable neutralizing antibody response after an acute viral infection is a key component of protective immunity, little is known about why some individuals generate high versus low neutralizing antibody titers to infection or vaccination. Infection with Zika virus (ZIKV) during pregnancy can cause devastating fetal outcomes, and efforts to understand natural immunity to this infection are essential for optimizing vaccine design. In this study, we leveraged the high-dimensional single-cell profiling capacity of mass cytometry (CyTOF) to deeply characterize the cellular immune response to acute and convalescent ZIKV infection in a cohort of blood donors in Puerto Rico incidentally found to be viremic during the 2015-2016 epidemic in the Americas. During acute ZIKV infection, we identified widely coordinated responses across innate and adaptive immune cell lineages. High frequencies of multiple activated innate immune subsets, as well as activated follicular helper CD4+ T cells and proliferating CD27-IgD-B cells, during acute infection were associated with high titers of ZIKV neutralizing antibodies at 6 months post-infection. On the other hand, low titers of ZIKV neutralizing antibodies were associated with immune features that suggested a cytotoxic-skewed immune "set-point." Our study offers insight into the cellular coordination of immune responses and identifies candidate cellular biomarkers that may offer predictive value in vaccine efficacy trials for ZIKV and other acute viral infections aimed at inducing high titers of neutralizing antibodies. One Sentence SummaryMass cytometry reveals acute ZIKV infection cellular immune signatures that predict high or low neutralizing antibody titers 6 months post-infection.

immunology↗