Biology subjects

Lyke, K. E.

Publications and source records attributed to Lyke, K. E..

7 recordsLinked to original sources

bioRxiv2026

A comparative analysis of the immunotranscriptomic features of DENV-1, -3, and -4 human challenge models

BackgroundDengue virus (DENV) infections cause a range of clinical symptoms, from a mild febrile illness to severe disease. Higher levels of DENV RNAemia are associated with severe dengue, although this relationship is incompletely understood. Dengue Human Infection Models (DHIMs), in which volunteers are experimentally infected with underattenuated DENV strains, provide an invaluable tool for studying early virologic, transcriptional, and immunologic features of infection. DHIM studies using DENV-1, DENV-3, and DENV-4 have demonstrated qualitatively distinct clinical features, however, the contribution of RNAemia and serotype to divergent transcriptional and clinical profiles in these challenge models remains unclear. MethodsWe performed a comparative analysis of DHIM-1, DHIM-3, and DHIM-4 studies to determine shared and unique features of the transcriptional response to infection and their associations with RNAemia and clinical symptoms. We then exposed primary human PBMC in vitro to DENV-1 or DENV-3 at varying titers and performed bulk RNA sequencing. FindingsAcross DHIMs, we identified a set of conserved, upregulated genes at day of peak RNAemia, representing a core antiviral response independent of serotype. Further, a unique gene signature indicating downregulated cytoplasmic translation emerged in a subset of DHIM-3 participants with elevated RNAemia and symptomatology. In vitro PBMC exposure to DENV demonstrated that conserved and unique gene expression signatures varied as a function of viral dose rather than serotype. InterpretationThese data show that viral burden correlates with transcriptional responses and clinical symptomatology following experimental DENV infection, contributing to our understanding of dengue pathogenesis and immunity. Research in ContextO_ST_ABSEvidence for this studyC_ST_ABSDengue virus (DENV) infections are known to elicit a range of clinical symptoms. Previous studies have demonstrated the association of higher DENV RNAemia with more pronounced symptoms and elevated risk for severe disease. Understanding the molecular features associated with RNAemia kinetics may provide insight into disease immunologic and clinical pathogenesis. Three live virus human challenge model studies employing underattenuated DENV-1, DENV-3, and DENV-4 have been conducted which demonstrate variance in clinical and virologic features. These experimental DENV infections serve as a valuable model to study early kinetics of infection and immunotranscriptomic features associated with RNAemia irrespective of serotype. Added value of this studyThis study is the first to conduct a head-to-head comparison of the transcriptional features of DHIM-1, -3 and -4 models, and to provide an in-depth analysis of these signatures with respect to RNAemia kinetics. These unique datasets provide a rare opportunity to investigate the longitudinal transcriptional signatures associated with peak symptomatology, serotype and RNAemia kinetics. Implications of all the available evidenceThese data support the existence of conserved gene expression features of DENV infection, irrespective of serotype and dependent on RNAemia levels. These transcriptional signatures are relevant for our understanding of early events after DENV infection and their relationship to RNAemia as a correlate of disease severity.

immunology↗

bioRxiv2024

Immune gene expression changes more during a malaria transmission season than between consecutive seasons.

Plasmodium parasites caused over 600,000 deaths in 2022. In Mali, P. falciparum is responsible for the majority of malaria cases and deaths and is transmitted seasonally. Anti-malarial immunity develops slowly over repeated exposures to P. falciparum but some aspects of this immunity (e.g., antibody titers) wane during the non-transmission, dry season. Here, we sequenced RNA from 33 pediatric blood samples collected during P. falciparum infections at the beginning or end of a transmission season and characterized the host and parasite gene expression profiles of paired, consecutive infections. Our analyses showed that human gene expression changes more over the course of one transmission season than it does between seasons, with signatures consistent with the partial development of adaptive immunity during one transmission season, contrasting with the stability in gene expression during the dry season. By contrast, P. falciparum gene expression did not seem to vary significantly and remained stable both across and between seasons. Overall, our results provide novel insights into the dynamics of anti-malarial immunity development over short timeframes.

bioinformatics↗

bioRxiv2023

Gene expression analyses reveal differences in children's response to malaria according to their age

In Bandiagara, Mali, children experience on average two clinical malaria episodes per season. However, even in the same transmission area, the number of uncomplicated symptomatic infections, and their parasitemia, vary dramatically among children. To examine the factors contributing to these variations, we simultaneously characterized the host and parasite gene expression profiles from 136 children with symptomatic falciparum malaria and analyzed the expression of 9,205 human and 2,484 Plasmodium genes. We used gene expression deconvolution to estimate the relative proportion of immune cells and parasite stages in each sample and to adjust the differential gene expression analyses. Parasitemia explained much of the variation in both host and parasite gene expression and revealed that infections with higher parasitemia had more neutrophils and fewer T cells, suggesting parasitemia-dependent neutrophil recruitment and/or T cell extravasation to secondary lymphoid organs. The childs age was also strongly correlated with gene expression variations. Plasmodium falciparum genes associated with age suggested that older children carried more male gametocytes, while host genes associated with age indicated a stronger innate response (through TLR and NLR signaling) in younger children and stronger adaptive immunity (through TCR and BCR signaling) in older children. These analyses highlight the variability in host responses and parasite regulation during P. falciparum symptomatic infections and emphasize the importance of considering the childrens age when studying and treating malaria infections. One Sentence SummaryHuman and P. falciparum gene expression differs according to the infections parasitemia and the childs age, highlighting an age-dependent response to malaria and complex cellular and molecular -host/parasite interactions.

microbiology↗

bioRxiv2022

Malian children infected with Plasmodium ovale and Plasmodium falciparum display very similar gene expression profiles.

Plasmodium parasites caused 241 million cases of malaria and over 600,000 deaths in 2020. Both P. falciparum and P. ovale are endemic to Mali and cause malaria illness, with P. falciparum infections typically being more severe. Here, we sequenced RNA from nine pediatric blood samples collected during uncomplicated, symptomatic infections with either P. falciparum or P. ovale and characterized the host and parasite gene expression profiles. We found that human gene expression varies more between individuals than according to the parasite species causing the infection, while parasite gene expression profiles cluster by species. Additionally, we characterized DNA polymorphisms of the parasites directly from the RNA-seq reads and found comparable levels of genetic diversity in both species despite dramatic differences in prevalence. Our results provide unique insights into host-pathogen interactions during malaria infections and their variations according to the infecting Plasmodium species, which will be critical to develop better elimination strategies against all human Plasmodium parasites. Author SummaryMultiple species of Plasmodium parasites can cause human malaria. Most studies and elimination efforts target P. falciparum, the most common cause of malaria worldwide and the species responsible for the vast majority of the mortality. Other Plasmodium species, such as P. ovale, typically lead to less severe forms of the disease but little is known about the molecular mechanisms at play during malaria infections with different parasites. We analyzed host and parasite gene expression from children successively infected with P. ovale and P. falciparum and found that, while the parasite gene expression differed significantly, the transcriptional profiles of the host immune cells were similar in P. ovale or P. falciparum infections. This suggests that infected individuals respond to uncomplicated malaria infections similarly, regardless of the Plasmodium species causing the infection, and that alternative immune processes may become important during the progression to severe P. falciparum malaria (rather than being inherent features of P. falciparum infections). Additionally, we observed similar levels of genetic diversity among P. ovale and P. falciparum parasites, suggesting that the P. ovale population might be larger than currently thought, possibly due to extensive misdiagnosis or the existence of hidden reservoirs of parasites.

microbiology↗

bioRxiv2020

Atypical B cells are a normal component of immune responses to vaccination and infection in humans

The full diversity of the circulating human B cell compartment is unknown. Flow cytometry analysis suggests that in addition to naive and memory B cells, there exists a population of CD11c+, CD27- CD21- "atypical" B cells, that are associated with chronic or recurrent infection and autoimmunity. We used single cell RNA-seq approaches to examine the diversity of both antigen-specific B cells and total B cells in healthy subjects and individuals naturally-exposed to recurrent malaria infections. This analysis revealed two B cell lineages: a classical lineage of activated and resting memory B cells, and an atypical-like lineage. Surprisingly, the atypical lineage was common in both malaria exposed individuals and non-exposed healthy controls. Using barcoded antibodies in conjunction with our transcriptomic data, we found that atypical lineage cells in healthy individuals lack many atypical B markers and thus represent an undercounted cryptic population. We further determined using antigen specific probes that atypical cells can be induced by primary vaccination in humans and can be recalled upon boosting. Collectively these data suggest that atypical cells are not necessarily pathogenic but can be a normal component of B responses to antigen.

immunology↗

bioRxiv2019

Antibody feedback limits the expansion of cognate memory B cells but drives the diversification of vaccine-induced antibody responses

Generating sufficient antibody to block infection is a key challenge for vaccines against malaria. Here we show that antibody titres to a key target, the repeat region of the Plasmodium falciparum circumsporozoite protein (PfCSP), plateaued after two immunizations in a clinical trial of the radiation-attenuated sporozoite vaccine. To understand the mechanisms limiting vaccine responsiveness, we developed Ig-knockin mice with elevated numbers of PfCSP-binding B cells. We determined that recall responses were inhibited by antibody feedback via epitope masking of the immunodominant PfCSP repeat region. Importantly, the amount of antibody that prevents boosting is below the amount of antibody required for protection. Finally, while antibody feedback limited responses to the PfCSP-repeat region in vaccinated volunteers, potentially protective subdominant responses to C-terminal regions did expand with subsequent boosts. These data suggest that antibody feedback drives the diversification of immune responses and that vaccination for malaria will require the targeting of multiple antigens.

immunology↗

bioRxiv2019

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

BackgroundPlasmodium falciparum (Pf) whole-organism sporozoite vaccines have provided excellent protection against controlled human malaria infection (CHMI) and naturally transmitted heterogeneous Pf in the field. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation of these results and understanding of their relevance to vaccine efficacy (VE) have been hampered by the lack of knowledge on genetic differences between vaccine and CHMI strains, and how these strains are related to parasites in malaria endemic regions.\n\nMethodsWhole genome sequencing using long-read (Pacific Biosciences) and short-read (Illumina) sequencing platforms was conducted to generate de novo genome assemblies for the vaccine strain, NF54, and for strains used in heterologous CHMI (7G8 from Brazil, NF166.C8 from Guinea, and NF135.C10 from Cambodia). The assemblies were used to characterize sequence polymorphisms and structural variants in each strain relative to the reference Pf 3D7 (a clone of NF54) genome. Strains were compared to each other and to clinical isolates from South America, Sub-Saharan Africa, and Southeast Asia.\n\nResultsWhile few variants were detected between 3D7 and NF54, we identified tens of thousands of variants between NF54 and the three heterologous strains both genome-wide and within regulatory and immunologically important regions, including in pre-erythrocytic antigens that may be key for sporozoite vaccine-induced protection. Additionally, these variants directly contribute to diversity in immunologically important regions of the genomes as detected through in silico CD8+ T cell epitope predictions. Of all heterologous strains, NF135.C10 consistently had the highest number of unique predicted epitope sequences when compared to NF54, while NF166.C8 had the lowest. Comparison to global clinical isolates revealed that these four strains are representative of their geographic region of origin despite long-term culture adaptation; of note, NF135.C10 is from an admixed population, and not part of recently-formed drug resistant subpopulations present in the Greater Mekong Sub-region.\n\nConclusionsThese results are assisting the interpretation of VE of whole-organism vaccines against homologous and heterologous CHMI, and may be useful in informing the choice of strains for inclusion in region-specific or multi-strain vaccines.

genomics↗