Biology subjects

Carre, A.

Publications and source records attributed to Carre, A..

7 recordsLinked to original sources

bioRxiv2026

Coxsackievirus B Escapes Antiviral CD8⁺ T Cells but Triggers Robust CD4⁺ Memory Responses

Coxsackieviruses B (CVBs) are plausible triggers of the pancreatic islet autoimmunity leading to type 1 diabetes. Islet autoantibody seroconversion correlates with persistent CVB infections in the gut and pancreas, suggesting defective antiviral control and the need to define immune mechanisms at the intestinal entry site. We investigated how CVB3 modulates antigen presentation, the viral immunopeptidome of enterocytes and antigen-presenting cells, and downstream T-cell immunity. CVB3-infected enterocytes escaped immune recognition by downregulating HLA Class I and viral peptide presentation, impairing CD8+ T-cell responses in vitro. In CVB-seropositive individuals, circulating CVB-reactive CD8+ T cells were stalled in naive-like and exhausted effector/memory states. In contrast, CVB3 induced HLA class II upregulation, promoting robust CD4 T-cell activation. Circulating CVB3-reactive CD4 T cells fully differentiated into polyfunctional T helper memory. These findings indicate that CVB3 antiviral control is predominantly CD4 T-cell-mediated and provide a rationale for mucosal vaccination strategies and immune monitoring tools to follow infection or vaccination. TeaserCoxsackievirus evades CD8+ T-cell immunity in the gut, leaving CD4+ T cells as the main line of antiviral defense.

immunology↗

bioRxiv2025

Decoding interaction-induced proteome changes in co-cultures with hybrid quantification and SILAC-directed real-time search

Intercellular communication between T cells and cancer cells plays a pivotal role in determining cancer cell survival or death. Yet, our understanding of this interaction remains incomplete. Methods to study heterotypic cell interactions are either limited to targeted studies relying on predefined set of proteins, or require cell separation, thus disrupting the native environment. Stable isotope labeling by amino acids in cell culture (SILAC) enables proteome distinction in heterologous co-cultures without the need for physical separation. But dynamic studies remain constrained by the need for numerous mass spectrometry (MS) runs, the challenges in detecting low-abundant proteins, particularly in immune cells and the limited data completeness due to the use of data-dependent MS1-based precursor quantification. To overcome these limitations, we evaluate the integration of SILAC with tandem mass tag (TMT) multiplexing and SILAC-directed real-time search (RTS). TMT labeling enables simultaneous analysis of multiple samples, while RTS-MS3 acquisition using SILAC-induced mass shifts as fixed modifications triggers MS3 scans for specific proteome populations within a mixed cell system, improving quantitative accuracy and proteome coverage for target protein populations. We benchmarked our acquisition methods using SILAC-labeled samples mixed at defined ratios and validated the approach in biologically relevant co-culture experiments. Additionally, we introduced a carrier channel to enhance detection of lower-abundant T cell proteins, while maintaining acceptable quantitative precision. Our results demonstrate that the combined SILAC-TMT-RTS strategy dramatically improves proteome depth, temporal resolution, and cell-type specificity for short-term co-culture interaction proteomics studies. In co-culture samples of T cells with non-small cell lung cancer cell lines that were either sensitive or resistant to T cell killing, our method revealed candidate mechanisms underlying their differential sensitivity. Our integrated approach combining SILAC, TMT and RTS to resolve cell-specific proteome dynamics in co-culture represents a novel and powerful advance.

cancer biology↗

bioRxiv2025

GGA2-depletion in beta cells by Enteroviruses causes Golgi acidification, premature activation of cathepsins and alters the MHC class I immunopeptidome

Enteroviruses (EVs), such as Coxsackievirus B5 (CVB5), are linked to pancreatic beta cell autoimmunity in type 1 diabetes (T1D). CVB5 infection of beta cells blocks their cap-dependent translation but spares cap-independent translation of insulin secretory granule (SG) cargoes, including major T1D autoantigens. Despite this, insulin SG stores are depleted. We show that CVB5 protease 2A rapidly depletes Golgi-associated sorting factor GGA2 in beta cells due to its short half-life. Immunostaining of pancreas sections from recent-onset T1D donors confirmed reduced GGA2 in beta cells expressing EV capsid protein VP1. Both GGA2 depletion and CVB5 2A expression impair SG biogenesis at the TGN without affecting MHC class I trafficking. They also disrupt the sorting of vacuolar ATPase and cathepsins, leading to TGN acidification and premature lysosomal hydrolase activation, which typically generate peptides presented in HLA-II alleles. Notably, the unique immunopeptidome of EV-infected, GGA2-depleted ECN90 beta-like cells is mainly presented via HLA-B alleles with an average isoelectric point (pI) of [~]5, compared to a pI of [~]7 of the prevailing HLA-I A allele immunopeptidome of non-infected cells. We propose that delayed sorting at the acidified TGN promotes cathepsin-mediated processing of in-transit secretory proteins, including SG cargoes, thereby generating novel peptides that may replace HLA class I antigens due to the acidic environment. This novel cross-presentation mechanism could have implications for T1D pathogenesis and antigen presentation in general.

cell biology↗

bioRxiv2023

The diallelic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene

Sexual reproduction in flowering plants is commonly controlled by self-incompatibility (SI) systems that are either homomorphic (and typically governed by large numbers of distinct allelic specificities), or heteromorphic (and then typically governed by only two allelic specificities). The SI system of the Oleaceae family is a striking exception to this rule and represents an evolutionary conundrum, with the long-term maintenance of only two allelic specificities, but often in the complete absence of morphological differentiation between them. To elucidate the genomic architecture and molecular bases of this highly unusual SI system, we obtained chromosome-scale genome assemblies of Phillyrea angustifolia individuals belonging to the two SI specificities and connected them to a genetic map. Comparison of the S-locus region revealed a segregating 543-kb indel specific to one of the two specificities, suggesting a hemizygous genetic architecture. Only one of the predicted genes in this indel is conserved with the olive tree Olea europaea, where we also confirmed the existence of a segregating hemizygous indel. We demonstrated full association between presence/absence of this gene and the SI groups phenotypically assessed across six distantly related Oleaceae species. This gene is predicted to be involved in catabolism of the Gibberellic Acid (GA) hormone, and experimental manipulation of GA levels in developing buds modified the male and female SI responses in an S-allele-specific manner. Thus, our results provide a unique example of a reproductive system where a single conserved gibberellin-related gene in a 500-700kb hemizygous indel underlies the long-term maintenance of two groups of reproductive compatibility.

evolutionary biology↗

bioRxiv2023

Interferon-α promotes neo-antigen formation andpreferential HLA-B-restricted antigen presentation in pancreatic β-cells

Interferon (IFN)- is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic {beta}-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN--exposed {beta}-cells. IFN- increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting {beta}-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN- only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and we identified islet-infiltrating CD8+ T-cells from T1D donors reactive to HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.

immunology↗

bioRxiv2023

Coxsackievirus infection induces direct pancreatic β-cell killing but poor anti-viral CD8+ T-cell responses

Coxsackievirus B (CVB) infection of pancreatic {beta} cells is associated with {beta}-cell autoimmunity. We investigated how CVB impacts human {beta} cells and anti-CVB T-cell responses. {beta} cells were efficiently infected by CVB in vitro, downregulated HLA Class I and presented few, selected HLA-bound viral peptides. Circulating CD8+ T cells from CVB-seropositive individuals recognized only a fraction of these peptides, and only another sub-fraction was targeted by effector/memory T cells that expressed the exhaustion marker PD-1. T cells recognizing a CVB epitope cross-reacted with the {beta}-cell antigen GAD. Infected {beta} cells, which formed filopodia to propagate infection, were more efficiently killed by CVB than by CVB-reactive T cells. Thus, our in-vitro and ex-vivo data highlight limited T-cell responses to CVB, supporting the rationale for CVB vaccination trials for type 1 diabetes prevention. CD8+ T cells recognizing structural and non-structural CVB epitopes provide biomarkers to differentially follow response to infection and vaccination.

immunology↗

bioRxiv2021

Genetic mapping of sex and self-incompatibility determinants in the androdioecious plant Phillyrea angustifolia

AO_SCPLOWBSTRACTC_SCPLOWThe diversity of mating and sexual systems in angiosperms is spectacular, but the factors driving their evolution remain poorly understood. In plants of the Oleaceae family, an unusual self-incompatibility (SI) system has been discovered recently, whereby only two distinct homomorphic SI specificities segregate stably. To understand the role of this peculiar SI system in preventing or promoting the diversity of sexual phenotypes observed across the family, an essential first step is to characterize the genetic architecture of these two traits. Here, we developed a high-density genetic map of the androdioecious shrub P. angustifolia based on a F1 cross between a hermaphrodite and a male parent with distinct SI genotypes. Using a double restriction-site associated digestion (ddRAD) sequencing approach, we obtained reliable genotypes for 196 offspring and their two parents at 10,388 markers. The resulting map comprises 23 linkage groups totaling 1,855.13 cM on the sex-averaged map. We found strong signals of association for the sex and SI phenotypes, that were each associated with a unique set of markers on linkage group 12 and 18 respectively, demonstrating inheritance of these traits as single, independent, mendelian factors. The P. angustifolia linkage map shows robust synteny to the olive tree genome overall. Two of the six markers strictly associated with SI in P. angustifolia have strong similarity with a recently identified 741kb chromosomal region fully linked to the SI phenotype on chromosome 18 of the olive tree genome, providing strong cross-validation support. The SI locus stands out as being markedly rearranged, while the sex locus has remained relatively more collinear between the two species. This P. angustifolia linkage map will be a useful resource to investigate the various ways by which the sex and SI determination systems have co-evolved in the broader phylogenetic context of the Oleaceae family.

evolutionary biology↗