Biology subjects

Auger, A.

Publications and source records attributed to Auger, A..

9 recordsLinked to original sources

bioRxiv2026

Sustained GnRH Agonism Alters Endocrine Dynamics and Pubertal Progression in Juvenile Rats

PurposeGonadotropin releasing hormone (GnRH) agonists are clinically used to delay pubertal progression by suppressing the hypothalamic-pituitary-gonadal (HPG) axis. While GnRH agonists have long been used clinically, the developmental characterization of HPG axis suppression during puberty remains incompletely understood. Thus, we examined the effects of GnRH receptor agonism in juvenile rats. HypothesisSustained GnRH receptor agonism will result in lower gonadal mass, blunt peripheral pubertal landmarks, and alter hormonal signaling dynamics within the HPG axis. MethodsAnimals received a single injection of extended-release leuprolide acetate depot (LA) or vehicle control on postnatal day (PND) 23. Animals were assessed for body mass and peripheral markers of puberty. On PND 44, animals were euthanized and tissues were evaluated to assess additional markers of pubertal maturation, pituitary gene transcript levels, and hormone concentrations in serum and gonads. ResultsIn females, LA treatment resulted in a smaller gonad size, increased body mass, and less vaginal openings. In males, LA treatment resulted in smaller gonads but did not significantly alter body mass or preputial separation. In the pituitary, LA-treated rats had lower Gnrhr, Fshb, and Lhb transcript levels regardless of sex, while females exhibited higher Cga and Nr5a1. Serum FSH and ACTH were lower in LA-treated animals, and treated females also had lower progestins and androstenedione, and higher LH. ConclusionsLA treatment reduced aspects of pubertal maturation and HPG axis output, with sex specific outcomes. These findings highlight the need for integrated, multi-level approaches to understand how altered GnRH signaling impacts pubertal and long-term physiology.

Developmental Biology↗

bioRxiv2026

Unpaired TCRα + TCRβ sequencing is sufficient for training machine learning TCR-epitope recognition predictors

T-cell recognition of infected and malignant cells is elicited by the binding of heterodimeric T-Cell Receptors (TCRs) to epitopes and both the TCR and the TCR{beta} chains play a key role in these interactions. Machine learning tools trained on databases of TCRs recognizing diverse epitopes are useful for identifying epitope-specific TCRs in large TCR repertoire datasets. However, collecting paired TCR{beta} sequences to train such tools is associated with significant sequencing costs. Here we demonstrate that unpaired TCR + TCR{beta} sequencing of epitope-specific T cells can be used for training TCR-epitope recognition predictors at a much reduced cost compared to standard single-cell TCR sequencing protocols and with no impact on prediction accuracy. Applying this approach to some unseen epitopes used in the IMMREP community benchmark demonstrates improved accuracy compared to both existing machine learning models and AlphaFold3-based predictions.

immunology↗

bioRxiv2026

Apoplast multi-omics profiling during fungal infection uncovers new players of basal and early induced immunity

The extracellular space in plant tissues, known as the apoplast, remains one of the least characterized cellular compartments. The apoplastic fluid (APF), akin to mammalian extracellular fluid, serves as the primary interface between pathogens and their host. It allows the exchange of signalling molecules, coordinates host cell responses, and enables the circulation of pathogen effectors that modulate the immune response. We describe here the first multi-omics analysis of the APF content just 6 h after the onset of A. thaliana infection with B. cinerea, a fast-killing necrotrophic fungus. By varying plant nitrogen nutrition, known to affect both plant defenses and pathogen virulence, we identify candidates that do not stand out under optimal conditions. Our analysis uncovers novel nitrogen-dependent mechanisms that regulate both basal and early induced apoplastic immunity, revealing the presence of previously unidentified, potentially protective apoplastic metabolites as well as the intercellular transport of nuclear proteins, thereby offering new insights into early apoplastic immune responses.

plant biology↗

bioRxiv2026

Applications of T-cell receptor specificity annotation models for quality control and immunomonitoring in adoptive T-cell therapies

Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TIL) is a powerful candidate immunotherapy. However, the personalized production process that underlies its potential also introduces an element of stochasticity, where the actual target of the TILs is variable across patients and protocols, and remains largely unknown. In this letter, we describe the application of T-cell receptor (TCR) sequencing in combination with computational tools for annotating epitope-specificity of the TCR repertoire of TIL products as a potent quality control. We highlight the potential of this approach by demonstrating the tumor antigen-specificity of TCR clusters within the TIL product in silico, and validating these responses in vitro. We also demonstrate screening for off-cancer reactivity against viral antigens, and immune monitoring of identified TCR clones. HighlightsO_LIT-cell receptor sequencing combined with epitope annotation tools are viable for quality control of TIL products by identifying tumor-specific clones. C_LIO_LIWe showed the additional utility of screening for off-cancer reactivity, such as viral antigens. C_LIO_LIThe identified tumor-specific TCR clones can be tracked in vivo providing a means of immune monitoring. C_LI

bioinformatics↗

bioRxiv2025

Affiliative behavioural phenotype and microglial activation predict social decision-making following immune activation

Social animals are faced with a critical decision when sick: to affiliate or withdraw. The behavioural response during an immune challenge varies by individual and species. However, the social and biological factors leading to variation in this decision during an immune challenge are unknown. Here, we explore the affiliative behavioural phenotype, "huddlers" and "non-huddlers," as a social predictor, and microglial activation and peripheral cytokine expression as biological predictors of social-decision making during an immune challenge. To measure social-decision making, we recorded social approach and time spent in proximity to a familiar same-sex conspecific versus a novel object in the social California mouse following lipopolysaccharide (LPS) treatment. Behavioural phenotype predicted both the social response to LPS and the relationship between cytokine activity and social behaviour, suggesting that social experience regulates social decision-making during sick versus healthy conditions. Additionally, we found that elevated microglia activity in the dentate gyrus (DG) and medial prefrontal cortex (mPFC) negatively correlated with social behaviour, positioning these regions for future exploration for the role of microglia on social decision-making. Our results identify the predictive power of behavioural phenotypes on social response to sickness and a link between microglia and decision-making during sickness.

neuroscience↗

bioRxiv2023

Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome.

Colletotrichum destructivum (Cd) is a phytopathogenic fungus causing significant economic losses on forage legume crops (Medicago and Trifolium species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from M. sativa using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises 10 core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15,631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of Cd relative to the closely-related Brassicaceae pathogen, C. higginsianum. In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of Cd that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen. Impact statementColletotrichum is a large genus of fungal phytopathogens that cause major economic losses on a wide range of crop plants throughout the world. These pathogens vary widely in their host specificity and may have either broad or narrow host ranges. Here, we report the first complete genome of the alfalfa (Medicago sativa) pathogen, Colletotrichum destructivum, which will facilitate the genomic analysis of host adaptation and comparison with other members of the Destructivum species complex. We identified a species-specific 1.2 Mb region within chromosome 1 displaying all the hallmarks of fungal accessory chromosomes, which may have arisen through the integration of a mini-chromosome into a core chromosome and could be linked to the pathogenicity of this fungus. We show this region is also a focus for segmental duplications, which may contribute to generating genetic diversity for adaptive evolution. Finally, we report infection by this fungus of the model legume, Medicago truncatula, providing a novel pathosystem for studying fungal-plant interactions. Data summaryAll RNA-seq data were submitted to the NCBI GEO portal under the GEO accession GSE246592. C. destructivum genome assembly and annotation are available under the NCBI BioProject PRJNA1029933 with sequence accessions CP137305-CP137317. Supplementary data (genomic and annotation files, genome browser) are available from the INRAE BIOGER Bioinformatics platform (https://bioinfo.bioger.inrae.fr/). Transposable Elements consensus sequences are also available from the French national data repository, research.data.gouv.fr with doi 10.57745/TOO1JS.

genomics↗

bioRxiv2023

Tumor-reactive clonotype dynamics underlying clinical response to TIL therapy in melanoma

The profiles, specificity and dynamics of tumor-specific clonotypes that are associated with clinical response to adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TILs) remain unclear. Using single-cell RNA/TCR-sequencing, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients treated with TIL-ACT. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, which were more effectively mobilized upon in vitro expansion, yielding products with higher numbers of tumor-specific CD8+ cells, which also preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes, and with cell products mostly composed of blood-borne clonotypes mainly persisting in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost the specific signatures of states originally exhibited in tumors, including exhaustion, and in responders acquired an intermediate exhausted effector state after tumor engraftment, revealing important functional cell reinvigoration.

cancer biology↗

bioRxiv2019

Integrated Proteogenomic Deep Sequencing and Analytics Accurately Identify Non-Canonical Peptides in Tumor Immunopeptidomes

Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides that derive from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass-spectrometry (MS)-based proteogenomics approaches are required to robustly identify these non-canonical peptides. We present an MS-based analytical approach that characterizes the non-canonical tumor HLA peptide repertoire, by incorporating whole exome sequencing, bulk and single cell transcriptomics, ribosome profiling, and a combination of two MS/MS search tools. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLA peptides and of an immunogenic peptide from a downstream reading frame in the melanoma stem cell marker gene ABCB5. It holds great promise for the discovery of novel cancer antigens for cancer immunotherapy.

cancer biology↗

bioRxiv2019

The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host-specialized and generalist populations

The host plant is often the main variable explaining population structure in fungal plant pathogens, because specialization contributes to reduce gene flow between populations associated with different hosts. Previous population genetic analysis revealed that French populations of the grey mould pathogen Botrytis cinerea were structured by hosts tomato and grapevine, suggesting host specialization in this highly polyphagous pathogen. However, these findings raised questions about the magnitude of this specialization and the possibility of specialization to other hosts. Here we report specialization of B. cinerea populations to tomato and grapevine hosts but not to other tested plants. Population genetic analysis revealed two pathogen clusters associated with tomato and grapevine, while the other clusters co-occurred on hydrangea, strawberry and bramble. Measurements of quantitative pathogenicity were consistent with host specialization of populations found on tomato, and to a lesser extent, populations found on grapevine. Pathogen populations from hydrangea and strawberry appeared to be generalist, while populations from bramble may be weakly specialized. Our results suggest that the polyphagous B. cinerea is more accurately described as a collection of generalist and specialist individuals in populations. This work opens new perspectives for grey mold management, while suggesting spatial optimization of crop organization within agricultural landscapes.

microbiology↗