Biology subjects

Perrin, A.

Publications and source records attributed to Perrin, A..

14 recordsLinked to original sources

bioRxiv2026

Functional diversity of Vγ9Vδ2 T cells overcomes glioblastoma state plasticity and antigen heterogeneity

Glioblastoma (GBM) is characterized by a high degree of cellular plasticity and intra-tumoral heterogeneity, which frequently leads to the failure of standard therapies, including immunotherapies. While chimeric antigen receptor (CAR) T cells offer a potent means of MHC-independent tumor recognition, their efficacy is hampered by the coexistence of distinct molecular states, gathered as proneural (PN) and mesenchymal (MES) phenotypes. Here, we demonstrate that gangliosides GD2 and O-acetylated GD2 (OAcGD2) are preferentially expressed by PN cells whereas MES cells display reduced expression due to upregulated ganglioside catabolism. Conversely, MES cells are known to exhibit high expression of stress-induced ligands recognized by V{gamma}9V{delta}2 T cells. We show that while engineering V{delta}2T cells with GD2- or OAcGD2-specific CAR enables the elimination of PN cells, it also facilitates the immune escape of MES cells in heterogeneous 3D-tumoroid models. Mechanistically, we reveal a hierarchy of receptor engagement, where CAR signaling predominates leading to the structural and functional exclusion of endogenous TCR from the immunological synapse. To address this receptor competition, we propose a strategy that leverages the functional effector diversity by combining untransduced and CAR-engineered V{delta}2T cells. This dual approach provides a dynamic safety net by ensuring the simultaneous elimination of PN and MES cells and preventing the selective outgrowth of resistant cells. Our findings establish a conceptual framework for designing off-the-shelf immunotherapies tailored to the metabolic and phenotypic plasticity of resistant solid tumors.

cancer biology↗

bioRxiv2025

Deciphering the Replication-Division Coordination in E. coli: A Unified Mathematical framework for Systematic Model Comparison

Despite extensive research, the quantitative principles that govern the coordination between DNA replication and cell division in bacteria remain debated. Multiple theoretical models have been proposed, some postulating that a single regulatory process is sufficient to ensure replication-division coordination, while others argue that two concurrent processes are required for robust control. In this work, we develop a unifying mathematical framework within which models can be consistently formulated, qualitatively analysed and quantitatively compared. This framework also allows us to propose a new double-process model. Through theoretical analysis, we establish the necessary and sufficient conditions under which single-process models can reproduce physiological cell behaviours. Beyond the correlation-based analyses extensively used to date, we further demonstrate within a comprehensive statistical framework that double-process models more accurately recapitulate experimental data across all growth conditions. Specifically, the new model we propose robustly captures the replication-division coordination in every growth regime, thereby providing a foundation for future mechanistic studies. Author SummaryHow bacteria regulate their cell size and ensure complete chromosome replication before division remains only partly understood, posing a fundamental question. A key challenge is understanding how bacterial cells reliably distribute their genetic material to daughter cells while managing randomness in division timing, especially since DNA replication is often initiated in earlier generations. Over the past decade, several models have been developed to describe the coordination of DNA replication and cell division in Escherichia coli, combining different mechanisms and levels of complexity. These models have mainly been evaluated through correlation analysis between cell cycle parameters, such as the size at which bacteria divide or initiate DNA replication. However, such analyses depend on strong underlying assumptions that are not always met by the experimental data. Here, we present a general framework that systematically integrates multiple models, allowing both qualitative analysis and quantitative comparison without relying on correlations. Our work concludes that under all growth conditions, E. coli cells most likely divide only after meeting two combined requirements: adding a critical size since birth and a critical size since the initiation of DNA replication.

cell biology↗

bioRxiv2025

Enhancing Embryo Stage Classification with Multi-Focal Plane Imaging and Deep Learning

PurposeAccurately identifying embryo developmental stages is crucial for improving success rates in in vitro fertilization (IVF). Traditional embryo assessment relies on 2D imaging with a single focal plane, which may overlook critical morphological details and lead to misclassification. This study investigates whether incorporating depth information through multi-focal plane imaging can enhance the accuracy of embryo stage classification. MethodsWe compared 2D and 3D convolutional neural network (CNN) architectures trained on a time-lapse embryo dataset containing seven focal planes. The models were evaluated based on their classification performance across different embryo developmental stages. Additionally, we used Gradient-weighted Class Activation Mapping (Grad-CAM) to analyze model attention and interpretability. ResultsThe findings demonstrate that 3D CNN models leveraging multi-focal plane data significantly outperform their 2D counterparts, particularly in complex stages such as Morula formation (tM) and expanded blastocyst (tSB, tB, and tEB). Grad-CAM visualization confirms that the models focus on relevant morphological structures, further validating the advantages of volumetric modeling. ConclusionMulti-focal plane imaging enhances embryo stage classification accuracy by providing richer morphological information. This study underscores the potential of volumetric modeling in embryo assessment and paves the way for extending this approach to full 3D time-lapse analysis.

developmental biology↗

bioRxiv2025

Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump

Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promises to enable the discovery and quantification of individual RNA isoforms at the single-cell level. However, highly multiplexed data such as from a single cell experiment only generates a limited number of reads for each cell, constituting a major challenge for transcript discovery and quantification with existing approaches that usually have limited power for samples with low sequencing depth. Here we present Bambu-Clump, a computational method that performs transcript discovery and quantification from single cell and spatial long read RNA-Seq data using information from both each cell and the cell cluster. Using this approach, Bambu-Clump provides the most accurate transcript discovery compared to other existing methods, and improves transcript quantification compared to methods that rely on estimates derived from single cells. We apply Bambu-Clump to identify fusion transcripts in single-cells, compare 5 and 3 selection protocols, and identify novel isoform cell-type markers in spatial mouse brain data. Together, Bambu-Clump provides an easy-to-use, efficient, and accurate method for analysing individual isoform expression for single cells and cell clusters across multiple datasets and replicates from long read RNA-Seq.

bioinformatics↗

bioRxiv2024

Highly enhanced transgene integration in human pluripotent stem cells by serine integrase BxbI

Genome engineering and especially integration of large DNA payloads in human pluripotent stem cells (hPSC) remains challenging largely due to the sensitive nature of hPSCs. Site specific recombinases such as the serine integrase Bxb1 have been utilised successfully to target hPSC, however the targeting efficiencies remain low. Here we leveraged codon optimisation, inclusion of a nuclear localisation signal, mRNA modality and co-introduction of p53 dominant negative fragment to increase the transgene payload integration efficiency by up to 20-fold in defined genomic safe harbours in hPSCs.

synthetic biology↗

bioRxiv2024

Comparative impact of porcine reproductive and respiratory virus and swine influenza A virus infections on respiratory lymph nodes B cells and macrophages.

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) strongly impacts the pig rearing sector due to its persistence in infected animals. Interestingly, although the PRRSV family exhibits considerable genome variability, with the PRRSV-1 and PRRSV-2 subtypes having been finally classified in two different species (Betaarterivirus suid 1 and 2). Both viruses, as well as their derived-attenuated vaccine strains, persist for months, due in part to their ability to delay the appearance of neutralizing antibodies. Thanks to extensive efforts over the past years, we have developed the capability to perform in-depth analysis of the previously poorly understood porcine inverted lymph node (LN). In this study, by comparing the early stages of LN B cell maturation upon PRRSV-1 infection to those induced upon the acute swine influenza A virus infection, we highlighted PRRSV-specific mechanisms, including the expression of PD-L1 in efferent macrophages, the induction of extrafollicular plasmocytes, and the influx of inflammatory monocytes/macrophages. Studies on PRRSV-2 infections report observations compatible with our results, that thus might be generalized to all PRRSV-strains. Moreover, these mechanisms can be compared with those used by the human immunodeficiency virus (HIV) and the murine chronic lymphocytic choriomeningitis virus (LCMV) to hijack the immune response. These similarities can be harnessed to develop new strategies to improve the development of more efficient anti-PRRSV vaccines.

immunology↗

bioRxiv2024

CyanoTag: Discovery of protein function facilitated by high-throughput endogenous tagging in a photosynthetic prokaryote

Despite their fundamental importance to aquatic ecosystems, global carbon cycling and exciting potential in sustainable bioindustries, the genomes of photosynthetic prokaryotes still contain large numbers of uncharacterised protein-coding genes. Here we present a high-throughput approach for scarless endogenous fluorescent protein tagging in the model cyanobacterium Synechococcus elongatus PCC7942. From 400 targets we successfully endogenously tag over 330 proteins corresponding to >10% of the proteome. We demonstrate how this resource can be used at scale to determine subcellular localisation, track relative protein abundances and to elucidate protein-protein interaction networks. Our data has provided biological insights into a diverse range of processes - from photosynthesis to cell division. Of particular interest, our CyanoTag lines enabled us to visualise in real time the rapid condensation of Calvin Cycle proteins Prk and Gap2 within seconds of withdrawal of light, effectively switching off photosynthesis in the dark. These insights, CyanoTag cell lines, associated data and optimised methods are intended to be shared as a resource to facilitate further discoveries relevant to cyanobacteria and more broadly to all photosynthetic life.

microbiology↗

bioRxiv2021

Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells

Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites in vitro using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easy targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.

bioengineering↗

bioRxiv2021

The novel conserved NAD+ binding micropeptide SGHRT regulates mitochondrial function and metabolism in human cardiomyocytes

AbstractsNicotinamide adenine dinucleotide (NAD) is a critical metabolite and coenzyme for multiple metabolic pathways and cellular processes (1-4). In this study, we identified Singheart, SGHRT as a nuclear genome-encoded NAD+-binding mitochondrial micropeptide. SGHRT, present in both monomeric and dimeric forms, binds directly to NAD, but not NADH or flavin adenine dinucleotide (FAD). Localized to the inner mitochondrial membrane and mitochondrial matrix, SGHRT interacts with the mitochondrial enzymes Succinate-CoA Ligase and Succinate Dehydrogenase. SGHRT deletion in human embryonic stem cell derived cardiomyocytes disrupted mitochondria morphology, decreased total NAD and ATP abundance, and resulted in defective TCA cycle metabolism, the electron transport chain and in Ox-Phos processes. These results comprise the first report of an NAD+-binding micropeptide, SGHRT, required for mitochondrial function and metabolism.

cell biology↗

bioRxiv2020

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Escherichia coli is a commensal of birds and mammals, including humans. It can act as an opportunistic pathogen and is also found in water and sediments. Since most population studies have focused on clinical isolates, we studied the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000, mostly non-clinical, isolates originating from humans, poultry, wild animals and water sampled from the Australian continent. These strains represent the species diversity and show large variations in gene repertoires within sequence types. Recent gene transfer is driven by mobile elements and determined by habitat sharing and by phylogroup membership, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. The phylogroups with smallest genomes had the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements, suggesting that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these small genomes were in freshwater isolates suggesting that some lineages are specifically adapted to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.

microbiology↗

bioRxiv2019

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and dont account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN. Author summaryMicroorganisms have the greatest biodiversity and evolutionary history on earth. At the genomic level, it is reflected by a highly variable gene content even among organisms from the same species which explains the ability of microbes to be pathogenic or to grow in specific environments. We developed a new method called PPanGGOLiN which accurately represent the genomic diversity of a species (i.e. its pangenome) using a compact graph structure. Based on this pangenome graph, we classify genes by a statistical method according to their occurrence in the genomes. This method allowed us to build pangenomes even for uncultivated species at an unprecedented scale. We applied our method on all available genomes in databanks in order to depict the overall diversity of hundreds of species. Overall, our work enables microbiologists to explore and visualize pangenomes alike a subway map.

bioinformatics↗

bioRxiv2019

Divergent DNA methylation signatures of juvenile seedlings grafts and adult apple trees

Plants are continuously exposed to environmental perturbations. Outcrossing annual plants can adapt rapidly to these changes via sexual mating and DNA mutations. However, perennial and clonally reproducing plants may have developed particular mechanisms allowing them to adapt to these changes and transmit this information to their offspring. It has been proposed that the mechanisms allowing this plasticity of response could come in the form of epigenetic marks that would evolve throughout a plants lifetime and modulate gene expression. To study these mechanisms, we used apple (Malus domestica) as a model perennial and clonally propagated plant. First, we investigated the DNA methylation patterns of mature trees compared to juvenile seedlings. While we did not observe a drastic genome-wide change in DNA methylation levels, we found clear changes in DNA methylation patterns localized in regions enriched in genes involved in photosynthesis. Transcriptomic analysis showed that genes involved in this pathway were overexpressed in seedlings. Secondly, we compared global DNA methylation of a newly grafted plant to its mother tree to assess if acquired epigenomic marks were transmitted via grafting. We identified clear changes, albeit showing weaker DNA methylation differences. Our results show that a majority of DNA methylation patterns from the tree are transmitted to newly grafted plants albeit with specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their mother tree.

plant biology↗

bioRxiv2019

CTCF controls imprinted gene activity at the mouse Dlk1-Dio3 and Igf2- H19 domains by modulating allele-specific sub-TAD structure

Mammalian genomic imprinting is essential for development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. Here, we compared chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints--the Igf2-H19 and the Dlk1-Dio3 domains--and assessed the involvement of the insulator protein CTCF. At both domains, CTCF binds the maternal allele of a differentially-methylated region (DMR), in addition to multiple instances of bi-allelic CTCF binding in their surrounding TAD (Topologically Associating Domain). On the paternal chromosome, bi-allelic CTCF binding alone is sufficient to structure a first level of sub-TAD organization. Maternal-specific CTCF binding at the DMRs adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal sub-TAD organisation. Genome-editing experiments at the Dlk1-Dio3 locus confirm that the maternal sub-TADs are essential during development to maintain the imprinted Dlk1 gene in an inactive state on the maternal chromosome.

molecular biology↗

bioRxiv2019

The NEDD8 cycle controlled by NEDP1 upon DNA damage is a regulatory module of the HSP70 ATPase activity

Ubiquitin and ubiquitin-like chains are finely balanced by the action of conjugating and de-conjugating enzymes. Alterations in this balance trigger signalling events required for the response to stress conditions and are often observed in pathologies. How such changes are detected is not well-understood. We show that upon DNA damage the induction of the de-NEDDylating enzyme NEDP1 restricts the formation of poly-NEDD8 chains, mainly through lysines K11/K48. This promotes APAF1 oligomerisation and apoptosis induction, a step that requires the HSP70 ATPase activity. We found that HSP70 binds to NEDD8 and in vitro, mono-NEDD8 stimulates the ATPase activity of HSP70, counteracted upon poly-NEDDylation. This effect is independent of NEDD8 conjugation onto substrates. The studies identify the HSP70 chaperone as sensor of changes in the NEDD8 cycle, providing mechanistic insights for a cytoplasmic role of NEDD8 in the DNA damage induced apoptosis. They also indicate that the balance between mono- versus poly-NEDDylation is a regulatory module of HSP70 function. The above findings may be important in tumorigenesis, as we find that NEDP1 levels are downregulated in Hepatocellular Carcinoma with concomitant accumulation of NEDD8 conjugates.

molecular biology↗