Biology subjects

Lemoine, S.

Publications and source records attributed to Lemoine, S..

11 recordsLinked to original sources

bioRxiv2026

The human-specific gene FRMPD2B couples postnatal experience to the expansion of cortical connectivity

The human neocortex is characterized by its uniquely prolonged postnatal developmental period during which experience sculpts neuronal circuits, a process essential to human cognitive abilities. Yet whether human-specific genetic innovations have shaped the activity-dependent mechanisms regulating circuit assembly remains unknown. Here, we identify the human-specific gene FRMPD2B as an activity- and experience-regulated modifier of cortical connectivity. FRMPD2B is primarily expressed in cortico-cortical projection neurons postnatally and throughout childhood. It promotes dendritic, axonal and synaptic development, and is required for proper morphogenesis in xenotransplanted human cortical neurons. FRMPD2B expression is bidirectionally regulated by neuronal activity and experience. This activity-responsiveness was gained after FRMPD2B arose through partial gene duplication, when a retrotransposon insertion remodeled its promoter. Our findings highlight how a series of genetic innovations have led to the emergence of a human-specific activity-regulated developmental program through which postnatal experience drives cortical connectivity expansion, linking genome evolution to human brain plasticity.

neuroscience↗

bioRxiv2025

Regeneration of distinct complex structures in the annelid Platynereis is partially based on common morphological, cellular, and molecular events

Many metazoan species harbor fascinating regenerative capabilities, but the underlying mechanisms remain poorly understood. Whether the capacity to regenerate complex structures successfully relies on common or divergent features is still an open question. To identify the key molecular and cellular elements necessary for successful regeneration, we investigated the efficient regeneration of two distinct complex structures in the annelid worm Platynereis dumerilli. By combining classical morphological and developmental approaches, with state-of-the-art single-cell RNA sequencing and analysis, we conducted a comprehensive comparison of locomotory appendage and posterior part regeneration. We uncovered the rich cell type diversity of this Platynereis appendage, over a third of which are nerve-related populations, highlighting the importance of its sensory function. We also described its regenerative process at the morphological and cellular levels, defining stages that include the formation of a proliferative blastema. We then compared posterior part and appendage blastemas, specifically assessing their cell diversity and cell differentiation trajectories. We found transcriptionally similar epithelial and mesodermal progenitors at play during posterior and appendage regeneration, although their specific trajectories differed to some extent. Our work, revealing partial morphological, molecular and cellular parallels between these two efficient regenerations within a single species, sets the foundation for addressing the fundamental question of regeneration success in animals.

developmental biology↗

bioRxiv2025

Common origin for effector and regulatory Follicular and Tissue-Adapted CD4+ T cells in Non-Small Cell Lung Cancer

Tumor-invaded lymph nodes (LNs) serve as critical hubs for anti-tumor immunity, yet their role in orchestrating immune responses remains poorly understood. Using integrated single-cell RNA sequencing, T cell receptor sequencing, and chromatin accessibility profiling, we analyzed CD4+ T cells from matched blood, tumor-invaded LNs, and tumors of treatment-naive non-small cell lung cancer patients. We identified distinct immunological landscapes across these compartments. Compared to blood, tumor-invaded LNs and tumors were enriched for follicular regulatory T cells (Treg-Tfr), conventional T cell subsets with Tfh-like characteristics (Tconv-Tfh and Tconv-CXCL13), and tissue-resident memory Tregs (Treg-Trm). These populations share a BATF-dependent transcriptional program that governs T-cell activation and tissue adaptation, while simultaneously engaging distinct, subset-specific regulatory networks. Integrative TCR-RNA analysis revealed that tumor-reactive, neoantigen-specific T cell clones were enriched within these subsets and demonstrated extensive LN-tumor clonal sharing, indicating active recirculation between compartments. Through clonal coupling analysis and trajectory inference, we uncovered that Treg-Tfr cells function as multipotent progenitors that bifurcate into tissue-resident Treg-Trm or into ex-Tregs adopting a Tfh-like CXCL13+ ewector phenotype. Remarkably, follicular CD4+ T subsets from LNs and tumor were transcriptionally and epigenetically similar and localized to analogous germinal center niches. These findings establish tumor-invaded LNs as functional extensions of the tumor microenvironment that generate and maintain tumor-reactive CD4+ lineages. The identification of tissue-resident Treg-Tfr plasticity reveals a critical developmental checkpoint that could be therapeutically targeted to redirect immunosuppressive programs toward anti-tumor ewector responses.

immunology↗

bioRxiv2025

A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data

Alternative splicing plays a crucial role in transcriptomic complexity, yet remains difficult to resolve at the single-cell level due to the limitations of short-read technologies. Coupling single-cell with long-read sequencing offers full-length transcript coverage, enabling more accurate isoform detection. Multiple specialized computational tools tailored for single-cell and spatial long-read transcriptomics have been developed, with diverse strategies. To compare the effectiveness of these approaches, we generated paired short-read and Nanopore long-read single-cell datasets, tailored for benchmarking bioinformatics tools. We evaluated ten state-of-the-art methods, spanning four analytical dimensions: barcodes and UMI detection, demultiplexing and UMI clustering, gene-level expression profiling, and isoform detection and quantification. Using real and simulated datasets across different protocols, sequencing depths and chemistries, we assessed the accuracy, robustness, and scalability of each tool. Our results revealed method-specific trade-offs, and highlight the importance of sequencing quality and UMI correction strategies. This benchmark provides a practical resource for optimizing isoform analysis and accurate gene expression profiling in single-cell and spatial transcriptomics using long-read sequencing. Our benchmarking workflow is designed to be reusable, thereby enabling method developers to compare their own approaches against the set of reference methods evaluated in this work.

bioinformatics↗

bioRxiv2025

Evolution of opsin genes in closely-related species of butterflies specialized in different microhabitats.

How do adaptive processes acting on the coevolution of opsin genes shape the evolution of colour vision in animals? At large phylogenetic scales, natural selection due to the contrasted light environments has been found to impact the evolution of photoreceptor genes. However, in closely-related species, species interactions due to sexual selection or competition may also influence opsin evolution. Here, we investigate the diversification of opsin sequences and their expression in closely-related blue Morpho butterfly species, living in different vertical strata within tropical forests, to shed light on the biotic and abiotic selective pressures shaping the coordinated evolution of opsin genes. We combined comparative genomics, transcriptomics, and immunochemistry to characterize the expression and the spatial distribution of the opsin proteins found in the eyes of Morpho helenor. We detected a double duplication of the LW opsin and found unique ommatidial types compared to other butterfly species. We then investigated the evolution of opsin genes among 21 Morpho species, found signatures of positive selection on two opsin genes (LW3Rh and BRh), and identified key co-evolving amino-acids within and among these two opsin genes. We showed that such opsin evolution was correlated with both light environment and wing coloration, highlighting the joint effect of several selective pressures in the coordinated evolution of proteins.

evolutionary biology↗

bioRxiv2025

A novel RNP compartment boosts translation in growing mouse oocytes to avoid cytoplasm dilution

Mammalian oocytes undergo a long growth phase in the ovary, during which transcriptional levels gradually decrease. Growing oocytes must therefore accumulate maternal stores and regulate their translation to achieve successful divisions and early embryo development. Using immunofluorescence, mass spectrometry and electron microscopy, we identified a novel and transient compartment, the Zollo Body, in late growing mouse oocytes, constituted of RNPs and organelles. Morphologically, this structure resembles the Balbiani body found in most vertebrate species but it stains positively for nascent translation and active phospho-mTOR. RNAseq analysis and dry mass measurements of growing oocytes with or without this compartment further support its key role in boosting translation, allowing growing oocytes to avoid cytoplasmic dilution despite their rapid size increase, ultimately ensuring their developmental potential.

cell biology↗

bioRxiv2021

A unique cerebellar pattern of microglia activation in a mousemodel of encephalopathy of prematurity

Preterm infants often show pathologies of the cerebellum, which are associated with impaired motor performance, lower IQ and poor language skills at school ages. Because 1 in 10 babies is born preterm cerebellar injury is a significant clinical problem. The causes of cerebellar damage are yet to be fully explained. Herein, we tested the hypothesis that perinatal inflammatory stimuli may play a key role in cerebellar injury of preterm infants. We undertook our studies in an established mouse model of inflammation-induced encephalopathy of prematurity driven by systemic administration of the prototypic pro-inflammatory cytokine interleukin-1{beta} (IL-1{beta}). Inflammation is induced between postnatal day (P) 1 to day 5, timing equivalent to the last trimester for brain development in humans the period of vulnerability to preterm birth related brain injury. We investigated acute and long-term consequences for the cerebellum on brain volume expansion, oligodendroglial maturation, myelin levels and the microglial transcriptome. Perinatal inflammation induced global mouse brain volume reductions, including specific grey and white matter volume reductions in cerebellar lobules I and II (5% FDR) in IL-1{beta} versus control treated mice from P15 onwards. Oligodendroglia damage preceded the MRI-detectable volume changes, as evidenced by a reduced proliferation of OLIG2+ cells at P10 and reduced levels of the myelin proteins MOG, MBP and MAG at P10 and P15. Increased density of Iba1+ cerebellar microglia was observed at P5 and P45, with evidence for increased microglial proliferation at P5 and P10. Comparison of the transcriptome of microglia isolated from P5 cerebelli and cerebrum revealed significant enrichment of pro-inflammatory markers in microglia from both regions, but in the cerebellum microglia displayed a unique type I interferon signalling dysregulation. Collectively, these data suggest that in our model that systemic inflammation causes chronic activation of microglia and maldevelopment of cerebellum that includes myelin deficits which is driven in the cerebellum by type I interferon signalling. Future protective strategies for preterm infants should consider sustained type I interferon signalling driven cerebellar inflammation as an important target.

neuroscience↗

bioRxiv2021

De novo germline mutation in the Dual Specificity Phosphatase 10 gene accelerates autoimmune diabetes in Non-Obese Diabetic (NOD) mice

Here we report the isolation by selective breeding of two sublines of Non-Obese Diabetic (NOD) mice exhibiting a significant difference in the incidence of autoimmune type 1 diabetes (T1D). Whole genome sequencing of the NOD/NckH (high T1D incidence) and NOD/NckL (low T1D incidence) revealed the presence of a limited number of variants specific to each subline. Treating the age of T1D onset as a quantitative trait and using automated meiotic mapping (AMM), enhanced susceptibility in the NOD/NckH subline was unambiguously attributed to a recessive allele of Dusp10 which encodes a dual specificity phosphatase. The causative effect of the mutation was verified with a high level of confidence by targeting Dusp10 with CRISPR/Cas9 in NOD/NckL mice: in these animals a higher incidence of diabetes was observed. Expression of wild-type Dusp10 correlated with higher levels of surface PD-L1 in the islets of NOD/NckL mice.

immunology↗

bioRxiv2019

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in histone H3 Lys-4 trimethylation independently from histone H2B monoubiquitination

The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in S. cerevisiae, where a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with Set1), in Arabidopsis thaliana this activity involves multiple histone methyltransferases (HMTs). Among these, the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. S2Lb co-purifies with the AtCOMPASS core subunit WDR5 from a high-molecular weight complex, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. Notwithstanding, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2 or H3 Lys-4 trimethylation, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been coopted by the plant-specific SDG2 HMT and mediates H3K4me3 deposition through an H2Bub-independent pathway in Arabidopsis.

plant biology↗

bioRxiv2018

Active intermixing of indirect and direct neurons builds the striatal mosaic

The striatum controls behaviors via the activity of direct and indirect pathway projection neurons (dSPN and iSPN) that are intermingled in all compartments. While such mosaic ensures the balanced activity of the two pathways, how it emerges remains largely unknown. Here, we show that both SPN populations are specified embryonically and progressively intermix through multidirectional iSPN migration. Using conditional mutants of the dSPN-specific transcription factor Ebf1, we found that inactivating this gene impaired selective dSPN properties, including axon pathfinding, whereas molecular and functional features of iSPN were preserved. Remarkably, Ebf1 mutation disrupted iSPN/dSPN intermixing, resulting in an uneven distribution. Such architectural defect was selective of the matrix compartment, revealing that intermixing is a parallel process to compartment formation. Our study reveals that, while iSPN/dSPN specification is largely independent, their intermingling emerges from an active migration of iSPN, thereby providing a novel framework for the building of striatal architecture.

neuroscience↗

bioRxiv2018

Active fluctuations modulate gene expression in mouse oocytes

In mammals, the nucleus is central in oocytes, not defining the future embryo axis. Nucleus centring depends on an F-actin mediated pressure gradient. In Fmn2-/- oocytes, lacking the F-actin nucleator Formin 2, the nucleus is off-centre and can be centred by re-expressing Formin 2. Here, we addressed the biological significance of nucleus positioning in mammalian oocytes. Using a dedicated computational 3D imaging approach, we observed nuclear architecture alterations in mouse Fmn2-/- oocytes. RNA sequencing of control versus Fmn2-/- oocytes detected 2285 mis-regulated genes. Rescue experiments showed that the process of nuclear positioning impacts nuclear architecture and gene expression. Using signal processing methods coupled to biophysical modelling allowing the extraction of in vivo mechanical properties of the nuclear envelope, we showed that F-actin-mediated activity promotes nuclear envelope shape fluctuations and chromatin motion. We thus propose a mechano-transduction model whereby nucleus positioning via microfilaments modulates oocyte transcriptome, essential for further embryo development.

cell biology↗