Biology subjects

Daunesse, M.

Publications and source records attributed to Daunesse, M..

9 recordsLinked to original sources

bioRxiv2026

Interspecies Differential Gene Expression Analysis with Regularized Phylogenetic Linear Models

Comparative transcriptomic datasets are increasingly used to investigate the molecular basis of phenotypic diversification across species. However, finding genes that are differentially expressed (DE) between lineages remains challenging, for two main reasons. First, the random evolutionary drift can blur the signal left by lineage-specific shifts in mean expression, and induces phylogenetic correlations that, if ignored, can widely inflate the False Discovery Rate (FDR), i.e., the amount of spuriously detected genes. Second, DE analysis from RNA-Seq data involves multiple testing on many genes for a small number of individual measurements with high noise, and requires dedicated statistical tools. Traditional DE tools, such as limma, and classical Phylogenetic Comparative Methods (PCMs), such as the Expression Variance and Evolution (EVE) model, are both designed to tackle one of these two challenges alone, but both fail in the context of inter-species RNA-Seq data. In this work, we present phyloDE, a new tool for inter-species DE, that aims at taking the best from both approaches. On simulations based on a recently published four-species rodent dataset, we show that, contrary to other methods, phyloDE correctly controls the FDR in all settings, while keeping a reasonable power. When reanalyzing the empirical dataset, phyloDE discovers more DE genes that exhibit consistent changes in their cis-regulatory landscape compared to EVE in all the experimental settings. The method is implemented in R, with an interface inheriting from limma.

evolutionary biology↗

bioRxiv2026

Evolution of the genetic architecture of uterine disorders

Uterine disorders and menstrual abnormalities are prevalent reproductive conditions with significant clinical consequences. Recent genome-wide association studies have identified hundreds of variants contributing to different uterine disorders, while epidemiological evidence suggests that these disorders co-occur more frequently than expected, implying shared genetic mechanisms. However, the specific genetic variants and biological pathways underlying this shared architecture remain poorly characterized. Here, we conducted a uterus-centric, multi-trait genome-wide association analysis across ten uterine disorders in a European cohort to elucidate this shared genetic architecture. Further, we embedded this architecture in a functional and population genomics framework to investigate its plausible biological mechanisms and its evolutionary history in humans. We confirm strong positive genetic correlations between major uterine disorders and identify 31 independent susceptibility loci jointly affecting the genetic risk of multiple uterine pathologies, substantiating an intertwined biological basis. Populational analyses demonstrated that several of these susceptibility variants exhibit pronounced allele frequency differentiation across global populations suggestive of recent polygenic selection, including variants with well-supported regulatory functions at the ESR1-CCDC170, WNT4, SFR1, FOXO1, ITPR1, DMRT1 and CDKN2B loci. Notably, we show that most derived alleles acquired during recent human evolution increase risk across multiple uterine disorders and may evolve under antagonistic selection. These findings provide functional annotation and population-level prioritization of genetic variants influencing multiple uterine disorders. They also highlight how past evolutionary histories may contribute to population differences in uterine disease prevalence and pathogenesis.

genetics↗

bioRxiv2026

NK cell receptor repertoires evolve under increased constraint butare not more diverse in menstruating mammals

The immune system plays key roles in the mammalian uterine cycle, particularly for menstruation, a dramatic tissue renewal mechanism independently acquired four times in eutherians. These roles specifically involve NK cells through the expression of surface killer cell immunoglobulin-like receptors (KIRs) and killer cell lectin-like receptors (KLRs), respectively part of the immunoglobulin-like and lectin-like gene superfamilies with poorly resolved phylogenetic histories. Acquisition of menstruation in primates seemingly coincides with a large expansion of the KIR family, suggesting that gains and losses in NK cell receptor families may have been crucial for the evolution of menstruation. To test this hypothesis, we performed an in-depth analysis of the evolutionary histories of the KIR and KLR gene families across 41 mammalian genomes, including all four clades that acquired menstruation. Our results reveal the existence of undescribed KIR and KLR genes across many mammalian species, including elephants, armadillos, rhinoceroses, and leaf-nosed bats, as well as a novel subfamily within the KLR phylogeny. Altogether, we identify more than twice as many NK cell receptor genes across mammals than currently reported in reference genomes. Further, we show that the KIR gene family has experienced intensified purifying selection in menstruating species compared to non-menstruating species, suggesting specific evolutionary pressures related to menstruation. Our data, however, do not support that menstruation coincides with expansions or contractions in NK cell receptor repertoires, except in primates, highlighting both shared and lineage-specific immune adaptations to rapidly evolving reproductive biology. Significance statementThe evolutionary history of the uterus in mammals is complex, with many traits acquired convergently. One of these traits is menstruation. There has, historically, been a dearth of research to better understand this physiological mechanism within an evolutionary context. Here, we tested whether two families of natural killer cell receptors, known to be implicated in successful human and murine pregnancies, have evolved in concert with acquisitions of menstruation in mammals. Our findings indicate that the immune system likely does not play the same role in catarrhine menstruation as in menstruation in other clades, such as bats and rodents. We also reconstructed the history of this trait and performed a thorough inventory of these receptor gene families across a wide range of mammals, including the identification of unreported expansions. This study places menstruation within an evolutionary context and provides a foundation to better understand the interactions between the mammalian immune system and uterus.

evolutionary biology↗

bioRxiv2025

Coordinated shifts in gene expression and regulation during mole-rat evolution

Changes in gene expression and regulation are central to mammalian phenotypic evolution. Yet, distinguishing adaptive gene expression shifts from neutral divergence remains challenging. Here, we integrate comparative transcriptomics and regulatory genomics to investigate how natural selection has shaped gene expression in African mole-rats, a group of subterranean rodents with phenotypic adaptations to underground environments. Using RNA-seq from liver and heart in two mole-rat species (naked mole-rat and Damaraland mole-rat) and two rodent outgroups (mouse and guinea pig), we leveraged phylogenetic models of expression evolution and identified hundreds of genes whose transcriptional levels have experienced accelerated evolution in each tissue and mole-rat species. These lineage-specific shifts account for only a small fraction of gene expression differences identified by classical differential expression analysis between species, underscoring the importance of phylogeny-aware inference to disentangle accelerated evolution from drift. To connect expression divergence with regulatory evolution, we integrated transcriptomic profiles with cis-regulatory landscapes. Genes with lineage-specific expression shifts displayed concordant changes in cis-regulatory activity, particularly at promoters, and the magnitude of expression divergence increased with the number of shifted cis-regulatory elements. Our results demonstrate that adaptive shifts in mole-rat gene expression are mirrored by regulatory evolution, providing genome-wide coordinated evidence of accelerated evolution on expression and regulation during mammalian evolution. Our approach thereby prioritises candidate loci that may have shaped adaptations specific to mole-rat physiology, including metabolic rewiring and stress responses.

evolutionary biology↗

bioRxiv2025

Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis

Hepatocellular carcinoma is the most prevalent primary liver cancer and arises from hepatocytes, which are very metabolically active and contain abundant mitochondria. Despite extensive characterisation of nuclear driver genes and pathways, the role of crosstalk between the mitochondrial and nuclear genomes in mitochondrial mutagenesis remains poorly understood. To address this, we leveraged a chemical carcinogenesis model of liver cancer in four mouse strains. We analysed hundreds of tumours with paired whole-genome sequencing and total RNA sequencing to comprehensively characterise mitochondrial mutations and expression. Following de novo assembly of strain-specific mitochondrial genomes, we devised an accurate and efficient heteroplasmy detection approach and analysed mitochondrial DNA (mtDNA) content and transcription. Across strains, there was high concordance of the number of heteroplasmies, mutation signatures, and variant allele frequencies. In contrast, the heteroplasmy rate and genic locations differed between strains, suggesting strain-specificity in DNA repair mechanisms in early tumour development. Independent of age or environmental factors, tumours had lower mtDNA content than adjacent normal liver, suggesting mitochondrial loss during tumourigenesis. Additionally, within individual strains, mtDNA content differences were associated with nuclear driver gene choice. Our comprehensive characterisation of mitochondrial genomes and expression patterns demonstrates that both germline and somatic genetic variation influence tumour mtDNA content, mutation patterns, and gene expression.

cancer biology↗

bioRxiv2025

Genetic background sets the trajectory of cancer evolution

Human cancers are heterogeneous. Their genomes evolve from genetically diverse germlines in complex and dynamic environments, including exposure to potential carcinogens. This heterogeneity of humans, our environmental exposures, and subsequent tumours makes it challenging to understand the extent to which cancer evolution is predictable. Addressing this limitation, we re-ran early tumour evolution hundreds of times in diverse, inbred mouse strains, capturing genetic variation comparable to and beyond that found in human populations. The sex, environment, and carcinogenic exposures were all controlled and tumours comprehensively profiled with whole genome and transcriptome sequencing. Within a strain, there was a high degree of consistency in the mutational landscape, a limited range of driver mutations, and all strains converged on the acquisition of a MAPK activating mutation with similar transcriptional disruption of that pathway. Despite these similarities in the phenotypic state of tumours, different strains took markedly divergent paths to reach that state. This included pronounced biases in the precise driver mutations, the strain specific occurrence of whole genome duplication, and differences in subclonal selection that reflected both cancer susceptibility and tumour growth rate. These results show that interactions between the germline genome and the environment are highly deterministic for the trajectory of tumour genome evolution, and even modest genetic divergence can substantially alter selection pressures during cancer development, influencing both cancer risk and the biology of the tumour that develops.

genomics↗

bioRxiv2024

Convergent gene expression in epithelial cells illuminates the evolution of uterine receptivity

The epithelium of the uterine endometrium is the first maternal interface encountered by the embryo, and plays crucial roles in the maternal-embryonic crosstalk necessary to embryo implantation. Mechanisms of embryo implantation are highly variable between mammals: humans and mice have convergently evolved similar embryo implantation phenotypes, where the embryo embeds in the maternal mucosa, which differs from the ancestral mammalian and primate phenotypes. This phenomenon is thought to be partly controlled by maternal epithelial receptivity signals during the window of implantation. Here, we combined endometrial epithelial organoid models and single-cell transcriptomics to investigate how gene expression has evolved in endometrial epithelial cells between human, non-human primates and mouse at key time points in the hormonal cycle. We discovered that many maternal genes involved in uterine receptivity and embryo implantation exhibit more similar expression patterns between human and mouse compared to macaque and marmoset. In particular, we show that the endometrial expression of LIF, a crucial actor of endometrial receptivity in both human and mouse, is likely an evolutionary convergence rather than a conserved feature as previously hypothesised.

evolutionary biology↗

bioRxiv2021

ChIPuana: from raw data to epigenomic dynamics

We present ChIPflow, a Snakemake-based pipeline for epigenomic data from the raw fastq files to the differential analysis. It can be applied to any chromatin factor, e.g. histone modification or transcription factor, which can be profiled with ChIP-seq. ChIPflow streamlines critical steps like the quality assessment of the immunoprecipitation using cross-correlation and the replicate comparison for both narrow and broad peaks. For the differential analysis ChIPflow provides linear and nonlinear methods for normalisation between samples as well as conservative and stringent models for estimating the variance and testing the significance of the observed binding/marking differences. ChIPflow can process in parallel multiple chromatin factors with different experimental designs, number of biological replicates and/or conditions. It also facilitates the specific parametrisation of each dataset allowing both narrow or broad peak calling, as well as comparisons between the conditions using multiple statistical settings. Finally, complete reports are produced at the end of the bioinformatic and the statistical part of the analysis, which facilitate the data quality control and the interpretation of the results. We explored the discriminative power of the statistical settings for the differential analysis, using a published dataset of three histone marks (H3K4me3, H3K27ac and H3K4me1) and two transcription factors (Oct4 and Klf4) profiled with ChIP-seq in two biological conditions (shControl and shUbc9). We show that distinct results are obtained depending on the sources of ChIP-seq variability and the dynamics of the chromatin factor under study. We propose that ChIPflow can be used to measure the richness of the epigenomic landscape underlying a biological process by identifying diverse regulatory regimes and the associated genes sets.

bioinformatics↗

bioRxiv2021

The CovR regulatory network drives the evolution of Group B Streptococcus virulence

Virulence of the neonatal pathogen Group B Streptococcus depends on the master regulator CovR. Inactivation of CovR leads to large-scale transcriptome remodeling and impairs almost every step of the interaction between the pathogen and the host. However, comparative analyses suggested a plasticity of the CovR signalling pathway in clinical isolates, probably due to the host selective pressure and leading to phenotypic heterogeneity in the bacterial population. Here, we characterize the CovR regulatory network in a strain representative of the hypervirulent lineage responsible of the majority of late-onset meningitidis. Genome-wide binding and transcriptome analysis demonstrated that CovR acts as a direct and global repressor of virulence genes, either as a primary regulator or with specialized co-regulators. Remarkably, CovR directly regulates genes of the pan-genome, including the two specific hypervirulent adhesins and horizontally acquired genes, as well as core-genes showing mutational biases in the population. Parallel analysis of the CovR network in a second isolate links strain-specificities to micro-evolutions in CovR-regulated promoters and to broad difference due to variability in CovR activation by phosphorylation. Our results highlight the direct, coordinated, and strain-specific regulation of virulence genes by CovR. This intra-species evolution of the signalling network reshapes bacterial-host interactions, increasing the potential for adaptation and the emergence of clone associated with specific diseases.

microbiology↗