Biology subjects

Subiran, N.

Publications and source records attributed to Subiran, N..

3 recordsLinked to original sources

bioRxiv2025

A Comparative Assessment of edgeR and methylKit Pipelines for DNA Methylation Detection

Despite the improvements in tool development for DNA methylation analysis, there is a lack of a consensus on computational and statistical models used for differentially methylated cytosine (DMC) identification. This variability complicates the interpretation of findings and raises concerns about the reproducibility and biological significance of the detected results. In this regard, the primary objective of this study was to compare the performance, concordance, and biological relevance of edgeR and methylKit tools in detecting DMCs (the first one based on fold change and the second one based on percentage), following morphine exposure model in mouse embryonic stem cells (mESCs). While a different number of total DMCs was identified by each tool, both pipelines detected a global hypomethylation as a result. Genomic analysis revealed a predominant distribution of DMCs in intergenic and intronic regions on one hand, and in open sea regions on the other hand. Despite the differences in sensitivity, both tools demonstrated moderate concordance in DMCs detection ([~]56%) and high concordance in gene level analysis ([~]90%), identifying similar differentially methylated genes (DMGs). Overall, the results underscore the complementary strengths of methylKit and edgeR and highlight the importance of tool selection for epigenetic studies. As a conclusion, integrating both pipelines is recommended for comprehensive analysis, particularly in studies with complex experimental designs.

bioinformatics↗

bioRxiv2025

Chronic morphine treatment leads to a global DNA hypomethylation via active and passive demethylation mechanisms in mESCs

Epigenetic changes are essential for normal development and ageing, but there is still limited understanding of how environmental factors can cause epigenetic changes that leads to health problems or diseases. Morphine is known to pass through the placental barrier and impact normal embryo development by affecting the neural tube, frontal cortex and spinal cord development, and, as a consequence, delaying nervous system development. In fact, in-utero morphine exposure has shown alterations in anxiety-like behaviours, analgesic tolerance, synaptic plasticity and the neuronal structure of offspring. However, how morphine leads to abnormal neurogenesis and other physiological consequences during embryo development is still unknown. Considering that DNA methylation is a key epigenetic factor crucial for embryo development, our aim is to elucidate the role of methylation in response to morphine. Chronic morphine treatment (24h, 10M) induces a global hypomethylation in mESC. WGBSeq identifies 16,808 sensitive to morphine which are involved in embryo development, signalling pathways, metabolism and/or gene expression, suggesting that morphine might impact methylation levels at developmental genes. Integrative analyses between WGBSeq and RNASeq identified Tet1 as morphine-sensitive gene. Morphine increased the gene expression of Tet1, modifying the methylation levels at the promoter. On the other hand, RNASeq and qRT-PCR analyses revealed that Dnmt1 gene expression decreased after morphine treatment, without altering the methylation patter at its promoters. By MS/MS approaches confirms a decrease in DNA methylation after chronic morphine treatment, together with an increase in hydroxymethylation global levels in mESCs. In conclusion, morphine induces a global hypomethylation in mESC through different mechanisms that involves passive demethylation and a self-regulatory mechanism via active demethylation. One Sentence SummaryUnderstanding how environmental epigenetics impact on embryo development aids to unravel changes that leads to health problems or diseases in the adulthood. Graphical abstractChronic morphine treatment induces a global hypomethylation in mESC through different mechanisms that involves passive demethylation and a self-regulatory mechanism via active demethylation in genes involved in embryo development. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/643512v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@e9d286org.highwire.dtl.DTLVardef@fc7066org.highwire.dtl.DTLVardef@1374039org.highwire.dtl.DTLVardef@598f05_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2024

Chronic inflammation drives epididymal tertiary lymphoid structure formation and autoimmune fertility disorders

The incomplete understanding of epididymal mucosal immunity is a significant contributing factor to the classification of many male infertility cases as idiopathic. Conditions that disrupt the immune balance in the male reproductive tract, such as vasectomy and infections, can expose sperm to the immune system, leading to increased production of anti-sperm antibodies (ASAs) and subsequent reproductive challenges. Regulatory T cells (Tregs) regulate inflammation and maintain sperm tolerance. In a murine model, we demonstrated that disrupting sperm immunotolerance induces chronic autoimmune responses characterized by antibody production targeting sperm and reproductive tissue autoantigens and unique tissue-specific immune cell signatures in the epididymis and testis. Such inflammatory features impair sperm function, contribute to epididymal damage, and drive sustained male subfertility. Tertiary lymphoid structures (TLSs) were formed within the epididymis after Treg depletion, defined by clusters of heterogenous B and T cells, fibroblasts, and endothelial cells. These ectopic structures perpetuate inflammation and lower the activation threshold for future immune threats. Similar isotypes of autoantibodies were detected in the seminal plasma of infertile patients, suggesting shared mechanistic pathways between mice and humans. Overall, we provide an in-depth understanding of the diverse B- and T-cell dynamics and TLS formation during epididymitis to develop precision-targeted therapies for infertility and chronic inflammation. Additionally, this immunological characterization of the epididymal microenvironment has the potential to identify novel targets for the development of male contraceptives. One Sentence SummaryUnderstanding the epididymal immune cell landscape dynamics aids in developing targeted therapies for infertility and contraception.

immunology↗