Search bioRxiv⌕ Search

Biology subjects

Jana, R.

Publications and source records attributed to Jana, R..

2 recordsLinked to original sources

LIF-LIFR/gp130 Survival Signaling and Connexin 47 Dysregulation upon Murine-β-Coronavirus Infection: Discovery of a Novel ERK2 Phosphorylation Site at Cx47 C-Terminal Domain

Oligodendrocyte (OLG) injury and loss are increasingly recognized as major determinants of demyelination and remyelination failure in multiple sclerosis (MS), alongside conventional immune-mediated processes. However, the mechanism underlying OLG injury and remyelination failure remains incompletely understood. Astrocyte-oligodendrocyte interactions mediated by Connexin (Cx)-43-Cx47 gap junction (GJ) communication and leukemia inhibitory factor (LIF)-LIFR/gp130 signaling are critical for oligodendroglial survival, homeostasis, and myelination. Despite their established role, how these pathways are altered during neuroinflammatory diseases remains unclear. To address this, we integrated a murine {beta}-coronavirus (RSA59)-induced in vivo model with enriched primary oligodendrocyte precursor cell (OPC) and mature OLG cultures to investigate the effect of RSA59 infection on OLGs, Cx47-mediated GJ communication, and LIF-LIFR/gp130 Signaling. We observed that RSA59 directly targets oligodendroglial lineage cells, including OPCs and mature OLGs, and induces apoptosis in mature OLGs. Despite increased OPC abundance, RSA59 infection reduces the expression of mature and myelinating markers CNPase and MBP, raising the possibility of impaired oligodendrocyte maturation and myelination. RSA59 infection also differentially regulates Cx47-mediated GJ communication and LIF-LIFR/gp130 signaling, crucial for OLG survival and homeostasis. Furthermore, our studies demonstrate that extracellular signal-regulated kinase (ERK), a downstream effector of LIF signaling, phosphorylates the Cx47 C-terminal domain (Cx47CT) at Serine-372 residue, identifying a previously unreported mechanism. Collectively, these findings reveal that RSA59 infection disrupts interconnected oligodendroglial communication and survival pathways, providing mechanistic insights into virus-induced chronic demyelination pathology. The study further identifies Cx47-mediated GJ communication and LIF-LIFR/gp130 signaling as crucial therapeutic targets, and highlights ERK-dependent Cx47CT phosphorylation as a potential regulatory mechanism.

neuroscience↗

Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation

Long read sequencing technologies such as Oxford Nanopore (ONT) offer direct, simultaneous detection of DNA base modifications. The recent migration of ONT to the upgraded R10 chemistry has spurred the development of diverse methylation detection models. However, their performance and accuracy remain unclear. Here, leveraging diverse bacterial, plant, and mammalian datasets, we systematically evaluate the current landscape of tools and models for studying DNA methylation using nanopore sequencing. Our results demonstrate that the older models remain the best choice for studying CpG methylation. We note substantial improvement of newer tools in identifying 5-methylcytosine in non-CG contexts, 6-methyladenine, and 4-methylcytosine. We highlight the sensitivity of various tools to confounding methylation nearby. We also assess the computational performance of various tools, and effects of sequencing depth, methylation abundance, read quality, and basecalling mode. Our reusable pipelines and fully open access datasets provide a framework of resources to empower future benchmarking efforts. Our work thus details the strengths and limitations of the state-of-the-art methylation models and outlines practical guidelines for researchers using nanopore sequencing to study DNA modifications.

genomics↗