Biology subjects

Choi, D.-J.

Publications and source records attributed to Choi, D.-J..

3 recordsLinked to original sources

bioRxiv2025

Mutant IDH impairs chromatin binding by PDGFB to promote chromosome instability

Non-canonical roles for growth factors in the nucleus have been previously described, but their mechanism of action and biological roles remain enigmatic. Platelet-derived growth factor B (PDGFB) can drive formation of low-grade glioma and here we show that it localizes to the nucleus of human glioma cells where it binds chromatin to preserve genome stability and cell lineage. Failure of PDGFB to localize to the nucleus leads to chromosomal abnormalities, aberrant heterochromatin architecture and accelerated tumorigenesis. Furthermore, nuclear localization of PDGFB is reliant upon the expression levels and mutation status of isocitrate dehydrogenase (IDH). Unexpectedly, we identified macrophages as the predominant source of PDGFB in human, finding that immune-derived PDGFB can localize to the nucleus of glioma cells. Collectively, these studies show that immune derived PDGFB enters the nucleus of glioma cells to maintain genomic stability, while identifying a new mechanism by which IDH mutations promote gliomagenesis.

cancer biology↗

bioRxiv2023

Activity-dependent induction of astrocytic Slc22a3 regulates sensory processing through histone serotonylation

Neuronal activity drives global alterations in gene expression within neurons, yet how it directs transcriptional and epigenomic changes in neighboring astrocytes in functioning circuits is unknown. Here we show that neuronal activity induces widespread transcriptional upregulation and downregulation in astrocytes, highlighted by the identification of a neuromodulator transporter Slc22a3 as an activity-inducible astrocyte gene regulating sensory processing in the olfactory bulb. Loss of astrocytic Slc22a3 reduces serotonin levels in astrocytes, leading to alterations in histone serotonylation. Inhibition of histone serotonylation in astrocytes reduces expression of GABA biosynthetic genes and GABA release, culminating in olfactory deficits. Our study reveals that neuronal activity orchestrates transcriptional and epigenomic responses in astrocytes, while illustrating new mechanisms for how astrocytes process neuromodulatory input to gate neurotransmitter release for sensory processing.

neuroscience↗

bioRxiv2022

Identification of functional immune and neuronal tumor cells in glioma

Despite advances in molecular profiling, therapeutic development has been hindered by the inability to identify and target tumour-specific mechanisms without consequence to healthy tissue. Correspondingly, a computational framework capable of accurately distinguishing tumour from non-tumour cells has yet to be developed and cell annotation algorithms are unable to assign integrated genomic and transcriptional profiles to single cells on a cell-by-cell basis. To address these barriers, we developed the Single Cell Rule Association Mining (SCRAM) tool that integrates RNA-inferred genomic alterations with co-occurring cell type signatures for individual cells. Applying SCRAM to glioma, we identified tumour cell trajectories recapitulate temporally-restricted developmental paradigms and feature unique co-occurring identities. Specifically, we validated two previously unreported tumour cell populations with immune and neuronal signatures as hallmarks of human glioma subtypes. In vivo modeling revealed a rare immune-like tumour cell population resembling antigen presenting cells can direct CD8+ T cell responses. In parallel, Patch sequencing studies in human tumours confirmed that neuronal-like glioma cells fire action potentials and represent 40% of IDH1 mutant tumor cells. These studies identified new glioma cell types with functional properties similar to their non-tumour analogues and demonstrate the ability of SCRAM to identify these cell types in unprecedented detail.

cancer biology↗