Biology subjects

Ko, C.

Publications and source records attributed to Ko, C..

9 recordsLinked to original sources

bioRxiv2026

Janus kinase 2 regulates Nurr1 protein stability in dopaminergic neurons of the aging midbrain

The nuclear receptor Nurr1 (NR4A2) is an essential transcription factor that governs the differentiation, maturation, and long-term maintenance of midbrain dopaminergic (mDA) neurons in the substantia nigra. Reduced Nurr1 expression has been closely linked to age-related dopaminergic neuronal loss and the pathogenesis of Parkinsons disease. However, the molecular mechanisms regulating Nurr1 expression and protein stability in the aging midbrain remain poorly understood. Here, we identify Janus kinase 2 (JAK2) as a previously unrecognized regulator of Nurr1 in mDA neurons. In the substantia nigra of aged mice (12-and 18-month-old), JAK2 was robustly expressed in Nurr1-positive mDA neurons, whereas its expression was minimal in young adult mice. In SK-N-BE(2)C neuroblastoma cells, overexpression of JAK2 modestly enhanced Nurr1 transcriptional activity, while the constitutively active mutant JAK2V617F markedly increased it. Notably, this effect was not blocked by pharmacological inhibition of STAT, PI3K, or Akt signaling pathways, indicating that JAK2 regulates Nurr1 independently of canonical JAK/STAT or PI3K/Akt signaling. Mechanistically, JAK2 did not promote tyrosine phosphorylation of Nurr1 but instead physically interacted with Nurr1, leading to enhanced nuclear stability of the Nurr1 protein. Consistent with this mechanism, expression of JAK2V617F increased Nurr1 protein levels without altering its mRNA expression. Functionally, co-expression of JAK2V617F and Nurr1 attenuated oxidative stress-induced cytotoxicity and reduced reactive oxygen species accumulation. Together, these findings reveal a phosphorylation-independent mechanism by which JAK2 stabilizes Nurr1 protein and enhances its transcriptional activity. Our results further suggest that age-associated induction of JAK2 in dopaminergic neurons may promote neuronal resilience by maintaining Nurr1 protein stability during aging.

neuroscience↗

bioRxiv2026

Minute-scale coupling of chromatin marks and transcriptional bursts

Histone modifications are often described as stable epigenetic marks that contribute to maintaining gene-expression programs during development and environmental responses 1-5. However, transcription of many genes is intermittent, switching between transcriptionally active and inactive episodes within minutes 6-10. Whether chromatin marks around individual genes change on these rapid timescales remains unclear. Here we show that local chromatin modification signals around endogenous genes in mouse embryonic stem cells fluctuate reversibly with transcriptional state, using live imaging of individual genes together with fluorescent probes that report histone modifications11-16. Activation-associated acetylation and methylation marks increased in association with transcriptional activation and decreased with inactivation, whereas a Polycomb-associated repressive mark behaved oppositely. Transcriptional coactivators and both histone acetyltransferase and deacetylase complexes were enriched during transcriptionally active state, consistent with opposing enzymatic activities shaping local acetylation levels 17,18. Inhibiting histone deacetylases altered the durations of active and inactive events, supporting a role for deacetylation in regulating transcriptional state transitions. Thus, histone modifications undergo reversible, minute-scale changes coupled to transcriptional activity. This framework helps explain how stochastic transcriptional bursts can occur with stable gene regulation over longer timescales.

molecular biology↗

bioRxiv2025

Reconstruction of Postures Using Partial Body Information Through a Self-supervised Transformer in Mice

The comprehensive interpretation of behavior from incomplete data represents a fundamental challenge in computational ethology. Here we present Masked Autoencoder for Transformer-based Estimation and Reconstruction (MATER), a self-supervised learning framework that extracts behaviorally relevant representations from unlabeled rodent pose data by reconstructing strategically masked body keypoints. This approach captures fundamental movement patterns without requiring extensive manual annotation, addressing common experimental challenges including occlusions during social interactions and tracking errors. We evaluate MATER across two-dimensional and three-dimensional rodent pose datasets, demonstrating its robustness under high levels of keypoint masking. The framework achieves high-fidelity reconstructions under these challenging conditions and produces latent representations that support accurate behavioral classification with minimal supervision. Our analyses further reveal that rodent movement exhibits intrinsic spatiotemporal structure, which can be computationally inferred without explicit labeling. Reconstruction performance is tightly linked to the temporal coherence of movement, highlighting the importance of temporal dynamics in behavioral representation. These findings reinforce the emerging view that animal behavior is hierarchically organized and governed by natural temporal dependencies. MATER offers a robust, scalable tool for neuroscientists seeking to analyze complex, naturalistic behaviors across diverse experimental contexts, ultimately advancing our understanding of behavioral architecture and its neural underpinnings.

neuroscience↗

bioRxiv2025

Cutaneous lupus features specialized stromal niches and altered retroelement expression

Cutaneous Lupus is an inflammatory skin disease causing highly morbid inflamed skin and hair loss. In order to investigate the pathophysiology of cutaneous lupus, we performed single-cell RNA and spatial sequencing of lesional and non-lesional cutaneous lupus skin compared to healthy controls. Pathway enrichment analyses of lesional keratinocytes revealed elevated responses to type I interferon, type II interferon, tumor necrosis factor, and apoptotic signaling. Detailed clustering demonstrated unique fibroblasts specific to lupus skin with likely roles in inflammatory cell recruitment and fibrosis. We also evaluated the association of retroelement expression with type I interferons in the skin. We observed increased retroelement expression which correlated with interferon-stimulated genes across multiple cell types. Moreover, we saw elevated expression of genes involved in RIG-I and cGAS-STING pathways, which transduce elevated nucleic acid signals. Treatment of active cutaneous lupus with Anifrolumab reduced RIG-I and cGAS-STING pathways in addition to the most abundant retroelement family, L2b. Our studies better define type I interferon-mediated immunopathology in cutaneous lupus and identify an association between retroelement expression and interferon signatures in cutaneous lupus.

immunology↗

bioRxiv2024

Inhibition of serine and arginine-rich splicing factor 3 induces epidermal differentiation and decreases cutaneous squamous cell carcinoma risk

Serine/Arginine-rich splicing factor 3 (SRSF3) is one of 12 SRSFs that regulate gene expression via alternative splicing. SRSF3 is upregulated in cutaneous squamous cell carcinoma (cSCC) and several squamous cancer cell lines in relation to normal keratinocytes. We suppressed SRSF3 with a specific inhibitor, SFI003, and observed an increase in epidermal differentiation. Our data suggests that in cSCC, SRSF3 overexpression suppresses cellular differentiation to enable cancer progression. In a clinical setting, patients taking known SRSF3 inhibitors digoxin and amiodarone exhibited higher cSCC-free survival compared to a propensity score-matched cohort treated with beta blockers. Thus, SRSF3 upregulation may be a novel therapeutic target in cSCC that can improve patient prognoses.

cancer biology↗

bioRxiv2024

Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin

Carcinogen-induced mutations are thought near-random, with rare cancer-driver mutations underlying clonal expansion. Using high-fidelity Duplex Sequencing to reach a mutation frequency sensitivity of 4x10-9 per nt, we report that sun exposure creates pervasive mutations at sites with [~]100-fold UV-sensitivity in RNA-processing gene promoters - cyclobutane pyrimidine dimer (CPD) hyperhotspots - and these mutations have a mini-driver clonal expansion phenotype. Numerically, human skin harbored 10-fold more genuine mutations than previously reported, with neonatal skin containing 90,000 per cell; UV signature mutations increased 8,000-fold in sun-exposed skin, averaging 3x10-5 per nt. Clonal expansion by neutral drift or passenger formation was nil. Tumor suppressor gene hotspots reached variant allele frequency 0.1-10% via 30-3,000 fold clonal expansion, in occasional biopsies. CPD hyperhotspots reached those frequencies in every biopsy, with modest clonal expansion. In vitro, tumor hotspot mutations arose occasionally over weeks of chronic low-dose exposure, whereas CPD hyperhotspot mutations arose in days at 1000-fold higher frequencies, growing exponentially. UV targeted mini-drivers in every skin cell.

genomics↗

bioRxiv2024

PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators

Spermatogenesis is a biological process within the testis that produces haploid spermatozoa for the continuity of species. Sertoli cells are somatic cells in the seminiferous epithelium that orchestrate spermatogenesis. Cyclic reorganization of Sertoli cell actin cytoskeleton is vital for spermatogenesis, but the underlying mechanism remains largely unclear. Here, we report that RNA-binding protein PTBP1 controls Sertoli cell actin cytoskeleton reorganization by programming alternative splicing of actin cytoskeleton regulators. This splicing control enables ectoplasmic specializations, the actin-based adhesion junctions, to maintain the blood-testis barrier and support spermatid transport and transformation. Particularly, we show that PTBP1 promotes actin bundle formation by repressing the inclusion of exon 14 of Tnik, a kinase present at the ectoplasmic specialization. Our results thus reveal a novel mechanism wherein Sertoli cell actin cytoskeleton dynamics is controlled post-transcriptionally by utilizing functionally distinct isoforms of actin regulatory proteins, and PTBP1 is a critical regulatory factor in generating such isoforms.

molecular biology↗

bioRxiv2024

Whole organism snRNA-seq reveals systemic peripheral changes in Alzheimer's Disease fly models

Peripheral tissues become disrupted in Alzheimers Disease (AD). However, a comprehensive understanding of how the expression of AD-associated toxic proteins, A{beta}42 and Tau, in neurons impacts the periphery is lacking. Using Drosophila, a prime model organism for studying aging and neurodegeneration, we generated the Alzheimers Disease Fly Cell Atlas (AD-FCA): whole-organism single-nucleus transcriptomes of 219 cell types from adult flies neuronally expressing human A{beta}42 or Tau. In-depth analyses and functional data reveal impacts on peripheral sensory neurons by A{beta}42 and on various non-neuronal peripheral tissues by Tau, including the gut, fat body, and reproductive system. This novel AD atlas provides valuable insights into potential biomarkers and the intricate interplay between the nervous system and peripheral tissues in response to AD-associated proteins.

genetics↗

bioRxiv2020

Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle.

Hepatitis B virus (HBV) is an enveloped DNA virus that contains a partially double-stranded relaxed circular (rc) DNA. Upon infection, rcDNA is delivered to the nucleus where it is repaired to covalently closed circular (ccc) DNA that serves as the transcription template for all viral RNAs. Our understanding of HBV particle entry dynamics and host pathways regulating intracellular virus trafficking and cccDNA formation is limited. The discovery of sodium taurocholate co-transporting peptide (NTCP) as the primary receptor allows studies on these early steps in viral life cycle. We employed a synchronized infection protocol to quantify HBV entry kinetics. HBV attachment to cells at 4{degrees}C is independent of NTCP, however, subsequent particle uptake is NTCP-dependent and reaches saturation at 12h post-infection. HBV uptake is clathrin- and dynamin dependent with actin and tubulin playing a role in the first 6h of infection. Cellular fractionation studies demonstrate HBV DNA in the nucleus within 6h of infection and cccDNA was first detected at 24h post-infection. Our studies show the majority (83%) of cell bound particles enter HepG2-NTCP cells, however, only a minority (<1%) of intracellular rcDNA was converted to cccDNA, highlighting this as a rate-limiting in establishing infection in vitro. This knowledge highlights the deficiencies in our in vitro cell culture systems and will inform the design and evaluation of physiologically relevant models that support efficient HBV replication.

microbiology↗