Biology subjects

Lee, S.-C.

Publications and source records attributed to Lee, S.-C..

7 recordsLinked to original sources

bioRxiv2026

Parabrachial-amygdala circuit cooperates with a posterior striatal area to drive opioid withdrawal aversion

Opioid addiction treatment is often hampered by the severe dysphoria of opioid withdrawal, but withdrawal treatments are limited by incomplete understanding of brain mechanisms involved. One area frequently implicated in withdrawal symptoms is the central amygdala, whose capsular portion (CeC) is particularly strongly activated during withdrawal. Additionally, a ventral posterior striatal region that resides near CeC, the interstitial nucleus of the posterior limb of the anterior commissure (IPACc), is also activated as strikingly as CeC. However, it is still unknown how these regions are activated, nor whether their activation explains the high intensity of withdrawal dysphoria. Using RNAscope, we found that c-fos expression is induced in the parabrachial nucleus (PB), a key glutamatergic afferent of CeC, after precipitated morphine withdrawal. Chemogenetic inhibition of PB glutamatergic neurons (VG2PB) nearly eliminated withdrawal-induced CeC c-Fos, without affecting IPACc c-Fos, indicating these two nuclei are activated by distinct sources. Furthermore, VG2PB inhibition markedly reduced somatic (jumping) and modestly reduced affective (place avoidance) withdrawal behavior. On the other hand, inhibition of CeC-projecting PB neuronal subtypes expressing calcitonin gene-related peptide (CGRP) or mu opioid receptor (MOR) reduced place avoidance without affecting jumping, indicating their specific role in withdrawal aversion. Strikingly, simultaneous inhibition of VG2PB and posterior striatal region containing IPACc robustly reduced withdrawal-induced place avoidance much more than the modest effects of either inhibition alone, suggesting their cooperative action in driving aversion. Our data suggests that PB-CeC circuit and posterior striatal area constitute a cooperative system driving opioid withdrawal aversion.

neuroscience↗

bioRxiv2026

V-SWITCH: A single-vector OFF-to-ON fluorescent reporter of live RNA virus infections

Fluorescent reporters of viral infection are powerful tools for studying viral pathogenesis and host-pathogen interactions. Here, we present V-SWITCH, a highly modular, single-vector, cell-based OFF-to-ON fluorescent reporter that enables robust detection of viral infection in living cells. V-SWITCH is based on a split mNeonGreen (mNG) system employing a release-and-capture mechanism. In the "OFF" state, the mNG3A(1-10) fragment is anchored to the endoplasmic reticulum via a Sec61 transmembrane domain, while the mNG(11) fragment, fused to BFP, is constitutively expressed in the nucleus. Upon infection, the viral protease cleaves a protease cleavage site (PCS) adjacent to the mNG3A(1-10) fragment, liberating it for translocation into the nucleus. There, it complements mNG(11) to reconstitute fluorescence. The constitutive BFP serves as both an expression control and a nuclear segmentation marker for image analysis. Each module in this dual-cassette design is flanked by unique restriction sites allowing rapid swapping of virus-specific PCS, split fluorophores, membrane anchors, and promoters. We demonstrate the versatility of the V-SWITCH reporter for several viruses (Dengue virus, Zika virus, West Nile virus and Human Coronavirus OC43) in several cell lines (A549, BJ-5 fibroblasts, HEK293T and HeLa). Reporter activation enables clear discrimination of infected and uninfected cells by flow cytometry and reveals time-dependent and heterogeneous infection dynamics by live-cell imaging at single-cell resolution. Importantly, we demonstrate the potential of V-SWITCH to support both rapid functional screening for host factor dependencies, as well as high-throughput compound screening to enable antiviral discovery and comparative evaluation of therapeutic strategies across multiple viruses and cell types.

microbiology↗

bioRxiv2024

Long-read Transcriptomics of Caviid Gammaherpesvirus 1: Compiling a Comprehensive RNA Atlas

Caviid gammaherpesvirus 1 (CaGHV-1), formerly known as the guinea pig herpes-like virus, is an oncogenic gammaherpesvirus with a sequenced genome but an as-yet uncharacterized transcriptome. Using nanopore long-read RNA sequencing, we annotated the CaGHV-1 genome and constructed a detailed transcriptomic atlas. Our findings reveal diverse viral mRNAs and non-coding RNAs, along with mapped promoter elements for each viral gene. We demonstrated that the CaGHV-1 RTA lytic cycle transcription factor activates its own promoter, similar to KSHV, and that the CaGHV-1 ORF50 promoter responds to RTA proteins from other gammaherpesviruses, highlighting the evolutionary conservation of RTA-mediated transcriptional mechanisms. Additionally, our analysis uncovered extensive transcriptional overlap within the viral genome, suggesting a role in regulating global gene expression. Given its tumorigenic properties, broad host range, and non-human pathogenicity, this work establishes CaGHV-1 as a promising small animal model for investigating human gammaherpesvirus pathogenesis. IMPORTANCEThe molecular underpinnings of gammaherpesvirus pathogenesis remain poorly understood, partly due to limited animal models. This study provides the first comprehensive transcriptomic atlas of CaGHV-1, highlighting both coding and non-coding RNAs and revealing regulatory elements that drive viral gene expression. Functional studies of the CaGHV-1 RTA transcription factor demonstrated its ability to self-activate and cross-activate promoters from homologous gammaherpesviruses, reflecting conserved mechanisms of transcriptional control. These findings solidify CaGHV-1 as a unique and versatile small animal model, offering new opportunities to investigate gammaherpesvirus replication, transcriptional regulation, and tumorigenesis in a controlled experimental system.

genomics↗

bioRxiv2019

Sustained modulation of emotion-related fibers after 8 weeks of mindfulness-based stress reduction training

An 8-week mindfulness-based stress reduction (MBSR) program enables novices to learn and practice mindfulness meditation. A longitudinal study design has been used in prior research to investigate the effect of short-term mindfulness meditation training on brain structures. Many studies have demonstrated microstructural changes in the white matter by comparing baseline measurements with measurements obtained immediately after short-term meditation training. However, these studies did not clarify the evolution of the modulated microstructures several months after mindfulness meditation practice is discontinued. Therefore, in this study, we recruited 13 novice practitioners and administered an 8-week MBSR training program. We extended the span of the longitudinal study by adding a third measurement taken approximately 6 months after the second time point. Diffusion indices derived from diffusion spectrum imaging were used to quantify the temporal changes in modulation across three time points. The analysis identified four tract bundles that were significantly modulated after the 8-week MBSR training program, namely the callosal fibers connecting the bilateral amygdalae and bilateral hippocampi, right thalamic radiation of the auditory nerve, and right uncinate fasciculus. At the third time point, at which the participants had discontinued practice for approximately 6 months, the diffusion indices of the four tract bundles still presented a significant difference compared with the baseline. Our results indicate that the modulation of microstructural properties of the white matter tract induced by the 8-week MBSR program was sustained after completion of the program and support that neuroplasticity in brain connection persists after the discontinuation of meditation training.

neuroscience↗

bioRxiv2019

Global kinome silencing combined with 3D invasion screening of the tumor microenvironment identifies fibroblast-expressed PIK3Cδ involvement in triple-negative breast cancer progression

As there is growing evidence for the tumor microenvironments (TME) role in tumorigenesis, we sought to investigate the role of fibroblast-expressed kinases in triple negative breast cancer (TNBC). Using a high-throughput kinome screen combined with 3D invasion assays, we identified fibroblast-expressed PIK3C{delta} (f-PIK3C{delta}) as a key regulator of progression. Although PIK3C{delta} has been mainly described in leucocytes, we detected high expression in primary fibroblasts derived from TNBC patients, while PIK3C{delta} was undetectable in cancer epithelial cell lines. Genetic and pharmacologic gain- and loss-of functions experiments verified the contribution of f-PIK3C{delta} in TNBC cell invasion. By employing an integrated secretomics and transcriptomics analysis, we revealed a paracrine mechanism via which f-PIK3C{delta} confers its pro-tumorigenic effects. Inhibition of f-PIK3C{delta} promoted the secretion of factors, including PLGF and BDNF, which subsequently led to upregulation of NR4A1 in TNBC cells where it acts as a tumor suppressor. Inhibition of PIK3C{delta} in an orthotopic BC mouse model reduced tumor growth only after inoculation with fibroblasts, indicating a role of f-PIK3C{delta} in cancer progression. Similar results were observed in the MMTV-PyMT transgenic BC mouse model, in addition to a decrease on tumor metastasis emphasizing the potential immune-independent effects of PIK3C{delta} inhibition. Finally, analysis of BC patient cohorts and TCGA datasets identified f-PIK3C{delta} (protein and mRNA levels) as an independent prognostic factor for overall and disease free survival, highlighting it as a therapeutic target for TNBC.

cancer biology↗

bioRxiv2018

Fast Parallel Algorithm for Large Fractal Kinetic Models with Diffusion

Chemical kinetic simulations are usually based on the law of mass action that applies to behavior of particles in solution. Molecular interactions in a crowded medium as in a cell, however, are not easily described by such conventional mathematical treatment. Fractal kinetics is emerging as a novel method for simulating kinetic reactions in such an environment. To date, there has not been a fast, efficient, and, more importantly, parallel algorithm for such computations. Here, we present an algorithm with several novel features for simulating large (with respect to size and time scale) fractal kinetic models. We applied the fractal kinetic technique and our algorithm to a canonical substrate-enzyme model with explicit phase-separation in the product, and achieved a speed-up of up to 8 times over previous results with reasonably tight bounds on the accuracy of the simulation. We anticipate that this technique and algorithm will have important applications to simulation of intra-cell biochemical reactions with complex dynamic behavior.

biophysics↗

bioRxiv2017

Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication

Transposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.

plant biology↗