Biology subjects

Jang, G.

Publications and source records attributed to Jang, G..

12 recordsLinked to original sources

bioRxiv2026

A representation of the visual environment in the human basolateral amygdala supports learning and choice

Animals continuously transform sensory inputs into representations that guide behavior. Although the amygdala is a brain structure critical for learning and choice, how natural sensory experience is represented within this circuit remains unknown. Here, we identify a representation of the visual environment in the human basolateral amygdala (BLA) that contains information relevant for learning and choice. Using image-computable encoding models trained on responses to naturalistic videos, we recover a continuous, low-dimensional representation of visual experience in the BLA. The representation generalizes across individuals and independent datasets and prospectively predicts BLA responses to novel visual stimuli generated through closed-loop image synthesis. Signals derived from the representation also informed reinforcement-learning models of human choice. Together, these findings show that the human BLA organizes complex visual experience into a structured representation that can support learning and flexible behavioral responses.

neuroscience↗

bioRxiv2025

Mutation-Agnostic Base Editing of the Progerin Farnesylation Site Rescues Hutchinson-Gilford Progeria Syndrome Phenotypes in Neuromuscular Organoids

Hutchinson Gilford progeria syndrome (HGPS) is a fatal premature aging disorder caused by pathogenic farnesylated lamin A variants that disrupt nuclear architecture and DNA repair. Current therapies, including farnesyltransferase inhibitors, provide only modest survival benefits and lack molecular specificity, while mutation-specific genome-editing strategies cannot address atypical laminopathies. Here, we develop Farnesylation Amino acid Targeted Editing (FATE), a mutation-agnostic base-editing platform that selectively disrupts the LMNA farnesylation motif without affecting other farnesylated proteins. Using isogenic human pluripotent stem cell derived neuromuscular organoids (NMOs), we reveal muscle-specific progerin accumulation that sequesters 53BP1 and abolishes DNA damage foci formation. FATE eliminates perinuclear progerin, restores 53BP1 mobility, reconstitutes DNA repair foci, and normalizes heterochromatin architecture. Importantly, transient delivery of FATE mRNA conjugated with lipid nanoparticles to HGPS NMOs achieves efficient base editing and phenotypic rescue. These findings establish FATE as a mutation-independent therapeutic strategy targeting a fundamental pathogenic mechanism in HGPS and provide a proof-of-concept for RNA-based in situ genome editing in progeroid disease.

pathology↗

bioRxiv2024

Shift from visceral to subcutaneous fat in Cyp17a1 knockout rats prevent the progression of metabolic syndrome

In this study, we investigated the effects of Cyp17a1 gene knockout (KO) on obesity and metabolic syndrome. Cyp17a1 KO in rats using CRISPR-Cas9 resulted in sex dimorphism and obesity, and interestingly, idiopathic accumulation was found in subcutaneous adipose tissue. Surprisingly, an insulin tolerance test and oral glucose tolerance test did not show any issues with insulin sensitivity and secretion despite hyperglycemia. In addition, Cyp17a1 KO rats showed normal plasma insulin and free fatty acid levels compared to wild-type rats, and blood biochemistry analysis revealed normal triglyceride, total cholesterol, high-density lipoprotein, and low-density lipoprotein levels. Cyp17a1 KO adipose-tissue-derived stem cells from subcutaneous fat showed increased expression of KLF5, an early adipogenesis marker, which implies enhanced adipogenic potential in subcutaneous adipose tissue. When gene expression associated with lipid, glucose, and insulin metabolism as well as inflammation in adipose tissue was examined, a metabolic shift to subcutaneous adipose tissue was discovered in the Cyp17a1 KO group. In conclusion, in the Cyp17a1 KO rat models we generated for the first time, the phenotype promoted by obesity reflected health obesity hypothesis, but this did not result in metabolic syndrome due to enhanced metabolism in the subcutaneous fats.

physiology↗

bioRxiv2024

Understanding human amygdala function with artificial neural networks

AbstractThe amygdala is a cluster of subcortical nuclei that receives diverse sensory inputs and projects to the cortex, midbrain and other subcortical structures. Numerous accounts of amygdalar contributions to social and emotional behavior have been offered, yet an overarching description of amygdala function remains elusive. Here we adopt a computationally explicit framework that aims to develop a model of amygdala function based on the types of sensory inputs it receives, rather than individual constructs such as threat, arousal, or valence. Characterizing human fMRI signal acquired as participants viewed a full-length film, we developed encoding models that predict both patterns of amygdala activity and self-reported valence evoked by naturalistic images. We use deep image synthesis to generate artificial stimuli that distinctly engage encoding models of amygdala subregions that systematically differ from one another in terms of their low-level visual properties. These findings characterize how the amygdala compresses high-dimensional sensory inputs into low-dimensional representations relevant for behavior.

neuroscience↗

bioRxiv2024

Efficient DNA base editing via an optimized DYW-like deaminase

CRISPR-based cytosine base editors enable precise genome editing without inducing double-stranded DNA breaks, yet traditionally depend on a limited selection of deaminases from the APOBEC/AID or TadA families. Here, we introduce SsCBE, a novel CRISPR-based cytosine base editor utilizing SsdAtox, a DYW-like deaminase derived from the toxin of Pseudomonas syringae. Strategic engineering of SsdAtox has led to remarkable improvements in the base editing efficiency (by up to 8.4-fold) and specificity for SsCBE, while concurrently reducing cytotoxicity. Exhibiting exceptional versatility, SsCBE was delivered and efficiently applied using diverse delivery methods, including the engineered virus-like particles (eVLPs). Its application has enabled targeted cytosine base editing in mouse zygotes and pioneering edits in mitochondrial DNA. The advent of SsCBE marks a significant advancement in the CRISPR toolkit, providing a versatile tool for advanced research and therapeutic strategies.

molecular biology↗

bioRxiv2023

Sensory encoding of emotion conveyed by the face and visual context

Humans rapidly detect and interpret sensory signals that have emotional meaning. The posterior temporal sulcus (pSTS) and amygdala are known to be critical for this ability, but their precise contributions--whether specialized for facial features or sensory information more generally--remain contentious. Here we investigate how these structures process visual emotional cues using artificial neural networks (ANNs) to model fMRI signal acquired as participants view complex, naturalistic stimuli. Characterizing data from two archival studies (Ns = 20, 45), we evaluated whether representations from ANNs optimized to recognize emotion from either facial expressions alone or the broader visual context differ in their ability to predict responses in human pSTS and amygdala. Across studies, we found that representations of facial expressions were more robustly encoded in pSTS compared to the amygdala, whereas representations related to visual context were encoded in both regions. These findings demonstrate how the pSTS operates on abstract representations of facial expressions such as fear and joy to a greater extent than the amygdala, which more strongly encodes the emotional significance of visual information more broadly, depending on the context.

neuroscience↗

bioRxiv2023

Ampk activation by glycogen expenditure primes the exit of naive pluripotency

Embryonic and epiblast stem cells in pre-and post-implantation embryos are characterized by their naive and primed states, respectively, which represent distinct phases of pluripotency. Thus, the cellular transition from naive to primed pluripotency recapitulates a drastic metabolic and cellular remodeling after implantation to adapt to changes in extracellular conditions. Here, we found that inhibition of Ampk occurred during naive transition with two conventional inhibitors (2i) of the Mek1 and Gsk3{beta} pathways. The accumulation of glycogen due to the inhibition of Gsk3{beta} was responsible for Ampk inhibition, which accounted for high de novo fatty acid synthesis in naive embryonic stem cells (ESCs). The knockout of glycogen synthase 1 (Gys1) in naive ESCs (GKO), resulting in a drastic glycogen loss, led to a robust Ampk activation and lowered the level of fatty acids. GKO lost the cellular characteristics of naive ESCs and rapidly transitioned to a primed state, as evidenced by a decrease in pluripotency markers in teratoma from GKO. The characteristics of GKO were restored by the simultaneous knockout of Ampk. These findings suggest that glycogen in naive ESCs within the blastocyst may act as a signaling molecule for the timely activation of Ampk, thus ultimately contributing to the transition to the epiblast stage. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/541467v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@118ea81org.highwire.dtl.DTLVardef@cbe4bforg.highwire.dtl.DTLVardef@16d5c1org.highwire.dtl.DTLVardef@12b825c_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

CRISPR prime editing for unconstrained correction of oncogenic KRAS variants

KRAS is the most commonly mutated RAS family gene and is a primary cause of the occurrence of several types of cancer. However, KRAS mutations have several unique and diverse molecular identities, making it difficult to find specific treatments. Here, we developed universal pegRNAs which can correct all types of G12 and G13 oncogenic KRAS mutations with CRISPR-mediated prime editors (PEs). The universal pegRNAs were found to be capable of correcting 12 types of KRAS mutations, accounting for 94% of all known KRAS mutations. Using our PE system, we successfully corrected 12 types of KRAS mutations with up to 54.7 % correction efficiency in HEK293T/17 cells. We also applied the universal pegRNA to correct endogenous KRAS mutations in pancreatic cancer cells and found that G12V and G12D KRAS mutations were successfully corrected to wild-type KRAS sequences with up to 18.7% correction efficiency without unwanted mutations. We propose prime editing with the universal pegRNA as a one-to-many potential therapeutic strategy for KRAS oncogene variants.

bioengineering↗

bioRxiv2021

Identification of the safe harbor locus, AAVS1, from porcine genome and site-specific integration of recombinase-mediated cassette exchange system in porcine fibroblasts using CRISPR/Cas9

Gene integration at site-specific loci, such as safe harbor regions for stable expression via transgenesis, is a critical approach for understanding the function of a gene in cells or animals. The AAVS1 locus is a well-known safe harbor site for human and mouse studies. In the present study, we found an AAVS1-like sequence in the porcine genome using the UCSC Genome Browser and designed TALEN and CRISPR/Cas9 to target AAVS1. The efficiency of CRISPR/Cas9 for targeting the AAVS1 locus in porcine cells was superior to that of TALEN. An AAVS1-targeting donor vector containing GFP was designed and cloned. We added a loxP-lox2272 cassette sequence to the donor vector for further exchange of various transgenes in the AAVS1-targeted cell line. The donor vector and CRISPR/Cas9 components targeting AAVS1 were transfected into a porcine fibroblast cell line. Targeted cells of CRISPR/Cas9-mediated homologous recombination were identified by antibiotic selection. Gene knock-in at the AAVS1 locus was confirmed by PCR analysis. To induce recombinase-mediated cassette exchange (RMCE), another donor vector containing the loxP-lox2272 cassette and inducible (Tet-on) Cre recombinase was cloned. The Cre-donor vector was transfected into the AAVS1-targeted cell line, and RMCE was induced by adding doxycycline to the culture medium. RMCE in porcine fibroblasts was confirmed using PCR analysis. In conclusion, gene targeting at the AAVS1 locus and RMCE in porcine fibroblasts was successful. This technology will be useful for future porcine transgenesis studies and the generation of stable transgenic pigs.

molecular biology↗

bioRxiv2021

Ketamine Produces a Long-Lasting Enhancement of CA1 Neuron Excitability

BackgroundKetamine is a clinical anaesthetic and a fast-acting, long-lasting antidepressant. Ketamine is known for its antagonistic actions on N-methyl-D-aspartate (NMDA) receptors, but mechanisms leading to antidepression are not clear. The present study examined synaptic, neuronal and circuit-level loci, the duration of ketamines actions, and the involvement of NMDA receptors in these actions. MethodsExtracellular evoked field potentials were recorded from the CA1 region of mouse hippocampal slices. Ketamine was tested at antidepressant (10 M) and anaesthetic (350 M) concentrations. Effects of NMDA receptor antagonists, DL-2-Amino-5-phosphonovaleric acid (APV) and MK-801, {gamma}-aminobutyric acid (GABA) receptor antagonist bicuculline, and a potassium channel blocker tetraethylammonium (TEA) were also studied. ResultsKetamine decreased population spike (PS) amplitudes during application, but a long-lasting increase in PS amplitudes was seen during washout of ketamine. While the acute effects of ketamine were reversed by bicuculline, the washout increase was not altered. This long-term increase was statistically significant (p<0.01, Wilcoxon Rank Test), sustained for >2 hours, and involved postsynaptic mechanisms. A similar, long-lasting effect was produced by MK-801 but was only partially evident with APV, demonstrating the importance of channel block downstream of NMDA receptors. Furthermore, TEA produced a lasting excitability increase, indicating possible involvement of potassium channel block in ketamines long-term effects. ConclusionsThis is this first report of a long-lasting increase in excitability following ketamine exposure. These results support a growing literature that increased GABA inhibition contributes to ketamine anaesthesia, while increased excitatory transmission contributes to its antidepressant effects. Published AbstractsSociety for Neuroscience Annual Meeting 2019 Association of University Anesthesiologists Annual Meeting 2020 International Anesthesia Research Society Annual Meeting 2020 The Science of Consciousness Conference 2020 International Society for Anaesthetic Pharmacology Annual Meeting 2020 Western Anesthesia Residents Conference 2021 Association of University Anesthesiologists Annual Meeting 2021 International Anesthesia Research Society Annual Meeting 2021

neuroscience↗

bioRxiv2020

Engineered Prime Editors with PAM flexibility

Although prime editors are a powerful tool for genome editing, which can generate various types of mutations such as nucleotide substitutions, insertions, and deletions in the genome without double-strand breaks or donor DNA, the conventional prime editors are still limited to its target scopes because of the PAM preference of the spCas9 protein. Here, we described the engineered prime editors to expand the range of their target sites using various PAM-flexible Cas9 variants.

bioengineering↗

bioRxiv2018

Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements

Determining cell lineage and function is critical to understanding human physiology and pathology. Although advances in lineage tracing methods have provided new insight into cell fate, defining cellular diversity at the mammalian level remains a challenge. Here, we developed a genome editing strategy using a cytidine deaminase fused with inactive Cas9 (dCas9) to specifically target endogenous interspersed repeat regions in mammalian cells. The resulting mutation patterns served as a genetic barcode, which was induced by targeted mutagenesis with single-guide RNA (sgRNA), leveraging substitution events, and subsequent read out by a single primer pair. By analyzing interspersed mutation signatures, we show the accurate reconstruction of cell lineage using both bulk cell and single-cell data. We envision that our genetic barcode system will enable fine-resolution mapping of organismal development in healthy and diseased mammalian states.

bioengineering↗