Biology subjects

Lim, G.

Publications and source records attributed to Lim, G..

10 recordsLinked to original sources

bioRxiv2026

Differential induction of 14-3-3 paralogs expression during early and late adipogenesis

Obesity is a major public health challenge of the 21st century, particularly in low- and middle-income populations. Adipogenesis plays a central role in the development of obesity and associated metabolic disorders, as it determines adipocyte number, size, and function. The 14-3-3 protein family comprises seven paralogs in mammals that regulate multiple cellular processes, yet their specific roles during adipogenesis remain poorly understood. In this study, we characterized the expression profiles of 14-3-3 paralogs during the early and late stages of adipogenic differentiation using quantitative PCR under standard adipogenic differentiation medium and modified drug-supplemented conditions. We found that the expression of specific paralogs is strongly influenced by the composition of the differentiation medium. The absence of insulin led to an early increase in Ywhaz, which could not be maintained during late adipogenesis and was associated with impaired adipogenic differentiation. In contrast, stimulation with incretins in combination with insulin induced late expression of Ywhag and Ywhab paralogs and promoted the formation of a greater number of smaller lipid droplets. These findings indicate that individual 14-3-3 paralogs exert distinct and context-dependent effects on adipogenesis, highlighting their potential roles as modulators of adipocyte differentiation and metabolic function.

biochemistry↗

bioRxiv2025

Predicting Metabolic Dysfunction Associated Steatotic Liver Disease Risk Using Patient-Derived Induced Pluripotent Stem Cells

Background and AimsMetabolic Dysfunction Associated Steatotic Liver Disease (MASLD) is reversible at early stages, making early identification of high-risk individuals clinically valuable. Previously, we demonstrated that patient-derived induced pluripotent stem cells (iPSCs) harboring MASLD DNA risk variants exhibit greater oleate-induced intracellular lipid accumulation than those without these variants. This study aimed to develop an iPSC-based MASLD risk predictor using functional lipid accumulation assessments. MethodsWe quantified oleate-induced intracellular lipid accumulation in iPSCs derived from three cohorts of diverse ancestry: 1) CIRM cohort (20 biopsy-confirmed MASH cases, 2 biopsy-confirmed MASLD cases, 17 controls), 2) POST cohort (18 MASLD cases, 17 controls), and 3) UCSF cohort (4 biopsy-confirmed MASH cases, 8 controls). Lipid accumulation levels in the CIRM cohort were used to define an iPSC-based MASLD risk score, which was used to predict case/control status in the POST and UCSF cohorts. ResultsIn all three cohorts, lipid accumulation was higher in MASLD/MASH cases vs. controls (CIRM cases vs. controls 3.32 {+/-} 0.25 vs. 2.70 {+/-} 0.19 -fold change, p=0.06; POST cases vs. controls 3.63 {+/-} 0.33 vs. 2.70 {+/-} 0.31, p=0.05; and UCSF cases vs. controls 4.39{+/-}0.46 vs. 2.03{+/-}0.20, p=0.0002). The iPSC-based MASLD risk score achieved a sensitivity of 44% and specificity of 75% in the POST cohort and 75% and 100%, respectively, in the UCSF cohort. Differences in cohort disease severity and cardiometabolic profiles may explain performance variability. ConclusionWhile validation in larger cohorts is needed, these findings suggest that oleate-induced intracellular lipid accumulation in subject-derived iPSCs is predictive of MASH development. Additional cellular phenotypes and donor information should be explored to improve predictive accuracy to inform MASLD surveillance and prevention strategies.

cell biology↗

bioRxiv2024

Loss of MEF2C function by enhancer mutation leads to neuronal mitochondria dysfunction and motor deficits in mice

Genetic changes and epigenetic modifications are associated with neuronal dysfunction in the pathogenesis of neurodegenerative disorders. However, the mechanism behind genetic mutations in the non-coding region of genes that affect epigenetic modifications remains unclear. Here, we identified an ALS-associated SNP located in the intronic region of MEF2C (rs304152), residing in a putative enhancer element, using convolutional neural network. The enhancer mutation of MEF2C reduces own gene expression and consequently impairs mitochondrial function in motor neurons. MEF2C localizes and binds to the mitochondria DNA, and directly modulates mitochondria-encoded gene expression. CRISPR/Cas-9-induced mutation of the MEF2C enhancer decreases expression of mitochondria-encoded genes. Moreover, MEF2C mutant cells show reduction of mitochondrial membrane potential, ATP level but elevation of oxidative stress. MEF2C deficiency in the upper and lower motor neurons of mice impairs mitochondria-encoded genes, and leads to mitochondrial metabolic disruption and progressive motor behavioral deficits. Together, MEF2C dysregulation by the enhancer mutation leads to mitochondrial dysfunction and oxidative stress, which are prevalent features in motor neuronal damage and ALS pathogenesis. This genetic and epigenetic crosstalk mechanism provides insights for advancing our understanding of motor neuron disease and developing effective treatments.

neuroscience↗

bioRxiv2024

14-3-3ζ regulates adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation

We previously established the scaffold protein 14-3-3{zeta} as a critical regulator of adipogenesis and adiposity, but the temporal specificity of its action during adipocyte differentiation remains unclear. To decipher if 14-3-3{zeta} exerts its regulatory functions on mature adipocytes or on adipose precursor cells (APCs), we generated Adipoq14-3-3{zeta}KO and Pdgfra14-3-3{zeta}KO mouse models. Our findings revealed a pivotal role for 14-3-3{zeta} in APC differentiation in a sex-dependent manner, whereby male and female Pdgfra14-3-3{zeta}KO mice display impaired or potentiated weight gain, respectively, as well as fat mass. To better understand how 14-3-3{zeta} regulates the adipogenic transcriptional program in APCs, CRISPR-Cas9 was used to generate TAP-tagged 14-3-3{zeta}-expressing 3T3-L1 preadipocytes. Using these cells, we examined if the 14-3-3{zeta} nuclear interactome is enriched with adipogenic regulators during differentiation. Regulators of chromatin remodeling, such as DNMT1 and HDAC1, were enriched in the nuclear interactome of 14-3-3{zeta}, and their activities were impacted upon 14-3-3{zeta} depletion. The interactions between 14-3-3{zeta} and chromatin-modifying enzymes suggested that 14-3-3{zeta} may control chromatin remodeling during adipogenesis, and this was confirmed by ATAC-seq, which revealed that 14-3-3{zeta} depletion impacted the accessibility of up to 1,244 chromatin regions corresponding in part to adipogenic genes, promoters, and enhancers during the initial stages of adipogenesis. Moreover, 14-3-3{zeta}-dependent chromatin accessibility was found to directly correlate with the expression of key adipogenic genes. Altogether, our study establishes 14-3-3{zeta} as a crucial epigenetic regulator of adipogenesis and highlights the usefulness of deciphering the nuclear 14-3-3{zeta} interactome to identify novel pro-adipogenic factors and pathways.

physiology↗

bioRxiv2024

Crossover Interference Mediates Multiscale Patterning Along Meiotic Chromosomes

The classical phenomenon of crossover interference is a one-dimensional spatial patterning process that produces evenly spaced crossovers during meiosis. Quantitative analysis of diagnostic molecules along budding yeast chromosomes reveals that this process also sets up a second, interdigitated pattern of related but longer periodicity, in a "two-tiered" patterning process. The second tier corresponds to a previously mysterious minority set of crossovers. Thus, in toto, the two tiers account for all detected crossover events. Both tiers of patterning set up spatially clustered assemblies of three types of molecules ("triads") representing the three major components of meiotic chromosomes (crossover recombination complexes and chromosome axis and synaptonemal complex components), and give focal and domainal signals, respectively. Roles are suggested. All observed effects are economically and synthetically explained if crossover patterning is mediated by mechanical forces along prophase chromosomes. Intensity levels of domainal triad components are further modulated, dynamically, by the conserved protein remodeler Pch2/TRIP13.

cell biology↗

bioRxiv2023

3-phenyllactic acid promotes healthspan through SKN-1/ATFS-1-mediated mitochondrial activation and stress resilience

The mechanisms underlying the impact of probiotic supplementation on health remain largely elusive. While previous studies have primarily focused on the discovery of novel bioactive bacteria and alterations in the microbiome environment to explain potential probiotic effects, our research delves into the role of living lactic acid bacteria (LAB) and their conditioned media, highlighting that only the former, not dead bacteria, enhance the healthspan of Caenorhabditis elegans. To elucidate the underlying mechanisms, we conducted transcriptomic profiling through RNA-seq analysis in C. elegans exposed to LAB or 3-phenyllactic acid (PLA), mimicking the presence of key candidate metabolites of LAB and evaluating healthspan. Our findings reveal that PLA treatment significantly extends the healthspan of C. elegans by promoting energy metabolism and stress resilience in a SKN-1/ATFS-1-dependent manner. Moreover, PLA-mediated longevity is associated with a novel age-related parameter, the Healthy Aging Index (HAI), introduced in this study, which comprises healthspan-related factors such as motility, oxygen consumption rate (OCR), and ATP levels. Extending the relevance of our work to humans, we observed an inverse correlation between blood PLA levels and physical performance in patients with sarcopenia, when compared to age-matched non-sarcopenic controls. Our investigation thus sheds light on the pivotal role of the metabolite PLA in probiotics-mediated enhancement of organismal healthspan, and also hints at its potential involvement in age-related sarcopenia. These findings warrant further investigation to delineate PLAs role in mitigating age-related declines in healthspan and resilience to external stressors. HighlightsO_LIMetabolites Produced by Lactic Acid Bacteria Function as Mediators of Longevity in C. elegans C_LIO_LI3-Phenyllactic Acid (PLA) Augmented Lifespan Extension and Elevated the Healthy Aging Index (HAI) C_LIO_LIPLA Facilitated Healthy Aging by Inducing Mitochondrial Activation and Stress Resistance Dependent on SKN-1/ATFS-1 C_LIO_LIPatients with Sarcopenia and Symptoms of Frailty Exhibited Reduced Blood PLA Levels. C_LI

molecular biology↗

bioRxiv2023

Fluorescent Peptide-based Probe for the Detection of Alpha-synuclein Aggregates in the Gut

BackgroundParkinsons disease (PD) is diagnosed clinically by motor symptoms, with no molecular diagnostic test currently available. By the time motor symptoms manifest, significant irreversible neurodegeneration has already occurred, limiting the effectiveness of neuroprotective therapies and drug interventions. Recent identification of pathological alpha-synuclein (-syn) aggregates in the gastrointestinal (GI) tract of prodromal PD patients offer a potential avenue for early disease diagnosis. This study aims to explore specific fluorescence labelling of -syn aggregates in the GI tract using a peptide-based probe for early diagnosis of PD. MethodsWe used primary hippocampal neuronal cells and wild-type mouse tissues with the addition of pre-formed -syn fibrils to identify the most suitable peptide fluorescent probe (P1) for staining -syn aggregates in cells and tissues. We validated the probe labelling in GI tract tissues from three mouse models, including PFF-injected mice and two transgenic PD mouse strains. We quantified labelling accuracy by confocal imaging and protein analysis. ResultsWe found that P1 labelled -syn aggregates with high accuracy (87% in comparison to Serine129-phosphorylated -syn antibody) and high specificity for labelling their aggregated forms over monomeric forms. In GI tract tissues, P1 labelled -syn aggregates across tissue layers (mucosa, sub-mucosa, muscularis externa) and achieved comparable performance to antibody staining. Higher degree of probe labelling was found in older mice due to increased accumulation of -syn aggregates with ageing. Notably, -syn aggregates were readily detectable in the colonic mucosae using P1, indicating the potential use of this probe for early PD diagnosis during colonic examinations like colonoscopy. ConclusionWe have developed a peptide-based fluorescent probe and demonstrated its rapid and specific labelling of -syn aggregates. We highlight the probes ability to label these aggregates rapidly over -syn monomers and survey the abundance of -syn aggregates throughout the entire length of the GI tract. These support the further development of P1 as a specific fluorescent imaging biomarker for colonic -syn aggregates for the early detection of PD.

neuroscience↗

bioRxiv2020

14-3-3ζ regulates lipolysis by influencing adipocyte maturity

One of the primary metabolic functions of a mature adipocyte is to supply energy via lipolysis, or the catabolism of stored lipids. Hormone-sensitive lipase (HSL) is a critical lipolytic enzyme, and its phosphorylation and subsequent activation by PKA generates phospho-binding sites for 14-3-3 proteins, a ubiquitously expressed family of molecular scaffolds. While we previously identified essential roles of the 14-3-3{zeta} isoform in murine adipogenesis, the presence of 14-3-3 protein binding sites on HSL suggests that 14-3-3{zeta} could also influence mature adipocyte processes like lipolysis. Herein, we demonstrate that 14-3-3{zeta} is necessary for lipolysis in male mice and fully differentiated 3T3-L1 adipocytes, as depletion of 14-3-3{zeta} significantly impaired glycerol and FFA release. Unexpectedly, this was not due to impairments in signaling events underlying lipolysis; instead, reducing 14-3-3{zeta} expression was found to significantly impact adipocyte maturity, as observed by reduced abundance of PPAR{gamma}2 protein and expression of mature adipocytes genes and those associated with de novo triglyceride synthesis and lipolysis. The impact of 14-3-3{zeta} depletion on adipocyte maturity was further examined with untargeted lipidomics, which revealed that reductions in 14-3-3{zeta} abundance promoted the acquisition of a lipidomic signature that resembled undifferentiated, pre-adipocytes. Collectively, these findings reveal a novel aspect of 14-3-3{zeta} in adipocytes, as reducing 14-3-3{zeta} was found to have a negative effect on adipocyte maturity and adipocyte-specific processes like lipolysis.

physiology↗

bioRxiv2019

14-3-3ζ over-expression improves tolerance to acute and chronic cold exposure in male mice via thermogenic-dependent and -independent mechanisms

Following prolonged cold exposure, adaptive thermogenic pathways are activated to maintain homeothermy, and elevations in body temperature are generally associated with UCP1-dependent and -independent increases in energy expenditure. One of the earliest, identified functions of the molecular scaffold, 14-3-3{zeta}, was its role in the synthesis of norepinephrine, a key endogenous factor that stimulates thermogenesis. This suggests that 14-3-3{zeta} may have critical roles in cold-induced thermogenesis. Herein, we report that transgenic over-expression of TAP-14-3-3{zeta} in mice significantly improved tolerance to prolonged cold. When compared to wildtype controls, TAP mice displayed significantly elevated body temperatures and paradoxical decreases in energy expenditure. No changes in {beta}-adrenergic sensitivity or oxidative metabolism were observed; instead, 14-3-3{zeta} over-expression significantly decreased thermal conductance via increased peripheral vasoconstriction. These findings suggest 14-3-3{zeta} mediates alternative, non-thermogenic mechanisms to mitigate heat loss for homeothermy. Our results point to an unexpected role of 14-3-3{zeta} in the regulation of body temperature. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=137 HEIGHT=200 SRC="FIGDIR/small/853184v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1f5b454org.highwire.dtl.DTLVardef@1219a7org.highwire.dtl.DTLVardef@523fb3org.highwire.dtl.DTLVardef@1d41780_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2017

Elucidation of the 14-3-3ζ interactome reveals critical roles of RNA splicing factors during adipogenesis

Adipogenesis is facilitated by a complex signaling network requiring strict temporal and spatial organization of effector molecules. Molecular scaffolds, such as 14-3-3 proteins, coordinate such events, and we have previously identified 14-3-3{zeta} as an essential scaffold in adipocyte differentiation. The interactome of 14-3-3{zeta} is large and diverse, and it is possible that novel adipogenic factors may be present within it. Mouse embryonic fibroblasts from mice over-expressing a TAP-epitope-tagged 14-3-3{zeta} molecule were generated, and following the induction of adipogenesis, TAP-14-3-3{zeta} complexes were purified, followed by mass spectrometry analysis to determine the 14-3-3{zeta} interactome. Over 100 proteins were identified as being unique to adipocyte differentiation, of which 56 were novel interacting partners. Previously established regulators of adipogenesis (ie, Ptrf/Cavin1 and Phb2) were found within the 14-3-3{zeta} interactome, confirming the ability of this approach to identify regulators of adipocyte differentiation. An enrichment of proteins in the interactome related to RNA metabolism, processing, and splicing was identified, and analysis of transcriptomic data revealed that 14-3-3{zeta} depletion in 3T3-L1 cells affected the alternative splicing of mRNA during adipocyte differentiation. Of the RNA splicing factors within the 14-3-3{zeta} interactome, depletion of Hnrnpf, Hnrnpk, Ddx6, and Sfpq by siRNA revealed essential roles of these proteins in adipogenesis and their roles in the alternative splicing of Lpin1. In summary, novel adipogenic factors can be detected within the 14-3-3{zeta} interactome, and further characterization of additional proteins within the 14-3-3{zeta} interactome has the potential of identifying novel targets to block the expansion of adipose tissue mass that occurs in obesity.

physiology↗